Pathogen diversity, host specificity and virulence
Lead Research Organisation:
University of Edinburgh
Department Name: The Roslin Institute
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
This project will examine the diversity of pathogen populations and identify factors that contribute to virulence and host tropism, define their mode of action and use this knowledge to develop strategies to detect, treat and prevent infections.
Planned Impact
unavailable
Organisations
- University of Edinburgh (Lead Research Organisation)
- James Hutton Institute (Collaboration)
- International Livestock Research Institute (ILRI) (Collaboration)
- Biomedicine Research Institute of Buenos Aires - CONICET - Partner Institute of the Max Planck Society (Collaboration)
- Liverpool School of Tropical Medicine (Collaboration)
- Friedrich Loeffler Institute (Collaboration)
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES) (Collaboration)
- OXFORD NANOPORE TECHNOLOGIES (Collaboration)
- NHS LOTHIAN (Collaboration)
- CENTRE FOR ENVIRONMENT, FISHERIES AND AQUACULTURE SCIENCE (Collaboration)
- University Libre Bruxelles (Université Libre de Bruxelles ULB) (Collaboration)
- National Institute for Agricultural and Food Research and Technology (Collaboration)
- THE PIRBRIGHT INSTITUTE (Collaboration)
- University of the Philippines Mindanao (Collaboration)
- Wageningen University & Research (Collaboration)
- Utrecht University (Collaboration)
- Hungarian Academy of Sciences (MTA) (Collaboration)
- PUBLIC HEALTH ENGLAND (Collaboration)
- National Scientific and Technical Research Council (Argentina) (Collaboration)
- Wellcome Trust (Collaboration)
- Scottish Environment Protection Agency (Collaboration)
- Adisseo (Collaboration)
- Erasmus MC (Collaboration)
- Public Health Scotland (Collaboration)
- AbacusBio (Collaboration)
- QUEEN'S UNIVERSITY BELFAST (Collaboration)
- Animal Health Service (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
- Chinese Academy of Agricultural Sciences (Collaboration)
- UNIVERSITY OF OXFORD (Collaboration)
- Pharmaq (Collaboration)
- National Veterinary School of Toulouse (Collaboration)
- Institute of Microbiology (Collaboration)
- Konkuk University (Collaboration)
- United States Geological Survey (Collaboration)
- National Veterinary Institute (Collaboration)
- Yale University (Collaboration)
- University of Georgia (Collaboration)
- National Food Chain Safety Office (Collaboration)
- Animal and Plant Quarantine Agency (Collaboration)
- Biomathematics and Statistics Scotland (BioSS) (Collaboration)
- University of Glasgow (Collaboration)
- Animal and Plant Health Agency (Collaboration)
- Moredun Research Institute (Collaboration)
- Complutense University of Madrid (Collaboration)
- Government of Canada (Collaboration)
- Sokoine University of Agriculture (Collaboration)
- Zoetis (Collaboration)
- Fleming Fund (Collaboration)
- Marine Scotland Science (MSS) (Collaboration)
- SalMar (Collaboration)
- Makerere University College of Health Sciences (Collaboration)
- University of Laval (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- University of Limoges (Collaboration)
- Experimental Zooprophylactic Institute of the Venezie (Collaboration)
- U.S. Department of Agriculture USDA (Collaboration)
- Cardiff University (Collaboration)
- Texas Tech University (Collaboration)
- National Academy of Sciences of the Republic of Armenia (Collaboration)
- University of Alberta (Collaboration)
- Fonds de la Recherche Scientifique (Collaboration)
- Makerere University (Collaboration)
- Genus plc (Collaboration)
- Établissement Français du Sang (Collaboration)
- Quadram Institute Bioscience (Collaboration)
- UNIVERSITY OF NOTTINGHAM (Collaboration)
- AB Vista (Collaboration)
- Scotland's Rural College (Collaboration)
- Hokkaido University (Collaboration)
- Vetline Services (Collaboration)
- Norwegian Veterinary Institute (Collaboration)
- Centers for Disease Control and Prevention (CDC) (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- Technical University of Denmark (Collaboration)
- Malawi Government (Collaboration)
- Grieg Group (Collaboration)
- NEWCASTLE UPON TYNE HOSPITALS NHS FOUNDATION TRUST (Collaboration)
- BANGOR UNIVERSITY (Collaboration)
- Animal Health Research Institute (Collaboration)
- Boehringer Ingelheim (Collaboration)
- Charoen Pokphand Group (Collaboration)
Publications
Abbas AH
(2018)
The Structure of a Conserved Telomeric Region Associated with Variant Antigen Loci in the Blood Parasite Trypanosoma congolense.
in Genome biology and evolution
Abouelhadid S
(2019)
Quantitative Analyses Reveal Novel Roles for N-Glycosylation in a Major Enteric Bacterial Pathogen.
in mBio
Adedeji AJ
(2021)
Household and animal factors associated with sheeppox and goatpox sero-prevalence and identification of high-risk areas in selected States of northern Nigeria.
in Preventive veterinary medicine
Akhmetova A
(2023)
Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland
in Microbial Genomics
Akram KM
(2018)
An innate defense peptide BPIFA1/SPLUNC1 restricts influenza A virus infection.
in Mucosal immunology
Alber A
(2021)
The bird's immune response to avian pathogenic Escherichia coli.
in Avian pathology : journal of the W.V.P.A
Alber A
(2019)
Avian Pathogenic Escherichia coli (APEC) Strain-Dependent Immunomodulation of Respiratory Granulocytes and Mononuclear Phagocytes in CSF1R-Reporter Transgenic Chickens.
in Frontiers in immunology
Alfituri OA
(2019)
Effects of host-derived chemokines on the motility and viability of Trypanosoma brucei.
in Parasite immunology
Alibhai JD
(2018)
Unravelling the glial response in the pathogenesis of Alzheimer's disease.
in FASEB journal : official publication of the Federation of American Societies for Experimental Biology
| Title | Additional file 1 of Probiotics mediated gut microbiota diversity shifts are associated with reduction in histopathology and shedding of Lawsonia intracellularis |
| Description | Additional file 1 Number of positive pigs/total pigs per group (group mean ± SEM) for log10 L. intracellularis DNA in rectal swabs at different days post L. intracellularis challenge [24]. Different superscripts (A,B,C) indicate significantly different group means on a certain day. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2021 |
| URL | https://springernature.figshare.com/articles/figure/Additional_file_1_of_Probiotics_mediated_gut_mic... |
| Title | Additional file 1 of Probiotics mediated gut microbiota diversity shifts are associated with reduction in histopathology and shedding of Lawsonia intracellularis |
| Description | Additional file 1 Number of positive pigs/total pigs per group (group mean ± SEM) for log10 L. intracellularis DNA in rectal swabs at different days post L. intracellularis challenge [24]. Different superscripts (A,B,C) indicate significantly different group means on a certain day. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2021 |
| URL | https://springernature.figshare.com/articles/figure/Additional_file_1_of_Probiotics_mediated_gut_mic... |
| Title | Additional file 14 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 14: Figure S5. siRNA/piRNA mapping against ASFV and ASFLI-element database. siRNA (22 nt) and piRNA (28-29 nt) fractions from Ornithodoros porcinus and Ornithodoros moubata, before and after deduplication, were individually mapped against ASFV whole-genome sequence and the O. moubata or O. porcinus ASFLI-element containing datasets using Bowtie 2 (2.3.0) in Geneious. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2020 |
| URL | https://springernature.figshare.com/articles/figure/Additional_file_14_of_Identification_of_African_... |
| Title | Additional file 14 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 14: Figure S5. siRNA/piRNA mapping against ASFV and ASFLI-element database. siRNA (22 nt) and piRNA (28-29 nt) fractions from Ornithodoros porcinus and Ornithodoros moubata, before and after deduplication, were individually mapped against ASFV whole-genome sequence and the O. moubata or O. porcinus ASFLI-element containing datasets using Bowtie 2 (2.3.0) in Geneious. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2020 |
| URL | https://springernature.figshare.com/articles/figure/Additional_file_14_of_Identification_of_African_... |
| Title | Additional file 18 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 18: Figure S6. The reconstructed ASFV-like A104R protein is highly similar to its ASFV homologue (A) A rabbit antiserum raised against the reconstructed A104 gene recognised a flag-tagged and an untagged version of A104R protein (lanes A104-Flag and A104, respectively), but showed no specific reaction with extracts of tick cell lines OME/CTVM21, OME/CTVM22, OME/CTVM24, and OME/CTVM27. In extracts of WSL-HP cells infected with ASFV Kenya 1033, the serum reacted with a single band of 12 kDa which is similar to the calculated molecular weight of ASFV A104R (11.6 kDa). (B) The Coomassie stained gel confirms equal loading with proteins. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2020 |
| URL | https://springernature.figshare.com/articles/figure/Additional_file_18_of_Identification_of_African_... |
| Title | Additional file 18 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 18: Figure S6. The reconstructed ASFV-like A104R protein is highly similar to its ASFV homologue (A) A rabbit antiserum raised against the reconstructed A104 gene recognised a flag-tagged and an untagged version of A104R protein (lanes A104-Flag and A104, respectively), but showed no specific reaction with extracts of tick cell lines OME/CTVM21, OME/CTVM22, OME/CTVM24, and OME/CTVM27. In extracts of WSL-HP cells infected with ASFV Kenya 1033, the serum reacted with a single band of 12 kDa which is similar to the calculated molecular weight of ASFV A104R (11.6 kDa). (B) The Coomassie stained gel confirms equal loading with proteins. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2020 |
| URL | https://springernature.figshare.com/articles/figure/Additional_file_18_of_Identification_of_African_... |
| Title | Additional file 4 of Probiotics mediated gut microbiota diversity shifts are associated with reduction in histopathology and shedding of Lawsonia intracellularis |
| Description | Additional file 4. Taxonomic characteristics of ileal microbiota. OTUs clustered according to their phylogenetic relationship and colored by abundance, also called a heat-tree. The core microbes can be identified by the dark green backbone while the transient/accessory microbes compose the rest of the tree branches and change by treatment groups. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2021 |
| URL | https://springernature.figshare.com/articles/figure/Additional_file_4_of_Probiotics_mediated_gut_mic... |
| Title | Additional file 4 of Probiotics mediated gut microbiota diversity shifts are associated with reduction in histopathology and shedding of Lawsonia intracellularis |
| Description | Additional file 4. Taxonomic characteristics of ileal microbiota. OTUs clustered according to their phylogenetic relationship and colored by abundance, also called a heat-tree. The core microbes can be identified by the dark green backbone while the transient/accessory microbes compose the rest of the tree branches and change by treatment groups. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2021 |
| URL | https://springernature.figshare.com/articles/figure/Additional_file_4_of_Probiotics_mediated_gut_mic... |
| Description | We utilise genome-wide studies of pathogens combined with detailed research on mechanisms to understand variation in microbial pathogens and infection outcomes in hosts. The work also contributes to development of novel diagnostics and interventions. Bacterial pathogens - We have developed a novel 3R approach to quantify the entry and persistence of diverse Salmonella serovars in the bovine lymphatic system by massively-parallel sequencing of polymorphic alleles of strains screened in pools. The approach has much potential to reduce animal use in screening strain phenotypes or evaluating cross-protective efficacy of vaccines or treatments. We have also retrospectively applied transposon-directed insertion-site sequencing to a library of Salmonella Typhimurium mutants screened for their ability to colonise the intestines of calves. The study independently validated the role of c. 3000 Salmonella genes in a key natural animal host using archived lymph node tissue without any further animal use. As such it also represents an advance of 3R principles. ISP-funded research contributed to ground-breaking collaborative work to describe the evolutionary history of host-switching by Staphylococcus aureus, including the identification of genetic signatures of host-adaptation. The work highlights humans as a major hub for the transmission of S. aureus to livestock and subsequent worldwide dissemination in the case of mastitis, but also the emergence of new human clones from a bovine reservoir, with important public health implications. Host-adaptation in S. aureus was also found to involve a novel mechanism of phage transduction in collaboration with the University of Glasgow. We characterised a staphylococcal fibrinogen-binding protein involved in host-adaptation, a novel superantigen that contributes to bacteraemia and a S. aureus lipase that enhances influenza virus replication but does not inhibit innate immunity. The lipase enhanced IAV yield in embryonated eggs, and a patent was filed for this purpose. We also identified a S. pseudintermedius adhesin that binds fibronectin in a host-specific way to promote biofilm formation and innate immune evasion. For some other bacterial pathogens, we reported a key role for the pgl N-glycosylation system in Campylobacter colonisation of chickens, that Shiga toxin 2a promotes transmission of E. coli O157 and restricts epithelial regeneration in bovine enteroids, defined a novel role for flagella in E. coli attachment and Salmonella invasion, and roles for capsular polysaccharide in lymphatic dissemination and immune evasion by Streptococcus. We further demonstrated the potential of machine learning to predict host tropism and differential virulence of bacterial pathogens, building on work supported by the last ISP that predicted that only a subset of E. coli O157 found in cattle pose zoonotic risk. A similar approach predicted variants of Salmonella Typhimurium that may differ in tropism for farm animals, virulence and zoonotic risk, and we plan to evaluate strain phenotypes using a novel 3Rs method developed with ISP support. In the middle of the ISP (3 years) we developed a joint appointment with Public Health England with ISP funds which facilitated translation of our research for prediction of zoonotic risk and source attribution. We have established a seconded post into Food Standards Scotland to work on threat prediction and source attribution for E. coli. Machine learning has also been applied to predict bacteriophage resistance, supported by high-density mutagenesis strategies to identify phage resistance genes, toward the selection of bacteriophage therapies for chronic bacterial infections. These computational approaches are complemented by genome-wide mutagenesis screens to assign functions to genes such as TraDIS, which we are applying to S. aureus and mastitis. We have developed methods for direct sequencing of Lawsonia intracellularis (LI) from clinical samples, enabling the first population-level view of genomic diversity and identifying candidate antigens for novel vaccines and diagnostics with a commercial partner. The limited diversity and broad geographical distribution from our sequencing indicate the recent emergence and clonal expansion of this important livestock pathogen. Recent work also provides evidence that modulation of the gut microbiome of pigs with a probiotic may also protect against LI infection. We also analysed the serotypes and genomes of the neglected pig pathogen Erysipelothrix rhusiopathiae towards an application to develop improved vaccines based on knowledge of diversity. We further dissected the regulation of the Type 3 secretion system in E. coli O157 that is critical for colonisation of cattle and a key target for vaccines. We have shown that different M. bovis strains can induce distinct transcriptional profiles, cytokines and cell death responses in bovine macrophages that may impact the effectiveness of bTB diagnostics and interventions. Under research using models and bacterial WGS for M bovis in cattle and wildlife, we provided the first demonstration using bacterial whole genome sequencing of the relationships between Tb in wildlife and cattle in the Republic of Ireland. We have also analysed M bovis bacterial sequence data in a long-term study area in England to identify likely badger-to-cattle and cattle-to-badger transmission pairs, using a new methodological approach that we developed. We also investigated the epidemiology of bTB in African countries and contributed to the WHO Roadmap for control of zoonotic TB. We are examining phenotypes of c. 4000 dairy cattle in Tanzania for brucellosis, Q fever and leptospirosis to provide epidemiological data on the risk of animal disease and zoonotic exposure, with host genotyping linked to Theme 1. Viral pathogens - For influenza, we have found mutations that affect the viral accessory proteins PA-X and PB1-F2 impacting on innate immune responses and modulation of virulence of an H9N2 virus in chickens and mice. Moreover, we have found that PA-X mutations can enhance the yield of human IAV vaccines from embryonated eggs, priming a UK patent to exploit our findings for practical gain. Similarly, we identified an epistatic interaction between viral polymerase genes that can also improve IAV vaccine yield in eggs and are exploring the impact of modulating CpG or UpA dinucleotide frequencies on viral fitness and vaccine yield. A swine-derived pandemic H1N1 strain of IAV was found to express a variant of the viral nucleoprotein that influences virulence in mice and pigs, and we assigned a new function to the IAV NS1 protein in mRNA transport. Work involving Core Scientists established a new paradigm for how chimeric proteins can be produced with contributions from cellular and viral transcripts and found that some contribute to virulence and T-cell responses. We also reported that 'snatching' of caps from the 5' end of host mRNAs during IAV transcription is not random as assumed, but biased to snRNAs and avoids transcripts for ribosomal proteins needed for viral replication Bioinformatic and phylodynamic tools have been developed and applied to avian IAV sequence data to define factors affecting transmission and evolution on a global scale, providing new insights into the origins and spread of novel variants. For example, together with international partners, especially the European Horizon 2020 project VEO ( https://www.veo-europe.eu ), we have been analysing the 2016/2017 and lately the 2020 autumn H5NX avian influenza outbreaks across Eurasia using phylodynamic and phylogeographic modelling with sequence data. This has generated an understanding of the generation and circulation of reassortant viruses in their reservoir and spill over populations (Lycett et al 2020 PNAS). With uplift funding via the BBSRC Ecology & Evolution of Infectious Diseases scheme with the US and China, we are now creating a predictive model to identify avian influenza viruses that pose the greatest risk to avian or human populations. We also secured funding from this source to apply phylodynamics to understand the diversity and spread of PRRSV, and the impact of imperfect vaccines, host genetics and non-genetic drivers on the evolution and transmission of MDV and IBV (®). We also defined the population structure of salmonid alphavirus, revealing previously unrecognized viral diversity to guide design of diagnostic tests, and identified novel lineages and anthropogenic disease transmission routes. Our expertise was rapidly deployed to understand the evolution, spread and risk of SARS-CoV-2 variants, including S protein variants that retain fitness while evading antibody-mediated immunity. Additionally, we were able to apply phylodynamic methods to improve the understanding of the evolution of serotype A and SAT2 FMDV and prospects for disease control, including the observation of rapidly diversifying strains in Africa that may be associated with vaccine use. We have also analysed transmission clusters using the phylodynamic methods from the Scottish Government EPIC III Bovine Viral Diarrhoea sequencing project to inform the Scottish eradication programme. We have established nanopore whole genome sequencing as a useful tool for the genomic surveillance of aquaculture pathogens, revealing novel strain diversity and potential routes of transmission for salmonid alphavirus on salmon farms. Towards control of Infectious bronchitis virus, we have used CLIPS epitope mapping we have identified novel immunogenic peptides on the spike protein of avian coronavirus of the three major strains circulating worldwide. These findings are being used to design broad-spectrum vaccines again IBV and commercial interest for patent filing and development. Protozoal pathogens - a small RNA species has been developed as a diagnostic target for animal trypanosomiasis, in partnership with Roslin Technologies. This target is sensitive, specific and uniquely detects active infections. A qPCR assay has been successfully developed with Roslin Technologies, and an application is currently under consideration that aims to identify a technology platform suitable for application to a pen-side diagnostic test (with Destina Genomics Ltd). We have made significant progress in understanding the metabolism of T. congolense, and have identified important key differences with the widely studied human pathogen T. brucei. We have also designed a new culture medium that enables propagation of the mammalian-infective bloodstream form of the parasite, and importantly efficiently allows growth of this form of parasite from infected blood. This has been a significant bottleneck. This work has also facilitated the development of genetic modification of T. congolense from an intractable to a routine process. This will be invaluable in dissecting the fundamental biology of T. congolense, as well as providing a foundation for furthering drug target discovery, drug mode of action and mode of resistance studies. Our analysis of parasite epidemiology in the tsetse fly vector, wildlife and livestock in Northern Tanzania has demonstrated that the low prevalence of AAT is due to farmer-led control by application of pyrethroid-based insecticides. This challenges findings from donor-led programmes indicating that insecticide control of AAT is ineffective. We have engaged with the FAO programme against AAT to update resources widely used by national control programmes, and reviewed issues associated with use of trypanocides. We have also developed reliable and scalable functional genetic tools for the bloodstream form of T. congelense, for example for genome-scale RNAi screens or production of transgenic fluorescent parasites. These tools are being used to identify drug targets, their mode of action and resistance mechanisms, as recently exemplified work on resistance to benzoxaboroles and diminazine. We have also analysed the basis of antigenic diversity in T. brucei with PacBio sequencing of trypanosome variant surface glycoprotein revealing unprecedented diversity of the types expressed, indicating the challenges that will need to be overcome for vaccines targeting this key surface antigen. Prions Toward an understanding of risk factors for prion disease, we have found that prion neuroinvasion after oral infection occurs independently of gut microbiota, or the level of PrPC expression in intestinal epithelial cells, involves delivery of prions to follicular dendritic cells by CXCR5-expressing DCs, and was influenced by co-infections with gut-restricted helminths. We also demonstrated that spermine can facilitate prion degradation by enhancing autolysosomal flux, thereby informing the design of therapies for protein mis-folding diseases. We provided the first evidence that PRNP codon 129 genotype of the host does not influence the strain characteristics of vCJD; specifically that vCJD strain properties are not affected by transmission through an individual with the PRNP methionine/valine codon 129 genotype and thus no alteration in virulence should be associated with the different host genotype. This has implications for public health as any changes in strain characteristics can lead to changes in clinical phenotype and diagnosis or changes in infectious potential. Application of organoids to study host-pathogen interactions Linked with ISP1, we have established a robust methodology to generate three-dimensional enteroids ('mini-guts') from small intestinal crypts of cattle. Histological and transcriptional analyses indicate that these comprise intestinal epithelial cell lineages, including intestinal stem cells, enterocytes, Paneth cells, goblet cells and enteroendocrine cells, that are stably maintained over long-term passage and can be cryopreserved and recovered. Protocols to obtain enteroids from pigs and chickens have also been devised with ISP support. Bovine enteroids have been used to establish that Shiga toxin produced by E. coli O157 inhibits host cell proliferation to colonise the rectal epithelium of cattle. This work is being extended to define interactions between bovine enteroids and Cryptosporidium, Salmonella serovars and Mycobacterium avium subsp. paratuberculosis. We have now developed avian 3D intestinal organoids or enteroids with a unique inside out orientation, which allows for easy manipulation without the need of micro injection. PCT patent application has been published and a licence option is under negotiation with the industrial partner. The versatile application of the culture model has led to follow up funding from an industrial partner (Novozymes) for who we further developed the 3D enteroid technology into a 2D model. The success of this avian model led to further funding from Novozymes to develop bovine 2D enteroids. The versatility of the 3D avian enteroid model will be tested in two newly awarded grants to investigate if enteroids can be applied as novel diagnostic tool to determine the virulence of emerging viruses and to investigate if we can model and predict the effect of innate immunity on emergence and evolution of avian influenza viruses. |
| Exploitation Route | Impact from our ISP-funded research frequently involves partnerships with animal breeding and health companies. Our five strategic alliances are advancing ISP-supported research to commercialisation, in particular PRRS-resistant pigs via Genus Plc., fish resistant to aquatic diseases via Hendrix Genetics and WorldFish, and research to dissect the architecture of Eimeria resistance and edit chickens for influenza resistance with Cobb. We have also worked with Zoetis and Boehringer on vaccines for PCV, PRRSV and Lawsonia in pigs. We expect industry interactions to grow via our role in nascent Agri-Tech Centres (CIEL & Agri-EPI), the recent formation of Roslin Technologies Ltd with £10m private equity funding, and the opening of the adjacent Roslin Innovation Centre in August 2017 which now has >80% occupancy and over 17 tenants. In terms of specific examples: 1. A roadmap to combat Zoonotic Tuberculosis was launched in 2017 at the Union World Conference on Lung Health in Mexico. Zoonotic Tuberculosis (TB) is a form of tuberculosis in people caused by Mycobacterium bovis, which is often transmitted to humans through contact with infected animals, mainly cattle, and consumption of infected products. Ending the global TB epidemic is part of the goals set by the United Nations, aiming at inclusive, multidisciplinary approaches to improving health throughout the world by 2030. Dr Adrian Muwonge chairs the Zoonotic TB section at the International Union Against Tuberculosis and Lung Disease (The Union) that has been key to developing the roadmap which defines 10 key priority areas for limiting the impact of this disease on humans and their livestock and calls on stakeholders such as government, donors, academia, non-governmental organisations and private partnerships to action. The roadmap advises stakeholders to prioritise: (i) Mitigation of risk of transmission of zoonotic TB; (ii) Strengthening diagnostic capability; (iii) Access to timely diagnosis and effective treatment; (iv) Fostering inter-sectoral collaboration. 2. In Northern Tanzania our preliminary data indicates the same farmer-led control having an impact upon tsetse population and trypanosome prevalence, as well as examining the sustainability of this approach in terms of insecticide use and trypanocide resistance. Findings are being disseminated through regular meetings with stakeholders, including both farmers, policy-level individuals in Tanzania and those involved in developing new control methods (GALVmed), in order to feed findings back and try to influence future sustainability of control. 3. Patents have been filed for our sRNA diagnostic for animal African trypanosomiasis and applications of avian enteroids to study host-pathogen interactions. Strategies to improve live-attenuated IAV vaccines based on mutation of M2, M42 and PA-X, have also resulted in patent applications. |
| Sectors | Agriculture Food and Drink Education Healthcare |
| URL | https://www.ed.ac.uk/roslin/research/isp/control-infectious-diseases/pathogen-diversity-host-specificity-and-virulence |
| Description | Our proposed outputs for this theme of the programme are: (1) New experimental models for pathogens in relevant hosts, including genome-edited cell lines and animals; (2) markers for improved diagnostics and risk analysis; (3) bioinformatic tools for assembling and analysing pathogen genomes and for modelling pathogen transmission on local and global scales; (4) new antigens and attenuated mutants as candidate vaccines; (5) novel targets for anti-infective agents and alternatives to antibiotics; (6) training in vulnerable capacities, in particular in vivo skills and bioinformatics. Specific non academic impacts to date include: 1. The first ever global Zoonotic TB roadmap. Zoonotic Tuberculosis (TB) is a form of tuberculosis in people caused by Mycobacterium bovis, which is often transmitted to humans through contact with infected animals, mainly cattle, and consumption of infected products. Ending the global TB epidemic is part of the goals set by the United Nations, aiming at inclusive, multidisciplinary approaches to improving health throughout the world by 2030. The roadmap defines 10 key priority areas for limiting the impact of this disease on humans and their livestock and calls on stakeholders such as government, donors, academia, non-governmental organisations and private partnerships to action. The roadmap advises stakeholders to prioritise: (i) Mitigation of risk of transmission of zoonotic TB; (ii) Strengthening diagnostic capability; (iii) Access to timely diagnosis and effective treatment; (iv) Fostering inter-sectoral collaboration. 2. Development of genome wide association and machine-learning approaches to dissect bacterial host adaptation and predict risk. Improved bioinformatics tools and sequence data are being used outbreak investigations with Public Health England and the Scottish E. coli reference laboratory. The tools are also defining specific targets for diagnostics and vaccine development. 3. Phylodynamic tools to integrate movement networks and cross host species transmission to quantify transmission patterns and strain evolution. This work has contributed to the Scottish Government EPIC III Bovine Viral Diarrhoea (BVD) sequencing project towards the Scottish eradication programme for BVD. 4. Building on our identification of PA-X mutants in influenza virus, it is apparent that such strains yield higher levels of the critical antigens for protection and a patent has been filed with interest in how this can be used commercially to improve flu vaccine production levels. |
| First Year Of Impact | 2017 |
| Sector | Agriculture, Food and Drink,Healthcare,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Economic Policy & public services |
| Description | A blue-print for One-health AMR surveillance in Uganda |
| Geographic Reach | Africa |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Description | Academy of Medical Sciences's "Preparing for a challenging winter 2020/21" report |
| Geographic Reach | National |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| URL | https://www.gov.uk/government/publications/covid-19-preparing-for-a-challenging-winter-202021-7-july... |
| Description | Discussion meeting on research gaps in avian influenza |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Description | Expert group for the National Integrated Sentinel Surveillance(NISS) in Uganda |
| Geographic Reach | Africa |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | This is yet to be realised |
| Description | Joining the MRC College of Global Health experts |
| Geographic Reach | Africa |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Description | Member of Defra's Science Advisory Council |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | All aspects of how science relates to future Defra policy are potentially commented on by Defra SAC, including the future of farming plan, the environmental land management plan, and many others. Such comments are considered by Defra's Chief Scientific Advisor and by the relevant policy teams developing policy agendas. This represents a 2nd term of activity starting in 2021. These activities cover actions across the Commonwealth. |
| URL | https://www.gov.uk/government/organisations/science-advisory-council/about |
| Description | Member of SAC-ED HPAI |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Member of the Bovine TB partnership |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | The Bovine TB partnerships provides strategic advice on all aspect of bovine TB related policy. Bovine TB is a disease with economic and animal health impact, and affects farmers mental health and well being. |
| URL | https://www.gov.uk/government/groups/bovine-tuberculosis-partnership |
| Description | Member of the Defra bovine Tuberculosis partnership |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| URL | https://www.gov.uk/government/groups/bovine-tuberculosis-partnership |
| Description | Models to inform Public Health Scotland Policy on COVID-19 controls |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Impact | Models developed at the Roslin Institute have been used to provide projections of COVID-19 in Scotland, to aid in the determination of Scottish tier levels (i.e. restrictions to control COVID-19). As these restrictions have widespread influence on Scotland as a whole, the impact is extremely broad. The projections used are based on a published preprint (currently under review) - doi: https://doi.org/10.1101/2020.11.25.20144139. Vaccine uptake analyses are used to improve planning for the COVID vaccination programme. |
| URL | https://www.gov.scot/collections/coronavirus-covid-19-modelling-the-epidemic/ |
| Description | Presentation to the Advisory Committee on Dangerous Pathogens TSE subgroup on chronic wasting disease in deer |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Report sent to Scientific Advisory Group for Emergencies (SAGE) by members of the COG-UK Consortium - Scotland Report - "Epidemic waves of COVID-19 in Scotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on SARS-CoV-2" |
| Geographic Reach | Local/Municipal/Regional |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| URL | https://www.cogconsortium.uk/news_item/two-new-reports-to-sage-on-the-genomic-analysis-of-epidemic-w... |
| Description | Reports on COVID-19 trajectories in Scotland |
| Geographic Reach | National |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| Impact | The reports provided to the Scottish government supported implementation of policy on COVID-19 controls. While the contribution of the reports are difficult to quantify, overall COVID-19 controls resulted in substantial reduction in severe illness and mortality due to COVID-19. |
| URL | https://www.gov.scot/collections/coronavirus-covid-19-modelling-the-epidemic/ |
| Description | Supporting digital contact tracing and early warning for COVID-19 |
| Geographic Reach | National |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| Impact | The tool allows for digital contact tracing without the need pf public health and security tracking down truck drivers. This process was extremely stressful for truck drivers especially during the second and third wave of the pandemic. It should also save the ministry of Health money as contact tracing was one of the components with the largest budget during the first COVID-19 wave |
| Description | World health Organisation global zoonotic tuberculosis road map |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| URL | http://www.who.int/tb/publications/2017/zoonotic_TB/en/ |
| Description | (CARE) - Corona Accelerated R&D in Europe |
| Amount | € 75,839,401 (EUR) |
| Funding ID | 101005077 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 03/2020 |
| End | 03/2025 |
| Description | 21-ICRAD: Tackling chronic wasting disease in Europe |
| Amount | £316,579 (GBP) |
| Funding ID | BB/V019880/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2021 |
| End | 03/2024 |
| Description | 21-ICRAD: Tackling chronic wasting disease in Europe |
| Amount | £1,417,216 (GBP) |
| Funding ID | BB/V019880/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2021 |
| End | 03/2024 |
| Description | A Bayesian spatial-temporal analysis of risk factors associated with foot-and-mouth disease outbreaks in Uganda |
| Amount | £10,198 (GBP) |
| Funding ID | 1915 |
| Organisation | Royal Society of Edinburgh (RSE) |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 08/2021 |
| End | 05/2022 |
| Description | A GeCKO library for candidate genes involved in Newcastle disease virus replication |
| Amount | £60,000 (GBP) |
| Organisation | TROPICAL ANIMAL GENETICS (UK) LTD |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 06/2019 |
| End | 10/2020 |
| Description | A UK underpinning platform to study immunology and immunopathology of COVID-19: The UK Coronavirus Immunology Consortium (UK-CIC) |
| Amount | £633,154 (GBP) |
| Funding ID | 1257927 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2020 |
| End | 08/2021 |
| Description | Advanced phage therapy for multidrug resistant E. coliassociated with canine urinary tract infections |
| Amount | £162,630 (GBP) |
| Organisation | Dogs Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2021 |
| End | 12/2022 |
| Description | Advanced phage therapy for multidrug resistantE. coliassociated withcanine urinary tract infections |
| Amount | £162,630 (GBP) |
| Organisation | Dogs Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2020 |
| End | 12/2021 |
| Description | Agritech- catalyst PigBoost: Sustainable data-driven pig production for Uganda |
| Amount | £520,000 (GBP) |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2020 |
| End | 03/2021 |
| Description | Alberta Prion Research Institute's Explorations Program Round VI |
| Amount | $493,700 (CAD) |
| Funding ID | PEX17009 |
| Organisation | Alberta Prion Research Institute |
| Sector | Charity/Non Profit |
| Country | Canada |
| Start | 06/2017 |
| End | 06/2020 |
| Description | An integrated approach to tackling drug resistance in livestock trypanosomes. |
| Amount | £159,757 (GBP) |
| Funding ID | 6326355 |
| Organisation | GALVmed |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2019 |
| End | 12/2021 |
| Description | Are coinfections a threat to drug control programmes for livestock trypanosomes? |
| Amount | £839,460 (GBP) |
| Funding ID | BB/X013650/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2023 |
| End | 03/2026 |
| Description | BBSRC Future Leader Fellowship |
| Amount | £304,886 (GBP) |
| Funding ID | BB/P007767/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2017 |
| End | 03/2019 |
| Description | BBSRC-A strategic approach to identifying and combating porcine reproductive and respiratory syndrome virus outbreaks and other porcine viral diseases |
| Amount | £983,771 (GBP) |
| Funding ID | BB/R013187/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 03/2021 |
| Description | BBSRC-SFI-Tackling a multi-host pathogen problem - phylodynamic analyses of the epidemiology of M. bovis in Britain and Ireland |
| Amount | £448,073 (GBP) |
| Funding ID | BB/P010598/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2017 |
| End | 09/2020 |
| Description | BBSRC_Understanding the CD163 - PRRS virus interaction to improve genetic engineering for resistance |
| Amount | £674,353 (GBP) |
| Funding ID | BB/R004463/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2017 |
| End | 11/2020 |
| Description | Boehringer Ingelheim The PCV2 European Research Award |
| Amount | € 25,000 (EUR) |
| Organisation | Boehringer Ingelheim |
| Department | Boehringer Ingelheim |
| Sector | Private |
| Country | Canada |
| Start | 02/2017 |
| End | 04/2018 |
| Description | CARE: Corona Accelerated R&D in Europe |
| Amount | £380,249 (GBP) |
| Funding ID | 101005077 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 03/2020 |
| End | 03/2025 |
| Description | Carnegie Research Incentive Grant |
| Amount | £9,886 (GBP) |
| Organisation | Carnegie Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 02/2018 |
| End | 07/2018 |
| Description | Carnegie Trust Research Incentive Grant |
| Amount | £9,740 (GBP) |
| Organisation | Carnegie Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 05/2018 |
| End | 05/2019 |
| Description | Cattle farming practices and the emergence of Escherichia coli O157 (Stx2a+): an international workshop award with INTA Argentina |
| Amount | £9,100 (GBP) |
| Funding ID | BB/T019743/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2020 |
| End | 07/2021 |
| Description | Center for Tropical Livestock Health and Genetics |
| Amount | £15,000,000 (GBP) |
| Organisation | Bill and Melinda Gates Foundation |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 02/2017 |
| End | 03/2020 |
| Description | Centre of Expertise in Animal Disease Outbreaks - UoG funded portion |
| Amount | £36,387 (GBP) |
| Funding ID | A16105930 / UoG Ref:70392/2 |
| Organisation | Government of Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 03/2018 |
| Description | Centre of Expertise in Animal Disease Outbreaks - UoG funded portion |
| Amount | £36,387 (GBP) |
| Funding ID | A16105930 / UoG Ref:70392/2 |
| Organisation | Government of Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 03/2018 |
| Description | Collaborative Award - Liam Morrison for RI - Challenging trypanosome antigenic variation paradigms using natural systems |
| Amount | £2,070,288 (GBP) |
| Funding ID | 206815/Z/17/Z |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 04/2022 |
| Description | Collaborative Award - Rold Kao - Thinking forward through the past: Linking science, social science and the humanities to inform the sustainable reduction of disease in British livestock farming |
| Amount | £218,525 (GBP) |
| Funding ID | 209818/C/17/Z |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 11/2018 |
| End | 11/2022 |
| Description | Combined influence of imperfect vaccines, host genetics, and non-genetic drivers on virus transmission and virulence evolution |
| Amount | £1,837,983 (GBP) |
| Funding ID | BB/V017411/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2021 |
| End | 12/2023 |
| Description | Cross-national genomic surveillance of viral pathogens to support disease control in Atlantic salmon aquaculture |
| Amount | £45,000 (GBP) |
| Organisation | Scottish Aquaculture Innovation Centre |
| Sector | Multiple |
| Country | United Kingdom |
| Start | 11/2022 |
| End | 10/2026 |
| Description | Cross-national genomic surveillance of viral pathogens to support disease control in Atlantic salmon aquaculture |
| Amount | £102,000 (GBP) |
| Organisation | Pharmaq |
| Sector | Private |
| Country | Norway |
| Start | 11/2022 |
| End | 10/2026 |
| Description | Cross-national genomic surveillance of viral pathogens to support disease control in Atlantic salmon aquaculture (studentship) |
| Amount | £102,000 (GBP) |
| Funding ID | Roslin Institute Project |
| Organisation | Zoetis |
| Sector | Private |
| Country | United States |
| Start | 11/2022 |
| End | 04/2026 |
| Description | Dairy niche adaptation by bovine mastitis pathogens: novel targets for control |
| Amount | £654,140 (GBP) |
| Funding ID | BB/W014920/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2022 |
| End | 05/2025 |
| Description | Dairy niche adaptation by bovine mastitis pathogens: novel targets for control |
| Amount | £540,914 (GBP) |
| Funding ID | BB/W014920/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2022 |
| End | 09/2025 |
| Description | Defining early entry mechanisms of Mycobacterium avium paratuberculosis into the host |
| Amount | £552,222 (GBP) |
| Funding ID | BB/T007354/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2020 |
| End | 12/2022 |
| Description | Determine the Therapeutic Potential of Sialylated Fc for Influenza Therapy |
| Amount | £42,192 (GBP) |
| Funding ID | 12RP -LSTM |
| Organisation | United Kingdom Research and Innovation |
| Department | Research England |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2021 |
| End | 09/2022 |
| Description | Determining the role of CSF1R-dependent macrophages in of Paneth cells and the |
| Amount | £520,952 (GBP) |
| Funding ID | MR/S000763/1 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2018 |
| End | 10/2021 |
| Description | Developing dairy-specific molecular screening tools to quantify the within herd dynamics of antimicrobial resistance |
| Amount | £9,090 (GBP) |
| Organisation | Hannah Dairy Research Foundation |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 05/2020 |
| Description | Developing dairy-specific molecular screening tools to quantify the within-herd dynamics of antimicrobial resistance |
| Amount | £9,820 (GBP) |
| Funding ID | HDRF E-mail- 28 June 2019 |
| Organisation | Hannah Dairy Research Foundation |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 11/2019 |
| End | 05/2021 |
| Description | Developing resilience in the fragile aquatic food systems of Bangladesh impacted by COVID-19. |
| Amount | £200,000 (GBP) |
| Organisation | Department For Environment, Food And Rural Affairs (DEFRA) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2020 |
| End | 03/2021 |
| Description | Development and testing of Operational Models of Bovine Tuberculosis in British Cattle and Badgers: Phase III & IV |
| Amount | £284,898 (GBP) |
| Funding ID | DEFRA SE3929 |
| Organisation | Department For Environment, Food And Rural Affairs (DEFRA) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2017 |
| End | 01/2020 |
| Description | Development of a 3Rs whole-genome sequencing method to evaluate vaccine efficacy against multiple bacterial strains simultaneously |
| Amount | £10,520 (GBP) |
| Funding ID | PIII080 - IAA |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2020 |
| End | 07/2021 |
| Description | Development of a 3Rs whole-genome sequencing method to evaluate vaccine efficacy against multiple bacterial strains simultaneously |
| Amount | £10,520 (GBP) |
| Funding ID | PIII080 - IAA |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2020 |
| End | 07/2021 |
| Description | Development of a PCR assay for the direct detection of Mycobacterium bovis DNA to improve the diagnosis of Bovine Tuberculosis |
| Amount | £4,567 (GBP) |
| Funding ID | Roslin2352 |
| Organisation | MV Diagnostics Ltd |
| Sector | Private |
| Country | United Kingdom |
| Start | 02/2019 |
| End | 05/2019 |
| Description | Development of genetic improvement tools to support tropical dairy and poultry small holder livestock systems (CTLGH 2.0) |
| Amount | £12,013,168 (GBP) |
| Funding ID | INV-040641 |
| Organisation | Bill and Melinda Gates Foundation |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 07/2022 |
| End | 08/2027 |
| Description | Dissecting the molecular pathways of MDV oncoprotein Meq for understanding pathogenesis and aid vaccine development |
| Amount | £384,966 (GBP) |
| Funding ID | BB/R007632/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 03/2021 |
| Description | ECAT-Plus/Wellcome Trust PhD Fellowship for Clinicians-Jenna Schafers-: Survival and adaptation of viruses within respiratory droplets: a c ombined molecular biological an d biophysical study |
| Amount | £247,098 (GBP) |
| Funding ID | ECAT-Plus -Schafers-12705842 |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 07/2022 |
| End | 07/2025 |
| Description | ENABLES: Enabling Livestock-keepers to Eliminate Sleeping Sickness |
| Amount | £71,556 (GBP) |
| Funding ID | BB/S01375X/1 (T74 03738) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2019 |
| End | 10/2020 |
| Description | EPIC 4 |
| Amount | £1,800,275 (GBP) |
| Funding ID | Case/56472 |
| Organisation | Government of Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2022 |
| End | 03/2025 |
| Description | EU-Dynamics of avian influenza in a changing world |
| Amount | £403,373 (GBP) |
| Funding ID | 727922 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 07/2017 |
| End | 09/2021 |
| Description | Edinburgh Global: Interdisciplinary workshop on peri-urban production |
| Amount | £13,000 (GBP) |
| Organisation | Edinburgh College |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 05/2018 |
| Description | Environmental and Economic Impacts of Improved Antibiotics Stewardship in Poultry Systems |
| Amount | £687,419 (GBP) |
| Funding ID | BB/T004436/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2019 |
| End | 05/2024 |
| Description | Environmental and Economic Impacts of Improved Antibiotics Stewardship in Poultry Systems |
| Amount | £687,419 (GBP) |
| Funding ID | BB/T004436/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2019 |
| End | 05/2024 |
| Description | Establishing the Mayuge-Iganga One Health Living laboratory as an exemplar for equitable implementation of Global Health (MIGOHILL) |
| Amount | £40,000 (GBP) |
| Organisation | University of Edinburgh |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 02/2024 |
| End | 10/2024 |
| Description | European Funds Knowledge Education Department |
| Amount | 12,656 zł (PLN) |
| Organisation | European Commission |
| Department | European Social Fund |
| Sector | Public |
| Country | European Union (EU) |
| Start | 05/2017 |
| End | 08/2017 |
| Description | Fleming Fund Fellowships Phase 2 |
| Amount | £3,240,000 (GBP) |
| Organisation | Mott Macdonald UK Ltd |
| Sector | Private |
| Country | United Kingdom |
| Start | 11/2023 |
| End | 12/2025 |
| Description | Fleming Fund fellowship scheme |
| Amount | £1,100,000 (GBP) |
| Organisation | Fleming Fund |
| Sector | Charity/Non Profit |
| Start | 02/2018 |
| End | 09/2022 |
| Description | Fleming fellowship fund for Uganda |
| Amount | £510,000 (GBP) |
| Organisation | Mott Macdonald UK Ltd |
| Sector | Private |
| Country | United Kingdom |
| Start | 01/2019 |
| End | 08/2020 |
| Description | Fleming fellowships for Malawi |
| Amount | £520,000 (GBP) |
| Organisation | Mott Macdonald UK Ltd |
| Sector | Private |
| Country | United Kingdom |
| Start | 02/2020 |
| End | 10/2021 |
| Description | Flexible Talent Mobility Account - 4 |
| Amount | £75,000 (GBP) |
| Funding ID | BB/X017613/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2023 |
| End | 03/2023 |
| Description | Food Standards Scotland Open Tender |
| Amount | £120,000 (GBP) |
| Funding ID | CRF:MRI/104/17 |
| Organisation | Government of Scotland |
| Department | Food Standards Agency (FSA), Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2017 |
| End | 06/2019 |
| Description | GCRF Global Challenges Research Fund - Tim Connelley - International Veterinary Vaccinology Network |
| Amount | £2,113,339 (GBP) |
| Funding ID | MR/R005958/1 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2017 |
| End | 06/2021 |
| Description | GCRF Impact Accelerator: A genomic map for bovine tuberculosis susceptibility in Bos indicus |
| Amount | £30,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2017 |
| End | 03/2018 |
| Description | General Scheme - Abigail Diack - A comparative platform for strain typing CWD |
| Amount | £131,947 (GBP) |
| Funding ID | RES0036432-S001 |
| Organisation | Alberta Prion Research Institute |
| Sector | Charity/Non Profit |
| Country | Canada |
| Start | 06/2017 |
| End | 06/2020 |
| Description | General Scheme - Consortium funding - David Gally for RI - The risk of STEC (Shiga Toxin-Producing E. coli) contamination in Wild Venison |
| Amount | £58,578 (GBP) |
| Funding ID | MRI/104/17 |
| Organisation | Scottish Parliament |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2017 |
| End | 06/2019 |
| Description | General Scheme - Fiona houston - Investigating the susceptibility of British deer to chronic wasting disease |
| Amount | £24,563 (GBP) |
| Organisation | Department For Environment, Food And Rural Affairs (DEFRA) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2017 |
| End | 03/2017 |
| Description | General Scheme - Jacqueline Smith - Genetic characterisation of Avian Leukosis Virus (ALV)-like tumours identified in commercial chicken lines |
| Amount | £8,896 (GBP) |
| Funding ID | wt 5448961 |
| Organisation | The Houghton Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 09/2018 |
| Description | General Scheme - Ross Fitzgerald - Direct diagnostic genomics towards effective antimicrobial stewardship |
| Amount | £242,381 (GBP) |
| Funding ID | WT 5613240 |
| Organisation | Dogs Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2019 |
| End | 12/2021 |
| Description | General Scheme - Tim Connelley - MHCI genotyping in horses |
| Amount | £5,800 (GBP) |
| Funding ID | SPrj028 |
| Organisation | Horserace Betting Levy Board |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 05/2018 |
| End | 02/2019 |
| Description | Genetically ENgineered BIOsensors to detect BIological Threats (GENBIOBIT): Influenza A Virus |
| Amount | £131,024 (GBP) |
| Funding ID | BB/V017365/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2021 |
| End | 05/2022 |
| Description | Genetically ENgineered BIOsensors to detect BIological Threats (GENBIOBIT): Influenza A Virus |
| Amount | £28,353 (GBP) |
| Funding ID | BB/V017365/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2021 |
| End | 05/2022 |
| Description | Genome-wide identification of novel therapeutic targets for the control of bovine Staphylococcus aureus infection |
| Amount | £54,627 (GBP) |
| Organisation | Zoetis |
| Sector | Private |
| Country | United States |
| Start | 08/2019 |
| End | 08/2023 |
| Description | Growth of avian leucosis virus stocks |
| Amount | £10,824 (GBP) |
| Funding ID | roslin 2107 |
| Organisation | Aviagen Group |
| Sector | Private |
| Country | United States |
| Start | 08/2019 |
| End | 11/2019 |
| Description | H2020 |
| Amount | € 5,500,000 (EUR) |
| Funding ID | DELTA-FLU |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 04/2017 |
| End | 04/2022 |
| Description | High-Resolution Ion Mobility enabled DART/LC-MS for metabolomics applications |
| Amount | £715,056 (GBP) |
| Funding ID | BB/X019608/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2023 |
| End | 07/2024 |
| Description | Horizon H2020 - Fast Track to Innovation - Lonneke Vervelde - Dynamics of avian influenza in a changing world |
| Amount | £403,373 (GBP) |
| Funding ID | 727922 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 05/2017 |
| End | 05/2022 |
| Description | Identification of interferon stimulated genes that control Toxoplasma in pig macrophages |
| Amount | £470,900 (GBP) |
| Funding ID | BB/W014807/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2023 |
| End | 12/2025 |
| Description | Identification of interferon stimulated genes that restrict cross-species transmission of influenza A virus. |
| Amount | £614,702 (GBP) |
| Funding ID | BB/S00114X/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 09/2023 |
| Description | Identification of virulence factors as novel vaccine targets for CBPP, by whole genome saturated mutagenesis |
| Amount | £4,881 (GBP) |
| Funding ID | 9486211 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2020 |
| End | 12/2020 |
| Description | Implementation of operationally useful models to analyse bacterial whole genome sequence data for control of bovine Tuberculosis in cattle and badgers |
| Amount | £7,147 (GBP) |
| Funding ID | FTMA Email-17/01/2020 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2020 |
| End | 03/2020 |
| Description | Improving implementation and operation of a One Health platform to combat rabies in Malawi |
| Amount | £12,000 (GBP) |
| Funding ID | 326267 |
| Organisation | Research Council of Norway |
| Sector | Public |
| Country | Norway |
| Start | 01/2022 |
| End | 12/2024 |
| Description | Industry Partnership Award (TR) - Liam Morrison - An integrated approach to tackling drug resistance in livestock trypanosomes. |
| Amount | £660,569 (GBP) |
| Funding ID | BB/S00243X/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2019 |
| End | 12/2021 |
| Description | Intended and unintended consequences of the ZnO ban from pig diets on antimicrobial resistance, post-weaning diarrhoea and the microbiome. |
| Amount | £1,110,610 (GBP) |
| Funding ID | BB/Y004086/1 (and linked consortium codes BB/Y003918/1; BB/Y004108/1; BB/Y003861/1) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2024 |
| End | 02/2027 |
| Description | Interferon-stimulated genes as resilience factors for PRRSV infection |
| Amount | £642,924 (GBP) |
| Funding ID | BB/T015179/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2020 |
| End | 11/2024 |
| Description | International Veterinary Vaccinology Network |
| Amount | £600,000 (GBP) |
| Funding ID | MC_PC_17219 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 03/2019 |
| Description | Investigating the Antimicrobial Properties of Scottish Honey: A Citizen Science Approach |
| Amount | £20,119 (GBP) |
| Funding ID | BB/T018984/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2020 |
| End | 05/2021 |
| Description | Investigation into the prevalence and aetiology of a novel form of feline meningoencephalitis: 'Robotic cat' disease |
| Amount | £7,974 (GBP) |
| Organisation | Petsavers Charitable Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 04/2020 |
| End | 05/2023 |
| Description | Investigation of proven vaccine breakthrough by SARS-CoV-2 variants in established UK healthcare worker cohorts: SIREN consortium & PITCH Plus Pathway |
| Amount | £1,585,765 (GBP) |
| Funding ID | MR/W02067X/1 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2021 |
| End | 08/2023 |
| Description | Large memory HPC infrastructure to underpin world-class biological research |
| Amount | £602,000 (GBP) |
| Funding ID | BB/S019367/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2019 |
| End | 06/2020 |
| Description | MSc by Research in Infectious Diseases |
| Amount | £4,000 (GBP) |
| Organisation | University of Edinburgh |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 09/2019 |
| End | 09/2020 |
| Description | Machine-learning to predict and understand the zoonotic threat of E. coli O157 isolates |
| Amount | £421,490 (GBP) |
| Funding ID | BB/P02095X/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 09/2020 |
| Description | Management of post-weaning diarrhoea and the implications for AMR in response to the upcoming ban on zinc supplementation in pigs. |
| Amount | £201,722 (GBP) |
| Funding ID | BB/W020467/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2022 |
| End | 12/2023 |
| Description | Market assessment for a novel diagnostic for Animal African |
| Amount | £10,000 (GBP) |
| Funding ID | PIII-041 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2019 |
| End | 12/2019 |
| Description | Metabolism And Drug Resistance Probed With New Genetic Tools In The Neglected Animal Pathogen Trypanosoma Vivax. |
| Amount | £117,505 (GBP) |
| Funding ID | BB/W000296/1 |
| Organisation | GALVmed |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2021 |
| End | 09/2024 |
| Description | Metabolism and drug resistance probed with new genetic tools in the neglected animal pathogen Trypanosoma vivax. |
| Amount | £414,291 (GBP) |
| Funding ID | BB/W000296/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2022 |
| End | 09/2025 |
| Description | Microbiology toolkit - Pondering pond life |
| Amount | £4,967 (GBP) |
| Funding ID | G002473 |
| Organisation | Microbiology Society |
| Sector | Learned Society |
| Country | United Kingdom |
| Start | 06/2020 |
| End | 06/2021 |
| Description | National COVID-19 Wastewater Epidemiology Surveillance Programme |
| Amount | £791,191 (GBP) |
| Funding ID | NE/V010441/1 |
| Organisation | Natural Environment Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2020 |
| End | 11/2021 |
| Description | Newton fund - Christine Tait-Burkard - A strategic approach to identifying and combating porcine reproductive and respiratory syndrome virus outbreaks and other porcine viral diseases |
| Amount | £983,771 (GBP) |
| Funding ID | BB/R013187/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 03/2021 |
| Description | Novel Tools for early diagnosis of mastitis in cattle |
| Amount | £29,982 (GBP) |
| Funding ID | BBSRC IAA PIII056 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2020 |
| End | 09/2020 |
| Description | One Health Models of Disease: Science, Ethics and Society |
| Amount | £5,328,962 (GBP) |
| Funding ID | 218471/Z/19/Z |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2020 |
| End | 09/2028 |
| Description | One Health Models of Disease: Science, Ethics and Society |
| Amount | £5,328,962 (GBP) |
| Funding ID | 218471/Z/19/Z |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2020 |
| End | 09/2028 |
| Description | Operational Optimization of Environmental FMD sampling |
| Amount | £26,145 (GBP) |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 12/2021 |
| End | 04/2023 |
| Description | Operational Optimization of Environmental FMD sampling |
| Amount | £26,145 (GBP) |
| Funding ID | 10868292 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 12/2021 |
| End | 04/2023 |
| Description | Outbreak Data Analysis Platform |
| Amount | £1,198,705 (GBP) |
| Funding ID | HDR UK 2021.0125 |
| Organisation | Health Data Research UK |
| Sector | Private |
| Country | United Kingdom |
| Start | 09/2021 |
| End | 09/2022 |
| Description | Paper based platform for onsite, rapid and multiplexed pathogen detection in shrimp farms |
| Amount | £10,098 (GBP) |
| Funding ID | U1875 (Glasgow) |
| Organisation | United Kingdom Research and Innovation |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2022 |
| End | 03/2023 |
| Description | Paper-based platform for onsite, rapid and multiplexed pathogen detection in shrimp farms |
| Amount | £252,639 (GBP) |
| Funding ID | BB/T012528/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2021 |
| End | 06/2022 |
| Description | PigBoost: Sustainable data-driven pig production for Uganda |
| Amount | £97,544 (GBP) |
| Funding ID | TS/T00763X/1 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2020 |
| End | 06/2021 |
| Description | Pilot project - Pre-emptive and non-invasive disease diagnostics to prevent the spread of shellfish disease. |
| Amount | £54,906 (GBP) |
| Funding ID | F S 042 |
| Organisation | Department For Environment, Food And Rural Affairs (DEFRA) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2020 |
| End | 01/2021 |
| Description | Piloting a digital one-health platform for AMR surveillance (Genopaths-Africa) |
| Amount | £69,541 (GBP) |
| Funding ID | RGS\R1\231137 |
| Organisation | The Royal Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2023 |
| End | 03/2024 |
| Description | Policy Research Programme - Abigail Diack for RI - Consortium Funding - Assessing and defining pre-clinical vCJD infectivity using transmission and protein aggregation models |
| Amount | £1,553,441 (GBP) |
| Funding ID | PR-R17-0916-23001 |
| Organisation | Department of Health (DH) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2017 |
| End | 03/2024 |
| Description | Policy Research Programme - Fiona Houston - Comparative evaluation of the performance of proposed diagnostic tests for vCJD in preclinical blood samples |
| Amount | £882,178 (GBP) |
| Funding ID | 3782585 |
| Organisation | Department of Health (DH) |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2017 |
| End | 02/2021 |
| Description | PorkMart v1.1: Data-driven market intelligence for a sustainable pork industry in Uganda |
| Amount | £34,997 (GBP) |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2022 |
| End | 03/2023 |
| Description | Post-hospitalisation COVID-19 study: a national consortium to understand and improve long-term health outcomes (PHOSP-COVID) |
| Amount | £1,101,992 (GBP) |
| Funding ID | MR/V027859/1 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2020 |
| End | 08/2022 |
| Description | Pre-emptive and non-invasive pathogen diagnostics to prevent the spread of shellfish disease |
| Amount | £189,967 (GBP) |
| Funding ID | WT 10899126 |
| Organisation | Centre For Environment, Fisheries And Aquaculture Science |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2021 |
| End | 12/2022 |
| Description | Precision bacteriophage identification through machine learning for mitigating persistent colonization of Escherichia coli O157:H7 in cattle |
| Amount | $136,857 (USD) |
| Funding ID | 60-3040-1-003 |
| Organisation | U.S. Department of Agriculture USDA |
| Sector | Public |
| Country | United States |
| Start | 01/2021 |
| End | 06/2023 |
| Description | Pump priming award |
| Amount | £19,200 (GBP) |
| Organisation | University of Edinburgh |
| Department | The Roslin Institute |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 07/2019 |
| End | 07/2020 |
| Description | Real-time monitoring and predictive modelling of the impact of human behaviour and vaccine characteristics on COVID-19 vaccination in Scotland |
| Amount | £321,960 (GBP) |
| Funding ID | ES/W001489/1 |
| Organisation | Economic and Social Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2021 |
| End | 09/2022 |
| Description | Redefining the role of the microglia in CNS prion disease pathogenesis |
| Amount | £3,624 (GBP) |
| Organisation | RS Macdonald Charitable Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 04/2018 |
| End | 12/2019 |
| Description | Regulatory approval and antigen production towards testing an experimental vaccine in a feedlot trial in the USA to limit E. coli O157 excretion from cattle. |
| Amount | £20,000 (GBP) |
| Funding ID | IAA PIII043 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2020 |
| End | 09/2020 |
| Description | Research Grant - Paul Digard - Tylvalosin as a porcine antiviral compound |
| Amount | £90,833 (GBP) |
| Funding ID | Roslin 1840 |
| Organisation | Eco Animal Health Ltd |
| Sector | Private |
| Country | United Kingdom |
| Start | 03/2017 |
| End | 09/2018 |
| Description | Research Grant - Ross Houston - Investigating genetic resistance to Bonamia in European flat oyster |
| Amount | £165,026 (GBP) |
| Organisation | Blue Marine Foundation |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 06/2018 |
| End | 06/2020 |
| Description | Research Incentive Grants - Liam Morrison - Unravelling the epidemiology of tropical theileriosis |
| Amount | £9,740 (GBP) |
| Funding ID | RIG007514 |
| Organisation | Carnegie Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 05/2018 |
| End | 06/2019 |
| Description | Research Incentive Grants - Robin Cassidy - Cloning, expression and characterisation of lymphostatin-like molecules from Chlamydia spp. |
| Amount | £9,886 (GBP) |
| Funding ID | RIG007401 |
| Organisation | Carnegie Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2018 |
| End | 02/2019 |
| Description | Responsive Mode - David Gally - Machine-learning to predict and understand the zoonotic threat of E. coli O157 isolates |
| Amount | £535,103 (GBP) |
| Funding ID | BB/P02095X/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 09/2021 |
| Description | Responsive Mode - Finn Grey - Identification of interferon stimulated genes that restrict cross-species transmission of influenza A virus. |
| Amount | £768,377 (GBP) |
| Funding ID | BB/S00114X/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2018 |
| End | 09/2021 |
| Description | Responsive Mode - Kellie Watson - The role of interleukin-10 (IL-10) in the regulation of innate immunity in the domestic chicken. |
| Amount | £801,119 (GBP) |
| Funding ID | BB/P022049/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2017 |
| End | 11/2020 |
| Description | Responsive Mode - Mick Watson - Dissecting the molecular pathways of MDV oncoprotein Meq for understanding pathogenesis and aid vaccine development |
| Amount | £391,146 (GBP) |
| Funding ID | BB/R007632/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2018 |
| End | 05/2021 |
| Description | Responsive Mode - Neil Mabbott - Role of distinct mononuclear phagocyte subsets in oral prion disease pathogenesis |
| Amount | £558,982 (GBP) |
| Funding ID | BB/S005471/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2018 |
| End | 11/2021 |
| Description | Responsive Mode - Rowland Kao - Joint estimation of epidemiological and genetic processes for Mycobacterium bovis transmission dynamics in cattle and badgers |
| Amount | £302,174 (GBP) |
| Funding ID | BB/L010569/2 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2017 |
| End | 06/2018 |
| Description | Responsive Mode - Rowland Kao Bilateral BBSRC-SF1: Tackling a multi-host pathogen problem - phylodynamic analyses of the epidemiology of M. bovis in Britain and Ireland |
| Amount | £560,091 (GBP) |
| Funding ID | BB/P010598/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2017 |
| End | 09/2020 |
| Description | Resposive Mode - Mike McGrew - Investigating the role of ANP32A in the replication of avain influenza virus |
| Amount | £520,795 (GBP) |
| Funding ID | BB/S006796/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2019 |
| End | 12/2021 |
| Description | Salmonid alphavirus genomic surveillance in Norwegian Aquaculture |
| Amount | £5,714 (GBP) |
| Organisation | Pharmaq |
| Sector | Private |
| Country | Norway |
| Start | 07/2020 |
| End | 03/2021 |
| Description | Scaling up a high throughput phenotypic screening platform |
| Amount | £155,560 (GBP) |
| Organisation | Government of Scotland |
| Department | Scottish Funding Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2020 |
| End | 07/2021 |
| Description | Sir Henry Dale Fellowship - Eleanor Gaunt - The role of CpG dinucleotides in regulating virus replication kinetics |
| Amount | £1,025,674 (GBP) |
| Funding ID | 211222/Z/18/Z |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2018 |
| End | 09/2023 |
| Description | Small Grants - Rowland Kao - US-UK Collab: Mycobacterial Transmission Dynamics in Agricultural Systems: Integrating Phylogenetics, Epidemiology, Ecology and Economics |
| Amount | £137,328 (GBP) |
| Funding ID | BB/M01262X/2 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2017 |
| End | 08/2019 |
| Description | Small RNA diagnostic for Trypanosoma Infection |
| Amount | £197,503 (GBP) |
| Organisation | Roslin Technologies |
| Sector | Private |
| Country | United Kingdom |
| Start | 01/2020 |
| End | 12/2020 |
| Description | Studentship - Fiona Houston - Modelling the susceptibility of British deer to chronic wasting disease |
| Amount | £26,782 (GBP) |
| Funding ID | RES2017FH |
| Organisation | British Deer Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 06/2017 |
| End | 06/2018 |
| Description | Sub-award from BBSRC Flexible Talent Mobility Award (BB/R506564/1). Professor Lonneke Vervelde & Dr Sam Ellis. 'Identification of protective epitopes for control of avian influenza virus'. |
| Amount | £14,138 (GBP) |
| Funding ID | BB/R506564/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2017 |
| End | 03/2019 |
| Description | Sub-award from BBSRC Impact Accelerator Account BB/S506722/1. Professor David Gally 'Using bacteriophage to remove Escherichia coli O157:H7 from cattle colonised at the terminal rectum' |
| Amount | £33,439 (GBP) |
| Funding ID | BB/S506722/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 03/2021 |
| Description | Sub-award from ISCF Transforming Food Production Seeding Award (ISCF-TFP-SA-Edinburgh). Dr Thibauld Porphyre 'Developing an online cost-estimator to support breeding and disease management decisions in the pig industry' |
| Amount | £15,744 (GBP) |
| Funding ID | ISCF-TFP-SA-Edinburgh |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2018 |
| End | 02/2019 |
| Description | The Dogs Trust |
| Amount | £242,000 (GBP) |
| Organisation | Dogs Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 05/2019 |
| End | 05/2022 |
| Description | The molecular biology of Rotavirus A |
| Amount | £63,000 (GBP) |
| Organisation | University of Edinburgh |
| Department | The Roslin Institute |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 04/2019 |
| End | 05/2023 |
| Description | Tracking Haulage in East Africa to support COVID-19 surveillance- THEA-C19 |
| Amount | £523,180 (GBP) |
| Funding ID | MR/V034952/1 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2020 |
| End | 05/2023 |
| Description | Tracking haulage in East Africa to support COVID-19 surveillance (THEA-c19) |
| Amount | £506,158 (GBP) |
| Funding ID | MR/V034952/1 |
| Organisation | National Institute for Health Research |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2020 |
| End | 04/2022 |
| Description | Tracking the rise and fall of Scottish SARS-CoV-2/COVID-19 using virus sequences |
| Amount | £62,000 (GBP) |
| Funding ID | COV/EDI/20/11 |
| Organisation | Chief Scientist Office |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2020 |
| End | 10/2020 |
| Description | U.V. irradiation as a means of sterilising bank notes |
| Amount | £72,016 (GBP) |
| Funding ID | 10195649 |
| Organisation | NCR Finnancial Systems |
| Sector | Private |
| Country | United States |
| Start | 07/2020 |
| End | 07/2021 |
| Description | UK Consortium on Avian Influenza Research Gaps |
| Amount | £224,832 (GBP) |
| Funding ID | BB/X006123/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2022 |
| End | 05/2023 |
| Description | UK International coronavirus network (UK-ICN) |
| Amount | £510,207 (GBP) |
| Funding ID | BB/W003287/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2021 |
| End | 09/2025 |
| Description | Understanding the E.Coli O157 strains associated with super-shedding and human disease |
| Amount | £14,360 (GBP) |
| Funding ID | FSS/2019/009 |
| Organisation | Government of Scotland |
| Department | Food Standards Agency (FSA), Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 11/2019 |
| Description | Using an experimentally induced ovine pulmonary adenocarcinoma model to advance human lung cancer research |
| Amount | £1,335,587 (GBP) |
| Organisation | Johnson & Johnson |
| Sector | Private |
| Country | United States |
| Start | 03/2023 |
| End | 03/2025 |
| Description | Using national whole-genome sequence data to inform epidemiological models of COVID-19 variant emergence and outbreak risks in Scotland |
| Amount | £77,530 (GBP) |
| Funding ID | HIPS/21/63 |
| Organisation | Chief Scientist Office |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2022 |
| End | 09/2023 |
| Description | VEO - Versatile Emerging infectious disease Observatory forecasting, nowcasting and tracking in a changing world |
| Amount | € 14,994,726 (EUR) |
| Funding ID | 874735 Proposal number |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 01/2020 |
| End | 12/2025 |
| Description | Vacation Scholarship - Paul Digard - Mechanisms of antiviral drug resistance in influenza A virus |
| Amount | £2,000 (GBP) |
| Funding ID | 208707/Z/17/Z |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 06/2017 |
| End | 08/2017 |
| Description | Virulent Non-Notifiable Avian Influenza; Determinants of virulence of emerging viruses |
| Amount | £506,806 (GBP) |
| Funding ID | BB/V019899/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2021 |
| End | 03/2024 |
| Description | Wastewater Epidemiology and Infectivity of SARS-CoV-2 (WELIES |
| Amount | £270,542 (GBP) |
| Funding ID | NE/V010441/1 |
| Organisation | United Kingdom Research and Innovation |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2020 |
| End | 09/2021 |
| Description | Wellcome Trust Collaborative Award |
| Amount | £2,021,766 (GBP) |
| Funding ID | 206815/Z/17/Z |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 03/2022 |
| Description | Wellcome Trust Institutional Strategic Support Fund-University of Edinburgh |
| Amount | £31,700 (GBP) |
| Funding ID | IS3-R1.09 19/20 |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2020 |
| End | 03/2021 |
| Description | Wellcome Trust Pathfinder Award |
| Amount | £129,709 (GBP) |
| Funding ID | 204521/Z/16/Z |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 04/2017 |
| End | 11/2018 |
| Description | Whole Genome Sequencing for Mycobacterium bovis to analyse bi directional transmission amongst badgers and cattle |
| Amount | £39,511 (GBP) |
| Funding ID | 31441 DEFRA |
| Organisation | Department For Environment, Food And Rural Affairs (DEFRA) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2021 |
| End | 12/2021 |
| Description | Whole room and workplace disinfection by means of electrogenerated oxidants delivered in the form of a fog, mist or spray |
| Amount | £250,607 (GBP) |
| Funding ID | 83701 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2020 |
| End | 03/2022 |
| Description | [18-EEID US-UK DDCOVMP] Drivers of diversity and transmission of co-circulating viral lineages in host meta-populations |
| Amount | £407,215 (GBP) |
| Funding ID | BB/T004401/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2019 |
| End | 08/2024 |
| Description | [18-EEID US-UK DDCOVMP] Drivers of diversity and transmission of co-circulating viral lineages in host meta-populations |
| Amount | £407,215 (GBP) |
| Funding ID | BB/T004401/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2019 |
| End | 08/2024 |
| Description | [YY-EEID US-UK XXXX] Predictive phylogenetics for evolutionary and transmission dynamics of newly emerging avian influenza viruses |
| Amount | £1,250,967 (GBP) |
| Funding ID | BB/V011286/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2021 |
| End | 12/2025 |
| Description | chicken synthetic microbiota (chisyn) |
| Amount | £77,801 (GBP) |
| Organisation | Technical University of Munich |
| Sector | Academic/University |
| Country | Germany |
| Start | 09/2023 |
| End | 05/2025 |
| Description | dissecting fatty acid metabolism in livestock trypanosomes |
| Amount | £507,271 (GBP) |
| Funding ID | BB/X009807/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2023 |
| End | 08/2026 |
| Description | evaluation of the scottish wastewater surveillance system for sars-cov-2 |
| Amount | £74,681 (GBP) |
| Funding ID | PHS2022-23R015 |
| Organisation | Public Health Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2023 |
| End | 03/2024 |
| Description | flu trailmap (transmission and risk of avian influenza: learning more to advance preparedness) |
| Amount | £864,340 (GBP) |
| Funding ID | BB/Y007352/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2023 |
| End | 11/2025 |
| Description | fluswitch: identification of factors driving the emergence and spread of avian influenza viruses with zoonotic potential |
| Amount | £389,623 (GBP) |
| Organisation | Department For Environment, Food And Rural Affairs (DEFRA) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2023 |
| End | 12/2027 |
| Description | investigating the potential of bacteriophages to kill scottish streptococcus uberis isolates as a primer for the development of phage therapy for bovine mastitis |
| Amount | £17,091 (GBP) |
| Funding ID | MMI/HA0514-0081 MMI |
| Organisation | Hannah Dairy Research Foundation |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 02/2024 |
| End | 01/2026 |
| Description | studentship: advancing phage therapy for human urinary tract infections |
| Amount | £113,009 (GBP) |
| Funding ID | PHD-50457-2021 |
| Organisation | Medical Research Scotland |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2022 |
| End | 10/2026 |
| Title | A Framework for Integrating Qualitative and Quantitative Data in Knowledge, Attitude, and Practice Studies |
| Description | As a quantitative epidemiologists, we know now that most of the risk factors of disease are driven by human behaviour fine tuned by context. So to fully understand the nuisances of disease dynamics we developed and test a framework for integrating socio-economic and anthropological data with quantitative data in order to understand biological dynamics at population level. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | It is a well cited paper, but also we have used the Framework to design grant applications for which we are awaiting results. |
| URL | https://www.frontiersin.org/articles/10.3389/fpubh.2017.00318/full |
| Title | Digital One health Framework |
| Description | The current implementation of One Health (OH) primarily focuses on multi-sectoral collaboration but often overlooks opportunities to integrate contextual and pathogen-related data into a unified data resource. This lack of integration hampers effective, data-driven decision-making in OH activities. In this perspective, we examine the existing strategies for data sharing and identify gaps and barriers to integration. To overcome these challenges, we propose the Digital OH (DOH) framework for data integration, which consolidates data-sharing principles within five pillars for the OH community of practice: (a) Harmonization of standards to establish trust, (b) Automation of data capture to enhance quality and efficiency, (c) Integration of data at point of capture to limit bureaucracy, (d) Onboard data analysis to articulate utility, and (e) Archiving and governance to safeguard the OH data resource. We discuss an upcoming pilot program as a use case focusing on antimicrobial resistance surveillance to illustrate the application of this framework. Our ambition is to leverage technology to create data as a shared resource using DOH not only to overcome current structural barriers but also to address prevailing ethical and legal concerns. By doing so, we can enhance the efficiency and effectiveness of decision-making processes in the OH community of practice, at a national, regional, and international level. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | The framework supports how data can be integrated across sector i.e human, veterinary and environment |
| URL | https://onehealth.ijidonline.org/article/S2949-9151(23)00011-2/fulltext |
| Title | ELISpot for PRRSV |
| Description | An ELISpot for PRRSV was developed to investigate cellular immune responses in vaccine development studies. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | The tool is essential to do vaccine efficacy studies. |
| Title | ELispot for PCV2 |
| Description | The assay is able to detect a cellular immune response to PCV2. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2017 |
| Provided To Others? | No |
| Impact | Improvement of vaccine efficacy assessment. |
| Title | In vitro infection model for Porcine Reproductive and Respiratory Syndrome |
| Description | Peripheral blood monocytes (PBMC) are isolated from blood and either cryopreserved or used immediately. PBMC are cultured in vitro in the presence of CSF1 for 5 days.Growth in the presence of CSF1 facilitates the differentiation of PBMC into macrophages. These in vitro differentiated macrophages are subsequently infected with Porcine Reproductive and Respiratory Syndrome Virus, |
| Type Of Material | Model of mechanisms or symptoms - in vitro |
| Year Produced | 2015 |
| Provided To Others? | No |
| Impact | The in vitro PRRS infection model facilitates studies of genetic variation in both host (pigs) and pathogen (e.g. PRRSV) simultaneously. Unlike for the laboratory mouse there is an absence of inbred strains or lines of pigs. The PBMC resource allows the same pig to be infected separately with multiple different pathogens or genetic variants of a pathogen. The PBMC resource and in vitro PRRS infection model also facilitates genetics studies that require population or sample sizes of hundreds to thousands that are not feasible through animal challenge experiments. Thus, the in vitro infection model also contributes to the 3Rs agenda. |
| Title | Informatic tools for clinical metagenomics |
| Description | This tool allows us to use changes in microbial variance to explain clinical and biological process. We use four previously published studies to demonstrate this utility. The tool is still under going refinement which should be ready for use in June 2021 |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | This is yet to be demonstrated |
| URL | https://clinical-metagenomics.shinyapps.io/clinical-metagenomics/ |
| Title | Nanopore sequencing of aquaculture viruses |
| Description | Methods for targeted whole genome sequencing were developed for several economically important aquaculture RNA viruses for use on nanopore MinION sequencing platform. No whole genome sequencing of these viruses had previously been performed using nanopore sequencing. This work also established this method for use in other experimental scenarios and is currently being used for other projects. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | NA |
| URL | https://www.nature.com/articles/s41598-018-34464-x |
| Title | Strategy for quantifying individual bacterial strains during mixed infections |
| Description | We devised a novel strategy to follow the fate of individual bacterial strains during mixed infections. Specifically, we wished to follow the fate of multiple Salmonella enterica serovars during colonisation of the bovine host. These are indistinguishable by culture, and while they can be specifically detected by serology, quantification of numbers of each serovar during mixed infection would involve analysis of many hundreds or thousands of individual colonies. We devised a method based on massively-parallel sequencing of a polymorphic allele (rpoB), whereby sequence reads can be used to identify the strain present (based on single nucleotide polymorphisms specific to each strain) and the number of sequence reads can be taken as a measure of the abundance of the cognate strain. Using this method we were able to simultaneously define the fate of 12 different S. enterica strains during infection of cattle, including as they colonised the gut over time and spread from the gut to the lymphatic system and other tissues. This 3R approach should allow phenotypes to be derived with reduced use of animals in experiments and could, for example, be used to see if vaccine-induced responses are effective in control of all the different members of a bacterial population present - in this case toward a pan-serovar cross-protective vaccine. A manuscript reporting these findings was published in late 2017 (Vohra et al). Though a direct output of BBSRC responsive-mode funding, the project was underpinned by core-strategic grants from 2012 and 2017 (e.g. via the involvement of core-funded staff in animal studies) and a BBSRC US-UK partnering award, where the ideas for following serovars based on massively-parallel sequencing of rpoB and ileS were jointly developed. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | Too early to say, but the method has the potential to reduce animal use in evaluating the cross-protective efficacy of vaccines or treatments as it enables many strains to be tested at once in a single animal rather than in separate groups that each receive a single strain. |
| Title | Targeted sequence capture of viruses in aquacultured fish |
| Description | Using a wide-ranging panel of probes, tiled across the genomes of several important aquaculture-related RNA viruses, a whole genome sequencing approach was established to efficiently enrich for viral nucleic acids. This was validated using a number of viral isolates to detect and characterise multi-viral infections which can produce important industry-regulator information. This approach has allowed us to study viral genetic diversity using an unbiased method unlike any other previously attempted. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | Not applicable yet - the paper is currently in preparation |
| Title | A putative genomic map for resistance of Bos indicus cattle in Cameroon to bovine tuberculosis |
| Description | Bovine Tuberculosis (bTB) caused by Mycobacterium bovis is a livestock disease of global economic and public health importance. There are currently no effective vaccines available for livestock and so control relies on animal level surveillance and pasteurisation of dairy products. A new alternative control approach is to exploit the genetic variability of the host; recent studies have demonstrated that breeding Bos taurus cattle for increased resistance to bTB is feasible. The utility of such an approach is still unknown for the Bos indicus cattle population. This study aims to assess genetic variation in bTB resistance and the underlying genomic architecture in Bos indicus breeds in Cameroon. We conducted a cross-sectional study of slaughter cattle in Cameroon and genotyped a sample of 213 cattle. Their genomic diversity was characterised using PCA, hierarchical clustering and admixture analysis. We assessed genetic variation in bTB resistance using heritability analysis and compared quantitative trait loci. Previous studies had found that breed was an important factor in explaining the epidemiology of bTB, with Fulani cattle appearing to be more susceptible than mixed breeds. However, we show that the apparent phenotypic differences in visual appearance between the breeds was not reflected by clear genomic differences. At the genetic level, cattle belonging to different hierarchical genomic clusters differed in their susceptibility to bTB. There was evidence of a genomic association between M. bovis infection status with specific SNPs. We highlight the need to understand the challenges faced by livestock in specific settings both in terms of pathogens and the environment, in addition to their intended purpose and how they fit into a defined management system. It is only at this point livestock keepers can then make informed breeding choices, not only for resistance to disease but also for increasing production. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | We highlight the need to understand the challenges faced by livestock in specific settings both in terms of pathogens and the environment, in addition to their intended purpose and how they fit into a defined management system. It is only at this point livestock keepers can then make informed breeding choices, not only for resistance to disease but also for increasing production. |
| URL | https://doi.org/10.7488/ds/2722 |
| Title | Additional file 1 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 1: Table S1. Overview of NGS experiments conducted in this study and data obtained from the literature. Ornithodoros moubata cell line names have been abbreviated by removal of "/CTVM" and Ornithodoros porcinus and Ornithodoros moubata have been abbreviated for convenience. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Identification_of_African_... |
| Title | Additional file 1 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 1: Table S1. Overview of NGS experiments conducted in this study and data obtained from the literature. Ornithodoros moubata cell line names have been abbreviated by removal of "/CTVM" and Ornithodoros porcinus and Ornithodoros moubata have been abbreviated for convenience. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Identification_of_African_... |
| Title | Additional file 1 of Temporal and nutritional effects on the weaner pig ileal microbiota |
| Description | Additional file 1. Taxonomic description of metagenomic data (day 13). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Temporal_and_nutritional_e... |
| Title | Additional file 1 of Temporal and nutritional effects on the weaner pig ileal microbiota |
| Description | Additional file 1. Taxonomic description of metagenomic data (day 13). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Temporal_and_nutritional_e... |
| Title | Additional file 10 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 10: Table S8. qRT-PCR results of Ornithodoros ticks experimentally infected with different ASFV-genotype isolate. Shown are ASFV-P72 transcript-specific Cq-values of third nymphal stage ticks fed with defibrinated pig blood, containing either 1 x 104 HAU/ml or 1 x 106 HAU/ml ASFV-ken.rie1 (GT X) (A-D), 1 x 105 HAU/ml ASFV-Ken06.bus (GT IX) (E-F) or 1 x 104 HAU/ml ASFV-Sardinia (GT I) (G-H). Due to the limited number of field ticks available and feeding under artificial conditions, fifteen Ornithodoros porcinus ticks were collected in each of three experiments and ten in two experiments while for the laboratory-reared Ornithodoros moubata, twenty-five individuals were collected in each of three experiments and fifteen in one experiment. All samples were stored at - 80 °C until RNA-extraction and ASFV transcript-specific qRT-PCR analysis as described in the 'Material and methods' section. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_10_of_Identification_of_African... |
| Title | Additional file 10 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 10: Table S8. qRT-PCR results of Ornithodoros ticks experimentally infected with different ASFV-genotype isolate. Shown are ASFV-P72 transcript-specific Cq-values of third nymphal stage ticks fed with defibrinated pig blood, containing either 1 x 104 HAU/ml or 1 x 106 HAU/ml ASFV-ken.rie1 (GT X) (A-D), 1 x 105 HAU/ml ASFV-Ken06.bus (GT IX) (E-F) or 1 x 104 HAU/ml ASFV-Sardinia (GT I) (G-H). Due to the limited number of field ticks available and feeding under artificial conditions, fifteen Ornithodoros porcinus ticks were collected in each of three experiments and ten in two experiments while for the laboratory-reared Ornithodoros moubata, twenty-five individuals were collected in each of three experiments and fifteen in one experiment. All samples were stored at - 80 °C until RNA-extraction and ASFV transcript-specific qRT-PCR analysis as described in the 'Material and methods' section. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_10_of_Identification_of_African... |
| Title | Additional file 15 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 15: Table S9. Results of small RNA sequencing and mapping against ASFV and ASFLI-elements. Small RNA was sequenced from Ornithodoros porcinus and Ornithodoros moubata nymphal stage ticks. After deduplication using BBMap, 22 nt siRNA and 28-29 nt piRNA fractions were extracted and mapped against ASFV and ASFLI-elements using Bowtie. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_15_of_Identification_of_African... |
| Title | Additional file 15 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 15: Table S9. Results of small RNA sequencing and mapping against ASFV and ASFLI-elements. Small RNA was sequenced from Ornithodoros porcinus and Ornithodoros moubata nymphal stage ticks. After deduplication using BBMap, 22 nt siRNA and 28-29 nt piRNA fractions were extracted and mapped against ASFV and ASFLI-elements using Bowtie. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_15_of_Identification_of_African... |
| Title | Additional file 16 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 16: Table S10. O. moubata piRNA ping-pong signature analysed by PingPongPro v1.0 with default parameters and -b option (creates additional browser track files, which are suitable for display in common genome browsers). The closer the Score-value (1 minus the FDR-value: estimated fraction of signatures that have the same combination of properties, but that are not true ping-pong signatures) which is calculated from adenine bias at pos. 10 of the piRNA, stack height - e.g. the number of reads that make up the stack and independence of local coverage is to 1, the more likely is a true ping-pong signature. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_16_of_Identification_of_African... |
| Title | Additional file 16 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 16: Table S10. O. moubata piRNA ping-pong signature analysed by PingPongPro v1.0 with default parameters and -b option (creates additional browser track files, which are suitable for display in common genome browsers). The closer the Score-value (1 minus the FDR-value: estimated fraction of signatures that have the same combination of properties, but that are not true ping-pong signatures) which is calculated from adenine bias at pos. 10 of the piRNA, stack height - e.g. the number of reads that make up the stack and independence of local coverage is to 1, the more likely is a true ping-pong signature. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_16_of_Identification_of_African... |
| Title | Additional file 17 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 17: Table S11. O. porcinus piRNA ping-pong signature analysed by PingPongPro v1.0 with default parameters and -b option (creates additional browser track files, which are suitable for display in common genome browsers). The closer the Score-value (1 minus the FDR-value: estimated fraction of signatures that have the same combination of properties, but that are not true ping-pong signatures) which is calculated from adenine bias at pos. 10 of the piRNA, stack height - e.g. the number of reads that make up the stack and independence of local coverage is to 1, the more likely is a true ping-pong signature. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_17_of_Identification_of_African... |
| Title | Additional file 17 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 17: Table S11. O. porcinus piRNA ping-pong signature analysed by PingPongPro v1.0 with default parameters and -b option (creates additional browser track files, which are suitable for display in common genome browsers). The closer the Score-value (1 minus the FDR-value: estimated fraction of signatures that have the same combination of properties, but that are not true ping-pong signatures) which is calculated from adenine bias at pos. 10 of the piRNA, stack height - e.g. the number of reads that make up the stack and independence of local coverage is to 1, the more likely is a true ping-pong signature. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_17_of_Identification_of_African... |
| Title | Additional file 19 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 19: Table S12.Primer and probe sequences used in this study. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_19_of_Identification_of_African... |
| Title | Additional file 19 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 19: Table S12.Primer and probe sequences used in this study. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_19_of_Identification_of_African... |
| Title | Additional file 2 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 2: Table S2. ASFV-like transcripts detected in data from six Ornithodoros moubata cell lines and O.moubata ticks by mRNA-sequencing and data analysis from published sequences ASFV-like sequences from tick cell libraries lib01543-46 und lib01610-11 (total RNA) were identified using RIEMS. The resulting reads were blasted against the NCBI BLASTn database for confirmation and annotation. Ornithodoros moubata transcriptome data from a previous study42 was downloaded from GenBank, and ASFV-like sequences were identified by mapping the data against a tailored database containing all known ASFV sequences and all previously obtained ASFV-like sequences. The resulting reads and contigs were annotated after a BLASTn search against the entire BLASTn database. Sequencing data from the mRNA enriched OME21 library lib02965 was mapped against a tailored database containing all known ASFV sequences and all previously obtained ASFV-like sequences, and resulting contigs were blasted against the entire BLASTn database. Per sequence, only the hit with the lowest e-value is shown. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_2_of_Identification_of_African_... |
| Title | Additional file 2 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 2: Table S2. ASFV-like transcripts detected in data from six Ornithodoros moubata cell lines and O.moubata ticks by mRNA-sequencing and data analysis from published sequences ASFV-like sequences from tick cell libraries lib01543-46 und lib01610-11 (total RNA) were identified using RIEMS. The resulting reads were blasted against the NCBI BLASTn database for confirmation and annotation. Ornithodoros moubata transcriptome data from a previous study42 was downloaded from GenBank, and ASFV-like sequences were identified by mapping the data against a tailored database containing all known ASFV sequences and all previously obtained ASFV-like sequences. The resulting reads and contigs were annotated after a BLASTn search against the entire BLASTn database. Sequencing data from the mRNA enriched OME21 library lib02965 was mapped against a tailored database containing all known ASFV sequences and all previously obtained ASFV-like sequences, and resulting contigs were blasted against the entire BLASTn database. Per sequence, only the hit with the lowest e-value is shown. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_2_of_Identification_of_African_... |
| Title | Additional file 2 of Temporal and nutritional effects on the weaner pig ileal microbiota |
| Description | Additional file 2. Alpha diversity statistical outputs from 16S rRNA gene sequencing data. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_2_of_Temporal_and_nutritional_e... |
| Title | Additional file 2 of Temporal and nutritional effects on the weaner pig ileal microbiota |
| Description | Additional file 2. Alpha diversity statistical outputs from 16S rRNA gene sequencing data. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_2_of_Temporal_and_nutritional_e... |
| Title | Additional file 3 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 3: Table S3. BLASTn results of SPAdes-assembled contigs containing ASFLI- and other endogenous viral elements detected in the OME/CTVM21 genome. Shown are hits with the lowest e-value for viral, tick and mobile genetic element-related genes, as obtained by Blastn against the entire NCBI database. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Identification_of_African_... |
| Title | Additional file 3 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 3: Table S3. BLASTn results of SPAdes-assembled contigs containing ASFLI- and other endogenous viral elements detected in the OME/CTVM21 genome. Shown are hits with the lowest e-value for viral, tick and mobile genetic element-related genes, as obtained by Blastn against the entire NCBI database. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Identification_of_African_... |
| Title | Additional file 3 of Temporal and nutritional effects on the weaner pig ileal microbiota |
| Description | Additional file 3. Statistical analysis of taxonomic changes by time point. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Temporal_and_nutritional_e... |
| Title | Additional file 3 of Temporal and nutritional effects on the weaner pig ileal microbiota |
| Description | Additional file 3. Statistical analysis of taxonomic changes by time point. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Temporal_and_nutritional_e... |
| Title | Additional file 4 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 4: Table S4. BLASTp results of all ORFs >500 bp on SPAdes-assembled contigs containing ASFLI- and other endogenous viral elements detected in the OME/CTVM21 genome Shown are hits with the lowest e-value for viral-, tick and mobile genetic element-related proteins, as obtained by Blastp of ORFs >500 bp against the entire NCBI database. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_4_of_Identification_of_African_... |
| Title | Additional file 4 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 4: Table S4. BLASTp results of all ORFs >500 bp on SPAdes-assembled contigs containing ASFLI- and other endogenous viral elements detected in the OME/CTVM21 genome Shown are hits with the lowest e-value for viral-, tick and mobile genetic element-related proteins, as obtained by Blastp of ORFs >500 bp against the entire NCBI database. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_4_of_Identification_of_African_... |
| Title | Additional file 4 of Temporal and nutritional effects on the weaner pig ileal microbiota |
| Description | Additional file 4. Full statistical analysis of metagenomic dataset highlighting taxonomic differences between diets at day 13. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_4_of_Temporal_and_nutritional_e... |
| Title | Additional file 4 of Temporal and nutritional effects on the weaner pig ileal microbiota |
| Description | Additional file 4. Full statistical analysis of metagenomic dataset highlighting taxonomic differences between diets at day 13. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_4_of_Temporal_and_nutritional_e... |
| Title | Additional file 5 of Temporal and nutritional effects on the weaner pig ileal microbiota |
| Description | Additional file 5. Pig metadata. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_5_of_Temporal_and_nutritional_e... |
| Title | Additional file 5 of Temporal and nutritional effects on the weaner pig ileal microbiota |
| Description | Additional file 5. Pig metadata. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_5_of_Temporal_and_nutritional_e... |
| Title | Additional file 6 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 6: Table S5. Results of tick and tick cell line screening for ASFLI-elements by qPCR. DNA from single ticks and every tick cell line (n=1) was extracted and analysed by qPCR for six ASFV-like genes as described in the 'Material and methods' section. All samples were tested with a qPCR control targeting a tick housekeeping gene to demonstrate successful DNA extraction and presence of tick DNA. Absence of ASFV in samples producing false positive results was proven by an OIE-listed qPCR. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_6_of_Identification_of_African_... |
| Title | Additional file 6 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 6: Table S5. Results of tick and tick cell line screening for ASFLI-elements by qPCR. DNA from single ticks and every tick cell line (n=1) was extracted and analysed by qPCR for six ASFV-like genes as described in the 'Material and methods' section. All samples were tested with a qPCR control targeting a tick housekeeping gene to demonstrate successful DNA extraction and presence of tick DNA. Absence of ASFV in samples producing false positive results was proven by an OIE-listed qPCR. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_6_of_Identification_of_African_... |
| Title | Additional file 7 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 7: Table S6. BLASTn results of SPAdes-assembled contigs from Ornithodoro porcinus France and Kenya17 containing ASFLI-elements. Shown are hits with the lowest e-value for ASFV-genes as obtained by Blastn against the entire NCBI database. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_7_of_Identification_of_African_... |
| Title | Additional file 7 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 7: Table S6. BLASTn results of SPAdes-assembled contigs from Ornithodoro porcinus France and Kenya17 containing ASFLI-elements. Shown are hits with the lowest e-value for ASFV-genes as obtained by Blastn against the entire NCBI database. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_7_of_Identification_of_African_... |
| Title | Additional file 9 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 9: Table S7. SPAdes-assembled contigs from deep sequencing data from libraries AGL001 and MPA001, as generated from museum-stored ticks. Data from libraries from museum-stored tick were mapped against ASFLI-element-containing databases of Ornithoidoros moubata (AGL001) and Ornithodoros porcinus (MPA001) using Bowtie2 (v.2.3.4.3) with default parameters. Subsequently, mapped reads were assembled using SPAdes and aligned to the corresponding ASFLI- element-contigs using MAFFT (v. 7.388) in Geneious. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_9_of_Identification_of_African_... |
| Title | Additional file 9 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution |
| Description | Additional file 9: Table S7. SPAdes-assembled contigs from deep sequencing data from libraries AGL001 and MPA001, as generated from museum-stored ticks. Data from libraries from museum-stored tick were mapped against ASFLI-element-containing databases of Ornithoidoros moubata (AGL001) and Ornithodoros porcinus (MPA001) using Bowtie2 (v.2.3.4.3) with default parameters. Subsequently, mapped reads were assembled using SPAdes and aligned to the corresponding ASFLI- element-contigs using MAFFT (v. 7.388) in Geneious. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_9_of_Identification_of_African_... |
| Title | Avianbase: a community resource for bird genomics |
| Description | The Avianbase Project is an initiative led by the Roslin Institute in collaboration with the Avian Phylogenomics Consortium and Ensembl to make the initial sequence and annotation available for 48 bird species within the Ensembl framework. The Avianbase Project is using the Ensembl infrastructure to share data brought together by the Avian Phylogenomics Consortium (as part of the Avian Genome Consortium) for 48 birds. Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore we announce Avianbase, a resource for bird genomics, which provides access to data released by the Avian Phylogenomics Consortium. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2015 |
| Provided To Others? | Yes |
| Impact | The Avianbase project was overviewed in the paper of 2015 (Lél Eöry, M Thomas P Gilbert, Cai Li, Bo Li, Alan Archibald, Bronwen L Aken, Guojie Zhang, Erich Jarvis, Paul Flicek and David W Burt (2015) Avianbase: a community resource for bird genomics. Genome Biology 16:21) which has been sited by over 18 times. It provides a valuable one-stop-shop to access a wealth of Avian genomic information to allow easy interrogation of genotype across species. |
| URL | http://avianbase.narf.ac.uk/index.html |
| Title | Bovine S. aureus sequence dataset |
| Description | Whole genome sequence data for 1080 S. aureus isolates from bovine mastitis |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | None yet |
| Title | COVID-19 spatial simulation model with inference |
| Description | A national model for COVID-19 spread in Scotland was constructed. This model uses publicly available data and further, where similar data is available, can immediately be used for other countries of similar or smaller size. The model development was in part funded by a re-purposing of this grant towards COVID-19 analysis (with permission from BBSRC). |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | This model is currently being used to inform Public Health Scotland on COVID controls. |
| URL | https://github.com/Kao-Group/SCoVMod |
| Title | Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii |
| Description | We deposited in ToxoDB, which is a database of Apicomplexan parasite genome and genomic data (such as RNA-seq, DNA-seq, proteomics, etc), whole genome ribosome profiling and RNA-sequencing data of intracellular and extracellular parasites to facilitate the identification of parasite genes that are essential for intercellular transmission. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | This is the first genome-wide ribosome profiling data on any strain of Toxoplasma and is helping research understand the role of translational regulation in the parasites's lifecycle. IT has informed current ongoing research in various aspects of Toxoplasma biology in many labs. |
| Title | Data for segment 4 subtype H5 - 1177 taxa from A brief history of bird flu |
| Description | Subsampled HA H5 sequences in fasta format, BEAST MCC tree, BEAUTI/BEAST xml configuration file, and sequence information as tables |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://rs.figshare.com/articles/Data_for_segment_4_subtype_H5_-_1177_taxa_from_A_brief_history_of_b... |
| Title | Data for segment 4 subtype H5 - 1177 taxa from A brief history of bird flu |
| Description | Subsampled HA H5 sequences in fasta format, BEAST MCC tree, BEAUTI/BEAST xml configuration file, and sequence information as tables |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://rs.figshare.com/articles/Data_for_segment_4_subtype_H5_-_1177_taxa_from_A_brief_history_of_b... |
| Title | Data for segments 1,2,3,5,7,8 - 10279 taxa from A brief history of bird flu |
| Description | Subsampled sequences in fasta format, corresponding trees in newick format and sequence information as tables |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://rs.figshare.com/articles/Data_for_segments_1_2_3_5_7_8_-_10279_taxa_from_A_brief_history_of_... |
| Title | Data for segments 1,2,3,5,7,8 - 10279 taxa from A brief history of bird flu |
| Description | Subsampled sequences in fasta format, corresponding trees in newick format and sequence information as tables |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://rs.figshare.com/articles/Data_for_segments_1_2_3_5_7_8_-_10279_taxa_from_A_brief_history_of_... |
| Title | Data for segments 1,2,3,5,7,8 - 8809 taxa for display from A brief history of bird flu |
| Description | Subsampled sequences in fasta format, corresponding trees in newick format, and sequence information for the display data sets as tables |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://rs.figshare.com/articles/Data_for_segments_1_2_3_5_7_8_-_8809_taxa_for_display_from_A_brief_... |
| Title | Data for segments 1,2,3,5,7,8 - 8809 taxa for display from A brief history of bird flu |
| Description | Subsampled sequences in fasta format, corresponding trees in newick format, and sequence information for the display data sets as tables |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://rs.figshare.com/articles/Data_for_segments_1_2_3_5_7_8_-_8809_taxa_for_display_from_A_brief_... |
| Title | Data from: A brief history of bird flu |
| Description | In 1918, a strain of influenza A virus caused a human pandemic resulting in the deaths of 50 million people. A century later, with the advent of sequencing technology and corresponding phylogenetic methods, we know much more about the origins, evolution and epidemiology of influenza epidemics. Here we review the history of avian influenza viruses through the lens of their genetic makeup: from their relationship to human pandemic viruses, starting with the 1918 H1N1 strain, through to the highly pathogenic epidemics in birds and zoonoses up to 2018. We describe the genesis of novel influenza A virus strains by reassortment and evolution in wild and domestic bird populations, as well as the role of wild bird migration in their long-range spread. The emergence of highly pathogenic avian influenza viruses, and the zoonotic incursions of avian H5 and H7 viruses into humans over the last couple of decades are also described. The threat of a new avian influenza virus causing a human pandemic is still present today, although control in domestic avian populations can minimize the risk to human health. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://datadryad.org/stash/dataset/doi:10.5061/dryad.5nb504n |
| Title | Data from: A field study evaluating the humoral immune response in Mongolian sheep vaccinated against sheeppox virus |
| Description | Sheeppox is a transboundary disease of sheep caused by infection with the capripoxvirus sheeppox virus (SPPV). Sheeppox is found in Africa, the Middle East and Asia and is characterised by fever, multifocal cutaneous raised lesions, and death, with substantial negative impact on affected flocks. Vaccination with live attenuated capripoxvirus (CPPV) strains is an effective and widely used means of controlling sheeppox outbreaks, however there are few reports of post-vaccination field surveillance studies of sheeppox. This study used a commercially available ELISA and a fluorescence-based neutralisation assay (FVNT) to examine quantitative and temporal features of the humoral response of sheep vaccinated with a live attenuated CPPV strain in Mongolia. 400 samples were tested using the ELISA, and a subset of 45 also tested with the FVNT. There was substantial agreement between the FVNT and ELISA tests. Antibodies to CPPV were detected between 40 and 262 days post vaccination. There was no significant difference between serological status (positive / negative) and sex or age, however an inverse correlation was found between the length of time since vaccination and serological status. Animals between 90 and 180 days post-vaccination were more likely to be positive than animals greater than 180 days post vaccination. This data provides temporal parameters to consider when planning sheeppox post-vaccination monitoring programmes. In summary, our results show a commercial CPPV ELISA kit is a robust and reliable assay for use in resource-restricted low and low-middle income countries for post CPPV vaccination surveillance on a regional or national level. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | http://datadryad.org/stash/dataset/doi:10.5061/dryad.msbcc2fvx |
| Title | MOESM1 of Effects of mutations in the effector domain of influenza A virus NS1 protein |
| Description | Additional file 1: Table S1. Mascot search results from LC-MS analysis of the novel polypeptide band in lane 8 of Fig. 2c. The data include a summary of protein IDs followed by details on the individual peptide hits. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/MOESM1_of_Effects_of_mutations_in_the_effector_domain_o... |
| Title | MOESM1 of Effects of mutations in the effector domain of influenza A virus NS1 protein |
| Description | Additional file 1: Table S1. Mascot search results from LC-MS analysis of the novel polypeptide band in lane 8 of Fig. 2c. The data include a summary of protein IDs followed by details on the individual peptide hits. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/MOESM1_of_Effects_of_mutations_in_the_effector_domain_o... |
| Title | Production system drivers of antibiotic resistance at the human-animal interface in Uganda |
| Description | This dataset and code are part of supplementary data for a manuscript Muwonge, A., Kakooza, T., Johnson, P.C.D., Kisuule, L., Kimaanga, M., Kankya, C., de Clare Bronsvoort, B.M., Lembo, T., "Production system drivers of antibiotic resistance at the human-animal interface in Uganda", The Lancet Planetary Health (in submission). They explore the role of livestock production systems in the epidemiology of antibacterial resistance (ABR) in sympatric human and livestock populations, which is poorly understood. Here, they examine ABR at the farmer-pig interface of Uganda, where the pig sector is rapidly growing, to quantify rates of resistance, understand associated human- and livestock-related factors, and investigate cross-species transmission. The motivation of this is to improve our understanding of the role of livestock production systems in the emergence and transmission of AMR, this paper uses phenotypic resistance profile from sentinel bacteria E.coli and Klebsiella, recovered from a faecal sample collected from farmers and their pigs across a one-year longitudinal study. This is mapped to AMR gene carriage of four selected genes measured using QPCR. Using the Metadata, they examine drivers of resistance in this setting, and also use the prevalence and sharing of MDR profiles to infer transmission. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | This dataset include data on AMR in livestock production systems. It allows us to elucidate how the transition from free range to semi-intensive livestock proaction will impact antibiotic use and resistance in developing countries |
| URL | https://datashare.ed.ac.uk/handle/10283/4833 |
| Title | Repurposing data to estimate livestock movements in developing countries |
| Description | The use of network analysis to support livestock disease control in low middle-income countries (LMICs) has historically been hampered by the cost of generating empirical data in the absence of animal movement recording schemes. To fill this gap, we have adopted methods which exploit freely available demographic and archived molecular data to generate livestock networks based on phylogeographic and gravity modelling techniques. We compare output from these network methodologies to empirical and randomly generated data. We simulate disease scenarios on the networks to evaluate the potential utility of our methodologies to inform robust livestock disease control strategies. The molecular network was the closest approximation to the empirical network, both in relation to topological and epidemic characteristics. The gravity network tended to overestimated disease epidemics. However, better agreement across all three networks was observed if less specific epidemic characteristics such as the size of outbreak were investigated. Moreover, these methods consistently identified the same important animal movement and trade hotspots as the empirical networks. We therefore consider this proof-of-concept that demographic data such as censuses and archived molecular data could be repurposed to inform livestock disease management in LMICs. |
| Type Of Material | Data analysis technique |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | We therefore consider this proof-of-concept that demographic data such as censuses and archived molecular data could be repurposed to inform livestock disease management in LMICs. |
| URL | https://doi.org/10.7488/ds/2780 |
| Title | The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps? |
| Description | Supplementary Material for 'The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps?' as published in Microbial Genomics. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://microbiology.figshare.com/articles/dataset/The_fall_and_rise_of_group_B_Streptococcus_in_dai... |
| Title | The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps? |
| Description | Supplementary Material for 'The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps?' as published in Microbial Genomics. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://microbiology.figshare.com/articles/dataset/The_fall_and_rise_of_group_B_Streptococcus_in_dai... |
| Title | Viral genome sequencing |
| Description | Whole genomes of salmonid alphavirus sequenced using second and third generation methods |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Ongoing collaborations with industry partners and Marine Scotland Science |
| URL | https://www.sciencedirect.com/science/article/pii/S0044848619321970 |
| Description | A comparative platform for strain typing CWD |
| Organisation | University of Alberta |
| Country | Canada |
| Sector | Academic/University |
| PI Contribution | This collaboration was funded by an award from the Alberta Prion Research Institute funding scheme. The contribution made my my team was to characterise samples from CWD infected deer. |
| Collaborator Contribution | Our collaborators provided us with brain material from CWD infected deer (either experimental deer or hunter harvested wild deer). |
| Impact | No outcomes to date |
| Start Year | 2017 |
| Description | A partnership to create a One health Living laboratory in Uganda |
| Organisation | Makerere University College of Health Sciences |
| Country | Uganda |
| Sector | Academic/University |
| PI Contribution | I have designed the project and invited the collaborative partners, this has emerged out of my BBSRC work interacting with farmers and their animals. We are propose to develop dedicated one health research similar to what we have for global health. We have received pilot funding from Edinburgh global through the Edinburgh-Africa partnerships call. This will bring together three research an training centres at Makerere University and three centres at Edinburgh University |
| Collaborator Contribution | Our partners own a health and demographic surveillance site that they have been managing since 2005. It has 100,000 individuals and it is this that will become the site for one health research. This is their contribution and of course the facilities we use for research ,most importantly the collaboration is fundamentally anchored on co-designing the centres have provided expertise in how this idea can and will be tested and implement elsewhere |
| Impact | We have conducted several workshops including the most recent on Nanopore sequencing: https://digital-one-health.github.io/doh-ont-workshop |
| Start Year | 2023 |
| Description | Adisseo consortium |
| Organisation | Adisseo |
| Country | France |
| Sector | Private |
| PI Contribution | Obtained a Adisseo Research grant |
| Collaborator Contribution | We will bring in our avian organoids technology to study the effect of microbiome on immune development of the gut and resilience to avian influenza. |
| Impact | Due to long start up time to set up a consortium agreement the project did not start in 20212 but end 2022, no out put yet. Collaboartive project with INRAE France and LMU Germany funded by Adisseo |
| Start Year | 2022 |
| Description | Canadian Big data centre University of Laval |
| Organisation | University of Laval |
| Country | Canada |
| Sector | Academic/University |
| PI Contribution | I am currently working with the Jacques Corbiel's group at the University of Laval. His group is providing capacity and training for me with regards to analysing big data. We are the fore collaborating on methodology as i contribute a rare insight into metagenomic dynamics in a resource limited setting. |
| Collaborator Contribution | The have given me access to one of Canada's super computer for my computing component. |
| Impact | None as yet |
| Start Year | 2017 |
| Description | Centre for Tropical Livestock Genetics and Health (CTLGH) |
| Organisation | International Livestock Research Institute (ILRI) |
| Country | Kenya |
| Sector | Charity/Non Profit |
| PI Contribution | Research contribution to the CTLGH result framework. |
| Collaborator Contribution | Research links and collaboration with its member partners in the UK and Africa. |
| Impact | No output to report yet. |
| Start Year | 2017 |
| Description | Centre for tropical livestock genetics and health (CTLGH) |
| Organisation | International Livestock Research Institute (ILRI) |
| Country | Kenya |
| Sector | Charity/Non Profit |
| PI Contribution | Mick Watson is co-leading programme 5 (informatics and bioresources) programme of CTLGH which aims to collect data on genotype and phenotype into a central database which can subsequently be mined for useful associations. So far we have ensured that scientists have access to the latest high performance computing environment for research, we have analysed and continue to analyse hundreds of farm animal genomes from LMIC countries, and we have built the data portal (http://data.ctlgh.org) |
| Collaborator Contribution | The partners are involved in all programmes, which include:Program 1: Harnessing genetic variability among indigenous and exotic breeds of cattle (as well as their crosses) to develop genetic and genomic tools that will be used to improve productivity under harsh tropical conditions and to mitigate the impact of cattle on climate change. Program 2: Harnessing genetic variability in tropical productivity and adaptation among various breeds of Chickens. Program 3: Development and application of precision breeding (through novel reproductive and germplasm technologies) to achieve step changes in livestock genetic improvement. Program 4: Understanding the genetic and molecular mechanisms underlying the tolerance of certain cattle and poultry breeds to tropical diseases and pests. Program 5: A shared global data and biological sample resource to support continued research and development on tropical livestock genetics and health. |
| Impact | The data portal so far: http://data.ctlgh.org The collaboration is multi-disciplinary, bringing together geneticists, parasitologists, virologists, epidemiologists and data scientists together. |
| Start Year | 2016 |
| Description | Centre for tropical livestock genetics and health (CTLGH) |
| Organisation | Scotland's Rural College |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Mick Watson is co-leading programme 5 (informatics and bioresources) programme of CTLGH which aims to collect data on genotype and phenotype into a central database which can subsequently be mined for useful associations. So far we have ensured that scientists have access to the latest high performance computing environment for research, we have analysed and continue to analyse hundreds of farm animal genomes from LMIC countries, and we have built the data portal (http://data.ctlgh.org) |
| Collaborator Contribution | The partners are involved in all programmes, which include:Program 1: Harnessing genetic variability among indigenous and exotic breeds of cattle (as well as their crosses) to develop genetic and genomic tools that will be used to improve productivity under harsh tropical conditions and to mitigate the impact of cattle on climate change. Program 2: Harnessing genetic variability in tropical productivity and adaptation among various breeds of Chickens. Program 3: Development and application of precision breeding (through novel reproductive and germplasm technologies) to achieve step changes in livestock genetic improvement. Program 4: Understanding the genetic and molecular mechanisms underlying the tolerance of certain cattle and poultry breeds to tropical diseases and pests. Program 5: A shared global data and biological sample resource to support continued research and development on tropical livestock genetics and health. |
| Impact | The data portal so far: http://data.ctlgh.org The collaboration is multi-disciplinary, bringing together geneticists, parasitologists, virologists, epidemiologists and data scientists together. |
| Start Year | 2016 |
| Description | Charoen Pokphand (CP) group |
| Organisation | Charoen Pokphand Group |
| Country | Thailand |
| Sector | Private |
| PI Contribution | Charoen Pokphand (CP) group are a large Asian conglomerate with an interest in farming, food production and feed additives. They have placed one of their staff members with me for PhD training, fully funded by them. We are training the staff member in laboratory and bioinformatics techniques related to microbiome research in chickens. |
| Collaborator Contribution | CP provide access to large chicken flocks both in at their farms and in their production facility. This enables us to study chicken breeds in the actual environments in which they live throughout Asia. |
| Impact | This is a multi-disciplinary project involving both laboratory and computational techniques. The major outcome so far include a review paper (http://aem.asm.org/content/early/2018/01/29/AEM.02627-17.abstract) and the technology transfer from our group into the commercial partner. |
| Start Year | 2017 |
| Description | Collaboration ANSES |
| Organisation | French Agency for Food, Environmental and Occupational Health & Safety (ANSES) |
| Country | France |
| Sector | Public |
| PI Contribution | My research team will work in the ANSES laboratories to set up organotypic avian cultures (intestinal organoids) of chicken, turkey and Guinea fowl which will be a unique opportunity. The organoids will then be infected with a variety of coronaviruses and avian influenza viruses (low and high pathogenic) and the viral replication will be analysed at different time points post infection. The RNA will be isolated and transported back to the UK to investigate the species specific immune responses using a high throughput qPCR array. The Roslin team will train the scientist at ANSES how to culture organoids whereas the team at ANSES will train the ECRs in virological techniques and working in a high containment laboratory. |
| Collaborator Contribution | The team at ANSES will contribute a lot of staff time, the animals, and will do the infection experiment in their high containment laboratory. In addition they will analyse the virus replication (RT-qPCR, egg titration and plaque assays) and we will write a joined publication describing the outcomes of this collaborative project. The data will feed in to many other projects related to avian corona and avian influenza viruses that are ongoing in the Vervelde group. |
| Impact | A collaborative project with ANSES, Ploufragan laboratory (reference lab for avian influenza), was initiated and funded by the BBSRC mitigation fund. This is a multidisciplinary collaboration in which the Roslin ECRs and PI will contribute their expertise in organotypic avian cultures (organoids) and the team at ANSES will contribute their virological expertise, the capacity to work with highly pathogenic avian influenza and their access to poultry species that we do not have in the U.K. (including guinea fowl, SPF turkeys and SPF ducks). The output of this collaboration will be joined peer reviewed publications on on host specific viral entry and immune responses (avian corona viruses and avian influenza viruses), preliminary data for follow on funding and future access to a wealth of virus strains and high containment laboratory and animal facilities. |
| Start Year | 2022 |
| Description | Collaboration on salmonid virus genomics |
| Organisation | Marine Scotland Science (MSS) |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Analysis of salmonid virus genomes to understand disease transmission and for strain/subtype diagnostics |
| Collaborator Contribution | Marine Scotland - co-supervision of PhD, sample and data provision, intellectual input PHARMAQ AS - sample provision, intellectual input |
| Impact | In process |
| Start Year | 2017 |
| Description | Collaboration on salmonid virus genomics |
| Organisation | Zoetis |
| Department | PHARMAQ AS |
| Country | Norway |
| Sector | Private |
| PI Contribution | Analysis of salmonid virus genomes to understand disease transmission and for strain/subtype diagnostics |
| Collaborator Contribution | Marine Scotland - co-supervision of PhD, sample and data provision, intellectual input PHARMAQ AS - sample provision, intellectual input |
| Impact | In process |
| Start Year | 2017 |
| Description | Collaboration with AB Vista |
| Organisation | AB Vista |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We are researching the activity of ovodefensins, naturally-occurring egg peptides with antimicrobial properties. With BBSRC LINK funding we are exploring the activity of diverse ovodefensins from multiple avian species, dissecting their structure and mode of action, and exploring their capacity to act as growth promoters and novel therapeutics. |
| Collaborator Contribution | AB Vista have made a substantial cash contribution to the LINK project (c. £460k) and also provide access to natural populations of broilers for feed trials using diets supplemented (or not) with Trichoderma-expressed ovodefensins. They also support analysis of the impact of such diets on intestinal microbiota and metabolites. |
| Impact | Commercially sensitive and to be disclosed following scrutiny for Intellectual Property. |
| Start Year | 2012 |
| Description | Collaboration with Boehringer Ingelheim |
| Organisation | Boehringer Ingelheim |
| Country | Germany |
| Sector | Private |
| PI Contribution | The collaboration is to advance diagnostics in relation to specific bacterial infections in pigs. We are carrying out basic science investigating antigens and immune responses |
| Collaborator Contribution | The company is providing reagents and expertise in this subject area |
| Impact | Part-funded PhD studentship |
| Start Year | 2017 |
| Description | Collaboration with Daniel Sordelli |
| Organisation | Biomedicine Research Institute of Buenos Aires - CONICET - Partner Institute of the Max Planck Society |
| Country | Argentina |
| Sector | Public |
| PI Contribution | Genome sequence analysis |
| Collaborator Contribution | Provision of bacterial isolates |
| Impact | Paper published in Scientific reports and one in preparation |
| Start Year | 2020 |
| Description | Collaboration with Frank Aarestrup |
| Organisation | Technical University of Denmark |
| Country | Denmark |
| Sector | Academic/University |
| PI Contribution | Analysis of Danish S. aureus genome sequences |
| Collaborator Contribution | Provision of bacterial isolates |
| Impact | Paper in preparation |
| Start Year | 2018 |
| Description | Collaboration with Jose Penades |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Evolutionary genomic analysis of host-adaptation, lateral transduction |
| Collaborator Contribution | Mechanistic analysis of host-adaptation, Lateral transduction |
| Impact | Numerous publications |
| Start Year | 2012 |
| Description | Collaboration with Michael Guttman |
| Organisation | University of Edinburgh |
| Department | Informatics Forum |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We are collaborating to examine the genetic basis of the capacity to cause disease- our role is to provide sequences and phylogenetic expertise |
| Collaborator Contribution | Expertise in Machine/Deep learning techniques |
| Impact | n/a |
| Start Year | 2020 |
| Description | Collaboration with Michael Guttman |
| Organisation | University of Edinburgh |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We are collaborating to examine the genetic basis of the capacity to cause disease- our role is to provide sequences and phylogenetic expertise |
| Collaborator Contribution | Expertise in Machine/Deep learning techniques |
| Impact | n/a |
| Start Year | 2020 |
| Description | Collaboration with Public Health England |
| Organisation | Public Health England |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Provision of animal and human STEC for sequencing, working with PHE to analyse strain phylogeny and epidemiology. We have contributed through further analysis of long read strain sequences to understand changes in strains that occur during outbreaks. We have co-upervised 2 PhD students on STEC bioinformatics projects. |
| Collaborator Contribution | Reduced rate sequencing of STEC, analysis of data, provision of metadata. Co-publication |
| Impact | Publications as in main list |
| Start Year | 2013 |
| Description | Collaboration with Texas Tech University |
| Organisation | Texas Tech University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Partner in this BBSRC US-UK Partnering Award related to Salmonella and E. coli infections in food-producing animals. |
| Collaborator Contribution | We hosted a visiting postdoctoral research fellow (Marie Bugarel from TTU) in 2015 and provided training in methods to study the basis of Salmonella virulence (inc. mutagenesis, cell-based assays & in vivo models). Drs Bugarel and Loneragan were co-authors on our manuscript describing the use of massively-parallel sequencing of polymorphic alleles to track the fate of Salmonella enterica serovars following inoculation of cattle. |
| Impact | A manuscript relating to a novel method to follow the fate of Salmonella enterica serovars during mixed infections was published in Applied and Environmental Microbiology in late 2017. This arose, in part, from the collaboration funded by a BBSRC US-UK partnering award (see tools), with resources from BBSRC- and Zoetis-funded project (BB/K015524/1) and core strategic grants to the Roslin Institute awarded in 2012 and 2017. |
| Start Year | 2014 |
| Description | Collaboration with USDA Nebraska |
| Organisation | U.S. Department of Agriculture USDA |
| Country | United States |
| Sector | Public |
| PI Contribution | Exchange of STEC sequence information. Analysis of PacBio long read sequencing of human and cattle isolates |
| Collaborator Contribution | Exchange of STEC sequence information. Carrying out of PacBio sequencing. Discussion of feedlot trials for E. coli O157 vaccine |
| Impact | Publications are provided in main list |
| Start Year | 2014 |
| Description | Collaboration with the Quadram Institute |
| Organisation | Quadram Institute Bioscience |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This is a joint project with the Quadram Institute, where the lead Principal Investigator is Dr Rob Kingsley. The BBSRC contribution to our component of the project is £123,594. It is envisaged that we will evaluate the virulence of variants of Salmonella enterica serovar Typhimurium in porcine models, both to quantify the magnitude and duration of intestinal colonisation in orally challenged pigs and the ability of strains to induce secretory and inflammatory responses in a porcine surgical model. |
| Collaborator Contribution | The Quadram Institute will select Salmonella strains for testing in vivo, based on analysis of their genome sequences, transcriptomes and the phenotypes of the strains in cell-based assays. |
| Impact | None at this stage. We await strains for testing. |
| Start Year | 2015 |
| Description | Collaboration: The dynamics of antimicrobial resistance gene prevalence on a commercial pig farm: implications for policy |
| Organisation | University of Edinburgh |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I am collaborating with data analysis of this project, which give me the opportunity to develop the bioinformatic pipelines needed for analysing my data when it comes. My first publication on AMR from pigs will be published using this data. |
| Collaborator Contribution | This would primarily be computing infra-struction to process the data. It takes about 1.6TB of space to per sample through the pipeline i am using so this sort of data would require significant robust computing infrastructure |
| Impact | Bio-informatic pipeline |
| Start Year | 2017 |
| Description | Collaborative research with Public Health England |
| Organisation | Public Health England |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | We provide samples and analysis of bacteria that are present in livestock that are the potential source of infections in humans |
| Collaborator Contribution | PHE analyse bacterial infections in humans and so by working in partnership we can improve our capacity to determine the source of particular infections in humans and hopefully prevent or limit these to improve public health |
| Impact | Outputs are publications as defined elsewhere as well as improved value to PHE surveillance |
| Start Year | 2015 |
| Description | Daniel Perez, University of Georgia |
| Organisation | University of Georgia |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | This grant is a joint programme with the USA component directly funded by the USDA, with money going to colleagues (Dr Daniel Perez) at the University of Georgia and The USDA SEPRL lab (Dr Darrell Kapcyznski). |
| Collaborator Contribution | Dr Perez primarily contributes to the animal challenge and viral evolution experiments |
| Impact | None yet |
| Start Year | 2021 |
| Description | Determine the therapeutic potential of sialylated Fc for influenza therapy |
| Organisation | Liverpool School of Tropical Medicine |
| Department | Parasite Immunology Liverpool |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Testing of sialylated Fcs in their ability to block influenza A virus causing haemagglutination and cell entry. |
| Collaborator Contribution | Design and synthesis of sialylated Fcs |
| Impact | N/A |
| Start Year | 2021 |
| Description | Developing tools for estimating AMR in developing Countries |
| Organisation | Yale University |
| Department | School of Public Health |
| Country | United States |
| Sector | Hospitals |
| PI Contribution | This group has supported my UKRI- Future Leader Fellowship application. They will be providing advance training for human microbial analysis. Through this group i also have access to the largest consortia of experts on AMR in the United State https://arlg.org this networking expertise would be much needed when the next fellowship is funded |
| Collaborator Contribution | The contribution has mainly been in Kind and mostly intellectual input for developing the next program of research |
| Impact | This has only just started, but i have used it write an application to the Soulsby Foundation to support efforts of developing an framework for estimating AMR in developing countries (Makerere University in Uganda, Edinburgh and Cambridge University in UK and Yale University in United States) |
| Start Year | 2019 |
| Description | Development of an optimised protocol for the sequencing of ASFV using ONT technology |
| Organisation | Oxford Nanopore Technologies |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We have developed primers, sequencing method and bioinformatics pipeline for the sequencing and assembly of whole genomes from African Swine Fever Virus (ASFV) samples for the purposes of research and epidemiological tracking of the virus. We used ONT sequencing for the broad applicability in ODA countries. |
| Collaborator Contribution | ONT have provided us with in kind contributions of their sequencing equipment and funding towards staff to test and validate the protocols developed with samples from different countries and using different ASFV genotypes. They have brought us in contact with different international partners, which we hope to further develop into established collaborations. |
| Impact | An ONT protocol is being finalised for publication on the Nanopore website following and referencing our preprint (10.1101/2021.12.01.470769v1?rss=1) soon to be submitted for publication. An international online seminar and Q&A on the use of this protocol and publicised and made available through the ONT website. Lilo, our assembly pipeline for tiled sequencing will be integrated within the Epi2me ONT platform for accessibility for people from ODA countries and people with limited bioinformatics background. |
| Start Year | 2021 |
| Description | EHEC O157 research groups in Argentina |
| Organisation | National Scientific and Technical Research Council (Argentina) |
| Country | Argentina |
| Sector | Public |
| PI Contribution | This award is a 'partnering award' and it has been successful in leading to research exchange trips and discussion between our laboratory and several groups in Argentina, primarily Dr Marina Palermo, CONICET, Buenos Aires and Dr Angel Cataldi, Instituto de Biotecnología, Hurlingham. We have provided genomics and gene expression expertise to aid their analysis of argentinian E. coli O157 isolates. |
| Collaborator Contribution | They have provided strains, immunological expertise and access to a mouse model to investigate Shiga toxin release and pathology |
| Impact | manuscript as presented in main section. The partnering award allows me to travel to Argentina, present our work and initiate discussions with Dr Angel Cataldi at an institute separate from Conicet. |
| Start Year | 2013 |
| Description | EPIC Consortium |
| Organisation | Biomathematics and Statistics Scotland (BioSS) |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Roslin Institute leads on improving veterinary surveillance (Prof Mark Bronsvoort, Dr Sam Lycett), analyses of disease control options (Dr Thibaud Porphyre) and horizon scanning for disease threats (Dr Paul Bessell). Through EPIC, Roslin staff will be providing expertise and the scientific evidence to policy makers, including during animal disease emergencies (should one occur). |
| Collaborator Contribution | The EPIC consortium delivers advice about livestock diseases to the Scottish Government under 5 themes: Topic 1 - Preparedness, Topic 2 - Risk, Topic 3 - Surveillance, Topic 4 - Control, Topic 5 - Futures. All Topics are co-lead with different combinations of partners from the collaborating institutes: Glasgow, Moredun, Roslin, James Hutton, BioSS, SRUC. |
| Impact | Multi-institution, multi-disciplinary collaboration |
| Start Year | 2016 |
| Description | EPIC Consortium |
| Organisation | James Hutton Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Roslin Institute leads on improving veterinary surveillance (Prof Mark Bronsvoort, Dr Sam Lycett), analyses of disease control options (Dr Thibaud Porphyre) and horizon scanning for disease threats (Dr Paul Bessell). Through EPIC, Roslin staff will be providing expertise and the scientific evidence to policy makers, including during animal disease emergencies (should one occur). |
| Collaborator Contribution | The EPIC consortium delivers advice about livestock diseases to the Scottish Government under 5 themes: Topic 1 - Preparedness, Topic 2 - Risk, Topic 3 - Surveillance, Topic 4 - Control, Topic 5 - Futures. All Topics are co-lead with different combinations of partners from the collaborating institutes: Glasgow, Moredun, Roslin, James Hutton, BioSS, SRUC. |
| Impact | Multi-institution, multi-disciplinary collaboration |
| Start Year | 2016 |
| Description | EPIC Consortium |
| Organisation | Moredun Research Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Roslin Institute leads on improving veterinary surveillance (Prof Mark Bronsvoort, Dr Sam Lycett), analyses of disease control options (Dr Thibaud Porphyre) and horizon scanning for disease threats (Dr Paul Bessell). Through EPIC, Roslin staff will be providing expertise and the scientific evidence to policy makers, including during animal disease emergencies (should one occur). |
| Collaborator Contribution | The EPIC consortium delivers advice about livestock diseases to the Scottish Government under 5 themes: Topic 1 - Preparedness, Topic 2 - Risk, Topic 3 - Surveillance, Topic 4 - Control, Topic 5 - Futures. All Topics are co-lead with different combinations of partners from the collaborating institutes: Glasgow, Moredun, Roslin, James Hutton, BioSS, SRUC. |
| Impact | Multi-institution, multi-disciplinary collaboration |
| Start Year | 2016 |
| Description | EPIC Consortium |
| Organisation | Scotland's Rural College |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Roslin Institute leads on improving veterinary surveillance (Prof Mark Bronsvoort, Dr Sam Lycett), analyses of disease control options (Dr Thibaud Porphyre) and horizon scanning for disease threats (Dr Paul Bessell). Through EPIC, Roslin staff will be providing expertise and the scientific evidence to policy makers, including during animal disease emergencies (should one occur). |
| Collaborator Contribution | The EPIC consortium delivers advice about livestock diseases to the Scottish Government under 5 themes: Topic 1 - Preparedness, Topic 2 - Risk, Topic 3 - Surveillance, Topic 4 - Control, Topic 5 - Futures. All Topics are co-lead with different combinations of partners from the collaborating institutes: Glasgow, Moredun, Roslin, James Hutton, BioSS, SRUC. |
| Impact | Multi-institution, multi-disciplinary collaboration |
| Start Year | 2016 |
| Description | EPIC Consortium |
| Organisation | University of Glasgow |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Roslin Institute leads on improving veterinary surveillance (Prof Mark Bronsvoort, Dr Sam Lycett), analyses of disease control options (Dr Thibaud Porphyre) and horizon scanning for disease threats (Dr Paul Bessell). Through EPIC, Roslin staff will be providing expertise and the scientific evidence to policy makers, including during animal disease emergencies (should one occur). |
| Collaborator Contribution | The EPIC consortium delivers advice about livestock diseases to the Scottish Government under 5 themes: Topic 1 - Preparedness, Topic 2 - Risk, Topic 3 - Surveillance, Topic 4 - Control, Topic 5 - Futures. All Topics are co-lead with different combinations of partners from the collaborating institutes: Glasgow, Moredun, Roslin, James Hutton, BioSS, SRUC. |
| Impact | Multi-institution, multi-disciplinary collaboration |
| Start Year | 2016 |
| Description | Epidemiology of integron genes in Scottish cattle |
| Organisation | University of Limoges |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Investigation of integron gene carriage by Scottish cattle through PCR and epidemiological analysis. |
| Collaborator Contribution | Provision of control strains and method expertise. |
| Impact | doi: 10.3389/fvets.2021.755833. PMID: 34778436; PMCID: PMC8585936. |
| Start Year | 2019 |
| Description | Evaluation of potential diagnostic tests for preclinical prion disease |
| Organisation | National Veterinary School of Toulouse |
| Country | France |
| Sector | Academic/University |
| PI Contribution | The collaboration was funded by an award to me from the UK Department of Health and Social Care. The contribution from my team is the adaptation of potential tests to sheep blood, and application of the tests to blinded panels of preclinical blood samples generated in a previous project. We have also supplied panels of samples from the same archive to our collaborators. |
| Collaborator Contribution | Our partners at ENVT have inoculated a panel of blood samples from sheep preclinically infected with BSE into a sensitive transgenic mouse model to determine infectious prion titres. The samples are identical aliquots of those tested in the blinded panels with potential diagnostic assays to determine comparative sensitivity and specificity. They are also supplying us with frozen transgenic mouse brains expressing sheep PrP for use in one of the assays under investigation. Our partners at EFS are testing an identical panel of preclinical BSE-infected sheep blood samples using their sensitive protein misfolding amplification assay (PMCA) developed for detection of variant Creutzfeldt-Jakob disease in human patients. |
| Impact | No outcomes to date |
| Start Year | 2017 |
| Description | Evaluation of potential diagnostic tests for preclinical prion disease |
| Organisation | Établissement Français du Sang |
| Country | France |
| Sector | Charity/Non Profit |
| PI Contribution | The collaboration was funded by an award to me from the UK Department of Health and Social Care. The contribution from my team is the adaptation of potential tests to sheep blood, and application of the tests to blinded panels of preclinical blood samples generated in a previous project. We have also supplied panels of samples from the same archive to our collaborators. |
| Collaborator Contribution | Our partners at ENVT have inoculated a panel of blood samples from sheep preclinically infected with BSE into a sensitive transgenic mouse model to determine infectious prion titres. The samples are identical aliquots of those tested in the blinded panels with potential diagnostic assays to determine comparative sensitivity and specificity. They are also supplying us with frozen transgenic mouse brains expressing sheep PrP for use in one of the assays under investigation. Our partners at EFS are testing an identical panel of preclinical BSE-infected sheep blood samples using their sensitive protein misfolding amplification assay (PMCA) developed for detection of variant Creutzfeldt-Jakob disease in human patients. |
| Impact | No outcomes to date |
| Start Year | 2017 |
| Description | Exchange of ASFV DNA samples for sequencing |
| Organisation | The Pirbright Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Sequencing of whole genome ASFV sequences from historic samples. |
| Collaborator Contribution | Provision of ASFV DNA samples. |
| Impact | ASFV sequences to aid epidemiological tracing and inform mutagenesis of the virus. |
| Start Year | 2021 |
| Description | Fleming Fellowship partnership for Malawi |
| Organisation | Government of Malawi |
| Country | Malawi |
| Sector | Public |
| PI Contribution | This collaboration, is similar to the one in Uganda. The application that attracted these funds is build on the one in Uganda which was developed around my fellowship. I am the deputy director for these fellowships at the University of Edinburgh |
| Collaborator Contribution | Malawi will be supported by the Fleming fund where we shall train stakeholders in AMR, the grant is ~£520,000 |
| Impact | This only started in January 2020, therefore we do not have any outcomes as yet |
| Start Year | 2019 |
| Description | Fleming Fund fellowship Kenya (Policy fellows) |
| Organisation | Fleming Fund |
| Sector | Charity/Non Profit |
| PI Contribution | I am the co-director of this fellowship scheme at the University of Edinburgh. My work in Uganda was the foundation on which the initial award was made and now we have Kenya awarded following Malawi Last Year |
| Collaborator Contribution | We use some the tools and study designs developed from my fellowship in the training and indeed this has been recognised globally see link https://icars-global.org/cta-resources/ |
| Impact | https://icars-global.org/cta-resources/ |
| Start Year | 2021 |
| Description | Flemings AMR training programme Uganda |
| Organisation | University of Edinburgh |
| Department | Edinburgh Infectious Diseases |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I am co-PI on an application to the Fleming's fund administered by Mott MacDonald on behalf of the UK department of Health and social care. This grant is for training AMR stakeholders in Uganda. This application is developed directly on the basis of my fellowship in Uganda |
| Collaborator Contribution | Edinburgh Infectious disease is the umbrella through which the University of Edinburgh applied to become a host institution for the Fleming's fund country training programme. The mentors for the training programme for the AMR stakeholders from Uganda(Mentees) are chose from the pool of experts in the Edinburgh infectious disease umbrella |
| Impact | We organised a fellow's workshop in Kampala in January this year to kick start the training activities https://www.ed.ac.uk/edinburgh-infectious-diseases/news/news/edinburgh-host-fleming-fund-fellows |
| Start Year | 2018 |
| Description | Generation of rotaviruses expressing SARS-CoV-2 peptides |
| Organisation | University of Cambridge |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We engineered and characterised rotaviruses expressing SARS-CoV-2 peptides. |
| Collaborator Contribution | They engineered rotaviruses expressing some different SARS-CoV-2 peptides and performed some mouse infection experiments. |
| Impact | Paper has been circulated to co-authors |
| Start Year | 2020 |
| Description | Genomic Epidemiology of Atlantic salmon viruses with Pharmaq (Zoetis) and a group of aquaculture production companies |
| Organisation | Grieg Group |
| Country | Norway |
| Sector | Private |
| PI Contribution | Genomic epidemiology was used to investigate genetic diversity and spread of salmonid alphavirus (SAV), the causative agent of pancreas disease (PD) in Atlantic salmon. The goal was to reconstruct SAV subtype-2 (SAV2) diversity and transmission dynamics in recent Norwegian aquaculture, including the origin of SAV2 in regions where this subtype is not tolerated under current legislation. We performed nanopore sequencing on ~100 field samples from 35 farms from 10 aquaculture production regions, shared by major aquaculture producers. Using time-calibrated phylogenetics we inferred novel genetic diversity in SAV and identified strongly supported disease transmission routes, including likely anthropogenic routes of transmission. The study demonstrated useful applications of genomic epidemiology for tracking viral disease spread in aquaculture. We are continuing the partnership through a new PhD due to start in Oct 2022 co-funded by Pharmaq, and will also seek grant funding to expand the work. |
| Collaborator Contribution | For the study above, Pharmaq AS - coordinated samples from industry partners and initiated the study with Sinkaberg Hansen AS. They also provided data and input to writing of manuscript reporting findings - https://www.mdpi.com/1999-4915/13/12/2549/htm Funding contributed by the following companies (in alphabetical order): Emilsen Fisk AS, Grieg Seafood ASA, Måsøval AS, Midt-Norsk Havbruk AS, Osland Havbruk AS, Pharmaq AS, Salmar ASA, and Sinkaberg Hansen AS. Samples used in the study were provided by (in alphabetical order): Alsaker Fjordbruk, Emilsen Fisk, Grieg Seafood Rogaland, Måsøval, Midt Norsk Havbruk, Mowi, Osland Havbruk, Salmar, and Salmonor |
| Impact | Publication on above study: https://www.mdpi.com/1999-4915/13/12/2549/htm Talks given at Pharmaqademy to industry stakeholders: - https://pharmaqademy.no/ - https://pharmaqademy.no/daniel-macqueen-genomic-epidemiology-of-sav2-in-norwegian-aquaculture-from-2018-to-2020/ Follow up funding - Pharmaq supporting PhD studentship starting Oct 2022 with £68,000 cash contribution (70% of studentship cost) |
| Start Year | 2020 |
| Description | Genomic Epidemiology of Atlantic salmon viruses with Pharmaq (Zoetis) and a group of aquaculture production companies |
| Organisation | Pharmaq |
| Country | Norway |
| Sector | Private |
| PI Contribution | Genomic epidemiology was used to investigate genetic diversity and spread of salmonid alphavirus (SAV), the causative agent of pancreas disease (PD) in Atlantic salmon. The goal was to reconstruct SAV subtype-2 (SAV2) diversity and transmission dynamics in recent Norwegian aquaculture, including the origin of SAV2 in regions where this subtype is not tolerated under current legislation. We performed nanopore sequencing on ~100 field samples from 35 farms from 10 aquaculture production regions, shared by major aquaculture producers. Using time-calibrated phylogenetics we inferred novel genetic diversity in SAV and identified strongly supported disease transmission routes, including likely anthropogenic routes of transmission. The study demonstrated useful applications of genomic epidemiology for tracking viral disease spread in aquaculture. We are continuing the partnership through a new PhD due to start in Oct 2022 co-funded by Pharmaq, and will also seek grant funding to expand the work. |
| Collaborator Contribution | For the study above, Pharmaq AS - coordinated samples from industry partners and initiated the study with Sinkaberg Hansen AS. They also provided data and input to writing of manuscript reporting findings - https://www.mdpi.com/1999-4915/13/12/2549/htm Funding contributed by the following companies (in alphabetical order): Emilsen Fisk AS, Grieg Seafood ASA, Måsøval AS, Midt-Norsk Havbruk AS, Osland Havbruk AS, Pharmaq AS, Salmar ASA, and Sinkaberg Hansen AS. Samples used in the study were provided by (in alphabetical order): Alsaker Fjordbruk, Emilsen Fisk, Grieg Seafood Rogaland, Måsøval, Midt Norsk Havbruk, Mowi, Osland Havbruk, Salmar, and Salmonor |
| Impact | Publication on above study: https://www.mdpi.com/1999-4915/13/12/2549/htm Talks given at Pharmaqademy to industry stakeholders: - https://pharmaqademy.no/ - https://pharmaqademy.no/daniel-macqueen-genomic-epidemiology-of-sav2-in-norwegian-aquaculture-from-2018-to-2020/ Follow up funding - Pharmaq supporting PhD studentship starting Oct 2022 with £68,000 cash contribution (70% of studentship cost) |
| Start Year | 2020 |
| Description | Genomic Epidemiology of Atlantic salmon viruses with Pharmaq (Zoetis) and a group of aquaculture production companies |
| Organisation | SalMar |
| Country | Norway |
| Sector | Private |
| PI Contribution | Genomic epidemiology was used to investigate genetic diversity and spread of salmonid alphavirus (SAV), the causative agent of pancreas disease (PD) in Atlantic salmon. The goal was to reconstruct SAV subtype-2 (SAV2) diversity and transmission dynamics in recent Norwegian aquaculture, including the origin of SAV2 in regions where this subtype is not tolerated under current legislation. We performed nanopore sequencing on ~100 field samples from 35 farms from 10 aquaculture production regions, shared by major aquaculture producers. Using time-calibrated phylogenetics we inferred novel genetic diversity in SAV and identified strongly supported disease transmission routes, including likely anthropogenic routes of transmission. The study demonstrated useful applications of genomic epidemiology for tracking viral disease spread in aquaculture. We are continuing the partnership through a new PhD due to start in Oct 2022 co-funded by Pharmaq, and will also seek grant funding to expand the work. |
| Collaborator Contribution | For the study above, Pharmaq AS - coordinated samples from industry partners and initiated the study with Sinkaberg Hansen AS. They also provided data and input to writing of manuscript reporting findings - https://www.mdpi.com/1999-4915/13/12/2549/htm Funding contributed by the following companies (in alphabetical order): Emilsen Fisk AS, Grieg Seafood ASA, Måsøval AS, Midt-Norsk Havbruk AS, Osland Havbruk AS, Pharmaq AS, Salmar ASA, and Sinkaberg Hansen AS. Samples used in the study were provided by (in alphabetical order): Alsaker Fjordbruk, Emilsen Fisk, Grieg Seafood Rogaland, Måsøval, Midt Norsk Havbruk, Mowi, Osland Havbruk, Salmar, and Salmonor |
| Impact | Publication on above study: https://www.mdpi.com/1999-4915/13/12/2549/htm Talks given at Pharmaqademy to industry stakeholders: - https://pharmaqademy.no/ - https://pharmaqademy.no/daniel-macqueen-genomic-epidemiology-of-sav2-in-norwegian-aquaculture-from-2018-to-2020/ Follow up funding - Pharmaq supporting PhD studentship starting Oct 2022 with £68,000 cash contribution (70% of studentship cost) |
| Start Year | 2020 |
| Description | IMCAS, Beijing |
| Organisation | Institute of Microbiology |
| Country | China |
| Sector | Public |
| PI Contribution | This award is a formal partnership with Dr Wenjun (Frank) Liu at IMCAS Beijing, whose research component is funded by the Chinese National Natural Science Foundation. |
| Collaborator Contribution | Our colleagues in China are providing input into the modelling, epidemiology and animal challenge aspects of the project |
| Impact | No outputs or outcomes yet |
| Start Year | 2021 |
| Description | Identification of AMR and virulence genes in Escherichia coli from cattle by high throughput microchip PCR |
| Organisation | French Agency for Food, Environmental and Occupational Health & Safety (ANSES) |
| Country | France |
| Sector | Public |
| PI Contribution | Expertise, provision of samples for testing, data analysis and interpretation. |
| Collaborator Contribution | Expertise, screening of samples through ANSES high throughput PCR facility, data analysis and interpretation. |
| Impact | No outputs yet. |
| Start Year | 2022 |
| Description | Identification of interferon stimulated genes that control Neospora caninum in bovine cells. |
| Organisation | Complutense University of Madrid |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | Using the tools from the project, specifically ISG screening protocol using fluorescent parasites, we are currently collaborating with Prof. Luis Ortega at University of Madrid to develop and bovine ISG library to screen for genes that control Neospora in bovine cells. |
| Collaborator Contribution | Prof. Luis leads the veterinary apicomplexan research at University of Madrid. He's evidence variable pathogenicity of different Neospora isolates in bovine cells and developed both fluorescent and transgenic parasites and cellular phenotypes that we can use to screen for both host and parasite genes controlling Neosporosis. |
| Impact | The collaboration has yet to produce an output. However, there's active research going on with a PhD student from Madrid visiting Roslin Institute and we will soon have a publication - currently under preparation. |
| Start Year | 2023 |
| Description | In vivo challenge of genome edited deltaSRCR5 pigs with PRRSV-1 |
| Organisation | Genus plc |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Following the successful generation of pigs lacking domain 5 (SRCR5) of the CD163 and the promising in vitro results, showing primary cells of these pigs to be resistant against PRRSV infection we obtained further funding from Genus plc. to conduct an in vivo study. 4 delta SRCR5 pigs and 4 wild type pigs were challenged with PRRSV-1. We conducted the study and analysed the outcomes. |
| Collaborator Contribution | Genus plc contributed funding to conduct the in vivo study to assess infectability of delta SRCR5 pigs with PRRSV-1 |
| Impact | We published the results of this study in a scientific publication, disseminated the results in a press release package, as well as presented the work at various scientific conferences and public engagement events. |
| Start Year | 2016 |
| Description | Inactivated SARS-CoV-2 for wastewater testing |
| Organisation | Bangor University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Generation of inactivated SARS-CoV-2 virus for wastewater testing. |
| Collaborator Contribution | Information |
| Impact | Improved testing for SARS-CoV-2 |
| Start Year | 2020 |
| Description | Inactivated SARS-CoV-2 for wastewater testing |
| Organisation | Cardiff University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Generation of inactivated SARS-CoV-2 virus for wastewater testing. |
| Collaborator Contribution | Information |
| Impact | Improved testing for SARS-CoV-2 |
| Start Year | 2020 |
| Description | Inactivated SARS-CoV-2 for wastewater testing |
| Organisation | Centre For Environment, Fisheries And Aquaculture Science |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Generation of inactivated SARS-CoV-2 virus for wastewater testing. |
| Collaborator Contribution | Information |
| Impact | Improved testing for SARS-CoV-2 |
| Start Year | 2020 |
| Description | Inactivated SARS-CoV-2 for wastewater testing |
| Organisation | Newcastle upon Tyne Hospitals NHS Foundation Trust |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Generation of inactivated SARS-CoV-2 virus for wastewater testing. |
| Collaborator Contribution | Information |
| Impact | Improved testing for SARS-CoV-2 |
| Start Year | 2020 |
| Description | Inactivated SARS-CoV-2 for wastewater testing |
| Organisation | Queen's University Belfast |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Generation of inactivated SARS-CoV-2 virus for wastewater testing. |
| Collaborator Contribution | Information |
| Impact | Improved testing for SARS-CoV-2 |
| Start Year | 2020 |
| Description | Inactivated SARS-CoV-2 for wastewater testing |
| Organisation | Scottish Environment Protection Agency |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Generation of inactivated SARS-CoV-2 virus for wastewater testing. |
| Collaborator Contribution | Information |
| Impact | Improved testing for SARS-CoV-2 |
| Start Year | 2020 |
| Description | Industrial partnership with Zoetis Animal Health |
| Organisation | Zoetis |
| Country | United States |
| Sector | Private |
| PI Contribution | Identification of conserved antigens expressed during infection which represent candidate vaccine components |
| Collaborator Contribution | Cash funding and challenge experiments in dairy cows |
| Impact | Subject to confidentiality agreement |
| Start Year | 2013 |
| Description | Influence of chronic stress condition on neuroinvasion of prions and progression of prion disease |
| Organisation | Hokkaido University |
| Country | Japan |
| Sector | Academic/University |
| PI Contribution | I was personally approached by Prof. Masaaki Murakami and Asso. Prof. Rie Hasebe at the Institute for Genetic Medicine at Hokkaido University, Sapporo, Japan to collaborate on a study to determine the influence of chronic stress condition on neuroinvasion of prions and progression of prion disease. I contributed my expertise in the study of oral prion disease pathogenesis and designed a series of in vivo studies to address the projects main aims. I also provided bioinformatics expertise and taught Asso. Prof. Rie Hasebe how to perform meta-analyses of multiple mRNA-seq data sets. During my visit I also gave an international seminar at Hokkaido University Medical School. |
| Collaborator Contribution | The Japanese partners, Prof. Masaaki Murakami and Asso. Prof. Rie Hasebe hosted my visit to their department at Hokkaido University. This lab will also provide the funding and consumables and conduct the in vivo experiments. |
| Impact | As a consequence of this collaboration, a General Joint Research Program grant was submitted to the Institute for Genetic Medicine, Hokkaido University. The aim of the project was to study the influence of chronic stress condition on neuroinvasion of prions and progression of prion disease. This application was successful and we received JPY 650,000 (approx. £5000). |
| Start Year | 2019 |
| Description | Knowledge exchange and primers for ASFV sequencing |
| Organisation | National Academy of Sciences of the Republic of Armenia |
| Country | Armenia |
| Sector | Academic/University |
| PI Contribution | Support with ASFV sequencing and analysis. |
| Collaborator Contribution | ASFV samples and sequencing from current outbreaks. |
| Impact | ASFV sequences to aid epidemiological tracing and inform mutagenesis of the virus. |
| Start Year | 2022 |
| Description | Knowledge exchange and primers for ASFV sequencing |
| Organisation | Sokoine University of Agriculture |
| Country | Tanzania, United Republic of |
| Sector | Academic/University |
| PI Contribution | Support with ASFV sequencing and analysis. |
| Collaborator Contribution | Archived ASFV samples sequenced at location. |
| Impact | ASFV sequences to aid epidemiological tracing and inform mutagenesis of the virus. |
| Start Year | 2022 |
| Description | Knowledge exchange and primers for ASFV sequencing |
| Organisation | University of the Philippines Mindanao |
| Country | Philippines |
| Sector | Academic/University |
| PI Contribution | Support with ASFV sequencing and analysis. |
| Collaborator Contribution | ASFV samples and sequencing from current outbreaks. |
| Impact | ASFV sequences to aid epidemiological tracing and inform mutagenesis of the virus. |
| Start Year | 2021 |
| Description | Pigboost consortium- Uganda |
| Organisation | AbacusBio |
| Country | New Zealand |
| Sector | Private |
| PI Contribution | This is an Agritec catalyst funded by Innovate UK. This projects builds on the work i do in Uganda and it is based in the same districts. It aims at developing data driven solution to support sustaibable pig production in Uganda |
| Collaborator Contribution | The three members are primary contributing expertise in breeding, quantitative data management and capture, farmer landscape mapping. This work provide the dept for me to understand the factors the drive the use of antibiotics in my study areas |
| Impact | It has just started |
| Start Year | 2020 |
| Description | Pigboost consortium- Uganda |
| Organisation | Makerere University |
| Country | Uganda |
| Sector | Academic/University |
| PI Contribution | This is an Agritec catalyst funded by Innovate UK. This projects builds on the work i do in Uganda and it is based in the same districts. It aims at developing data driven solution to support sustaibable pig production in Uganda |
| Collaborator Contribution | The three members are primary contributing expertise in breeding, quantitative data management and capture, farmer landscape mapping. This work provide the dept for me to understand the factors the drive the use of antibiotics in my study areas |
| Impact | It has just started |
| Start Year | 2020 |
| Description | Pigboost consortium- Uganda |
| Organisation | Vetline Services |
| Country | Uganda |
| Sector | Private |
| PI Contribution | This is an Agritec catalyst funded by Innovate UK. This projects builds on the work i do in Uganda and it is based in the same districts. It aims at developing data driven solution to support sustaibable pig production in Uganda |
| Collaborator Contribution | The three members are primary contributing expertise in breeding, quantitative data management and capture, farmer landscape mapping. This work provide the dept for me to understand the factors the drive the use of antibiotics in my study areas |
| Impact | It has just started |
| Start Year | 2020 |
| Description | Pirbright Institute |
| Organisation | The Pirbright Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | As BBSRC Institutes within the National Institutes of Bioscience umbrella we collaborate on a variety of virology projects, pooling expertise, facilities and data. |
| Collaborator Contribution | Please see the specific publications involving joint authors |
| Impact | Toward the aim of defining the basis of resistance of poultry to viral diseases (DO1.2), we analysed the early immune response of Brown Leghorn and inbred line 61 chickens housed by the National Avian Research Facility to infection by Infectious Bursal Disease Virus, in collaboration with The Pirbright Institute. This identified candidate genes and pathways associated with resistance (DOI: 10.1128/JVI.02828-14). Uplift funding totalling >£800k linking Pirbright and Roslin Institute researchers will use epitope fingerprinting to investigate the genetic plasticity of infectious bronchitis virus strains to develop improved cross-protective vaccines (BB/M012069/1). Toward making disease-resistant animals, research linking ISPG2 and ISPG4 aims to define the contribution of RelA polymorphism to resistance to African Swine Fever Virus in pigs. Challenge experiments at The Pirbright Institute are ongoing at the time of writing. We currently have two joint PhD students shared between the Institutes - one (Miss Anabel Clements, supervised by Professor Paul Digard [RI] and Drs Munir Iqbal and Holley Shelton [PI]) is working on virulence determinants of avian influenza virus, while the other (Miss Laura Dunn, supervised by Dr Pip Beard [RI] and Dr Linda Dixon [PI]) is studying miRNA modification by African swine fever virus. Dr Beard, a senior virologist and pathologist has been appointed to a joint Roslin / Pirbright position, starting 1st May, 2016. |
| Description | Research consortium investigating chronic wasting disease in Europe |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | This consortium has been funded under an Era-Net ICRAD (International coordination of research on infectious diseases) call. I am the project leader, and my research team will be involved in developing in vitro techniques to predict the effect of sequence variants found in the prion protein gene (PRNP) of British/European cervid species on susceptibility to chronic wasting disease (CWD). CWD is a prion disease similar to scrapie in sheep and BSE in cattle, that has become widespread in North America, and was identified in Norway and other Scandinavian countries since 2016. A team from the National CJD Research and Surveillance Unit in Edinburgh will also participate in analysis of the potential for cross-species transmission of CWD using in vitro assays. |
| Collaborator Contribution | The Norwegian Veterinary Institute and Swedish National Veterinary Institute will collaborate in investigating the epidemiology and projected spread of CWD in Scandinavian cervid populations, and supplying material from CWD cases to other partners. FLI, INRA and NVI will contribute to PRNP genotyping of wild cervid populations in their respective countries. INIA, INRA and FLI will investigate the potential for cross-species transmission of CWD by experimental infection of transgenic mice expressing prion protein (PrP) from the respective host species (cattle, sheep, pig, human), and in vitro amplification of CWD in brain substrate from these mice. INRA will also participate in development of in vitro techniques to predict the effect of cervid PRNP sequence variants on susceptibility to CWD. |
| Impact | PMID: 34564054; DOI: https://doi.org/10.1002/2688-8319.12203 The collaboration involves scientists with expertise in a number of disciplines, including epidemiology, wildlife ecology and disease monitoring, genetics, neuropathology, prion biology (including biochemistry, cell biology in vitro assays and rodents model of disease). |
| Start Year | 2021 |
| Description | Research consortium investigating chronic wasting disease in Europe |
| Organisation | Friedrich Loeffler Institute |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | This consortium has been funded under an Era-Net ICRAD (International coordination of research on infectious diseases) call. I am the project leader, and my research team will be involved in developing in vitro techniques to predict the effect of sequence variants found in the prion protein gene (PRNP) of British/European cervid species on susceptibility to chronic wasting disease (CWD). CWD is a prion disease similar to scrapie in sheep and BSE in cattle, that has become widespread in North America, and was identified in Norway and other Scandinavian countries since 2016. A team from the National CJD Research and Surveillance Unit in Edinburgh will also participate in analysis of the potential for cross-species transmission of CWD using in vitro assays. |
| Collaborator Contribution | The Norwegian Veterinary Institute and Swedish National Veterinary Institute will collaborate in investigating the epidemiology and projected spread of CWD in Scandinavian cervid populations, and supplying material from CWD cases to other partners. FLI, INRA and NVI will contribute to PRNP genotyping of wild cervid populations in their respective countries. INIA, INRA and FLI will investigate the potential for cross-species transmission of CWD by experimental infection of transgenic mice expressing prion protein (PrP) from the respective host species (cattle, sheep, pig, human), and in vitro amplification of CWD in brain substrate from these mice. INRA will also participate in development of in vitro techniques to predict the effect of cervid PRNP sequence variants on susceptibility to CWD. |
| Impact | PMID: 34564054; DOI: https://doi.org/10.1002/2688-8319.12203 The collaboration involves scientists with expertise in a number of disciplines, including epidemiology, wildlife ecology and disease monitoring, genetics, neuropathology, prion biology (including biochemistry, cell biology in vitro assays and rodents model of disease). |
| Start Year | 2021 |
| Description | Research consortium investigating chronic wasting disease in Europe |
| Organisation | National Institute for Agricultural and Food Research and Technology |
| Country | Spain |
| Sector | Public |
| PI Contribution | This consortium has been funded under an Era-Net ICRAD (International coordination of research on infectious diseases) call. I am the project leader, and my research team will be involved in developing in vitro techniques to predict the effect of sequence variants found in the prion protein gene (PRNP) of British/European cervid species on susceptibility to chronic wasting disease (CWD). CWD is a prion disease similar to scrapie in sheep and BSE in cattle, that has become widespread in North America, and was identified in Norway and other Scandinavian countries since 2016. A team from the National CJD Research and Surveillance Unit in Edinburgh will also participate in analysis of the potential for cross-species transmission of CWD using in vitro assays. |
| Collaborator Contribution | The Norwegian Veterinary Institute and Swedish National Veterinary Institute will collaborate in investigating the epidemiology and projected spread of CWD in Scandinavian cervid populations, and supplying material from CWD cases to other partners. FLI, INRA and NVI will contribute to PRNP genotyping of wild cervid populations in their respective countries. INIA, INRA and FLI will investigate the potential for cross-species transmission of CWD by experimental infection of transgenic mice expressing prion protein (PrP) from the respective host species (cattle, sheep, pig, human), and in vitro amplification of CWD in brain substrate from these mice. INRA will also participate in development of in vitro techniques to predict the effect of cervid PRNP sequence variants on susceptibility to CWD. |
| Impact | PMID: 34564054; DOI: https://doi.org/10.1002/2688-8319.12203 The collaboration involves scientists with expertise in a number of disciplines, including epidemiology, wildlife ecology and disease monitoring, genetics, neuropathology, prion biology (including biochemistry, cell biology in vitro assays and rodents model of disease). |
| Start Year | 2021 |
| Description | Research consortium investigating chronic wasting disease in Europe |
| Organisation | National Veterinary Institute |
| Country | Sweden |
| Sector | Public |
| PI Contribution | This consortium has been funded under an Era-Net ICRAD (International coordination of research on infectious diseases) call. I am the project leader, and my research team will be involved in developing in vitro techniques to predict the effect of sequence variants found in the prion protein gene (PRNP) of British/European cervid species on susceptibility to chronic wasting disease (CWD). CWD is a prion disease similar to scrapie in sheep and BSE in cattle, that has become widespread in North America, and was identified in Norway and other Scandinavian countries since 2016. A team from the National CJD Research and Surveillance Unit in Edinburgh will also participate in analysis of the potential for cross-species transmission of CWD using in vitro assays. |
| Collaborator Contribution | The Norwegian Veterinary Institute and Swedish National Veterinary Institute will collaborate in investigating the epidemiology and projected spread of CWD in Scandinavian cervid populations, and supplying material from CWD cases to other partners. FLI, INRA and NVI will contribute to PRNP genotyping of wild cervid populations in their respective countries. INIA, INRA and FLI will investigate the potential for cross-species transmission of CWD by experimental infection of transgenic mice expressing prion protein (PrP) from the respective host species (cattle, sheep, pig, human), and in vitro amplification of CWD in brain substrate from these mice. INRA will also participate in development of in vitro techniques to predict the effect of cervid PRNP sequence variants on susceptibility to CWD. |
| Impact | PMID: 34564054; DOI: https://doi.org/10.1002/2688-8319.12203 The collaboration involves scientists with expertise in a number of disciplines, including epidemiology, wildlife ecology and disease monitoring, genetics, neuropathology, prion biology (including biochemistry, cell biology in vitro assays and rodents model of disease). |
| Start Year | 2021 |
| Description | Research consortium investigating chronic wasting disease in Europe |
| Organisation | Norwegian Veterinary Institute |
| Country | Norway |
| Sector | Private |
| PI Contribution | This consortium has been funded under an Era-Net ICRAD (International coordination of research on infectious diseases) call. I am the project leader, and my research team will be involved in developing in vitro techniques to predict the effect of sequence variants found in the prion protein gene (PRNP) of British/European cervid species on susceptibility to chronic wasting disease (CWD). CWD is a prion disease similar to scrapie in sheep and BSE in cattle, that has become widespread in North America, and was identified in Norway and other Scandinavian countries since 2016. A team from the National CJD Research and Surveillance Unit in Edinburgh will also participate in analysis of the potential for cross-species transmission of CWD using in vitro assays. |
| Collaborator Contribution | The Norwegian Veterinary Institute and Swedish National Veterinary Institute will collaborate in investigating the epidemiology and projected spread of CWD in Scandinavian cervid populations, and supplying material from CWD cases to other partners. FLI, INRA and NVI will contribute to PRNP genotyping of wild cervid populations in their respective countries. INIA, INRA and FLI will investigate the potential for cross-species transmission of CWD by experimental infection of transgenic mice expressing prion protein (PrP) from the respective host species (cattle, sheep, pig, human), and in vitro amplification of CWD in brain substrate from these mice. INRA will also participate in development of in vitro techniques to predict the effect of cervid PRNP sequence variants on susceptibility to CWD. |
| Impact | PMID: 34564054; DOI: https://doi.org/10.1002/2688-8319.12203 The collaboration involves scientists with expertise in a number of disciplines, including epidemiology, wildlife ecology and disease monitoring, genetics, neuropathology, prion biology (including biochemistry, cell biology in vitro assays and rodents model of disease). |
| Start Year | 2021 |
| Description | SARS-CoV-2 standards for testing |
| Organisation | NHS Lothian |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Isolation and cultivation of clinical isolate SARS-CoV-2 from clinical isolate. Provision of cultured virus for testing standards. |
| Collaborator Contribution | Patient samples of SARS-CoV-2 and relevant information. |
| Impact | Improved testing for SARS-CoV-2 |
| Start Year | 2020 |
| Description | SARS-CoV-2 standards for testing |
| Organisation | Public Health Scotland |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Isolation and cultivation of clinical isolate SARS-CoV-2 from clinical isolate. Provision of cultured virus for testing standards. |
| Collaborator Contribution | Patient samples of SARS-CoV-2 and relevant information. |
| Impact | Improved testing for SARS-CoV-2 |
| Start Year | 2020 |
| Description | Scotland's Rural College, Epidemiology Unit |
| Organisation | Scotland's Rural College |
| Department | Inverness Veterinary Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Laboratory investigations, data analysis and interpretation, sharing of results, generation of publications. |
| Collaborator Contribution | Sample and epidemiological metadata provision, expertise. |
| Impact | doi: 10.3389/fvets.2021.755833. PMID: 34778436; PMCID: PMC8585936. doi: 10.1128/AEM.03142-20. PMID: 33712425; PMCID: PMC8117755. |
| Start Year | 2015 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Animal Health Research Institute |
| Country | Taiwan, Province of China |
| Sector | Public |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Animal Health Service |
| Country | Netherlands |
| Sector | Public |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Animal and Plant Health Agency |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Animal and Plant Quarantine Agency |
| Country | Korea, Republic of |
| Sector | Public |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Centers for Disease Control and Prevention (CDC) |
| Country | United States |
| Sector | Public |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Chinese Academy of Agricultural Sciences |
| Department | Harbin Veterinary Research Institute (HVRI) |
| Country | China |
| Sector | Public |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Erasmus MC |
| Department | Department of Viroscience |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Experimental Zooprophylactic Institute of the Venezie |
| Country | Italy |
| Sector | Public |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Fonds de la Recherche Scientifique |
| Country | Belgium |
| Sector | Public |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Friedrich Loeffler Institute |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Government of Canada |
| Department | Canadian Food Inspection Agency (CFIA) |
| Country | Canada |
| Sector | Public |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Government of Canada |
| Department | Canadian Food Inspection Agency (CFIA) |
| Country | Canada |
| Sector | Public |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Hokkaido University |
| Department | Graduate School of Veterinary Medicine |
| Country | Japan |
| Sector | Academic/University |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Hokkaido University |
| Department | Research Center for Zoonosis Control |
| Country | Japan |
| Sector | Academic/University |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Hungarian Academy of Sciences (MTA) |
| Country | Hungary |
| Sector | Academic/University |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | International Livestock Research Institute (ILRI) |
| Country | Kenya |
| Sector | Charity/Non Profit |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Konkuk University |
| Country | Korea, Republic of |
| Sector | Academic/University |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | National Food Chain Safety Office |
| Department | Veterinary Diagnostic Directorate |
| Country | Hungary |
| Sector | Public |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | National Veterinary Institute |
| Country | Sweden |
| Sector | Public |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | U.S. Department of Agriculture USDA |
| Department | National Wildlife Research Center |
| Country | United States |
| Sector | Public |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | U.S. Department of Agriculture USDA |
| Department | Southeast Poultry Research Laboratory |
| Country | United States |
| Sector | Public |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | U.S. Department of Agriculture USDA |
| Country | United States |
| Sector | Public |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | US Geological Survey |
| Country | United States |
| Sector | Public |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | University Libre Bruxelles (Université Libre de Bruxelles ULB) |
| Department | Spatial Epidemiology Laboratory |
| Country | Belgium |
| Sector | Academic/University |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | University of Oxford |
| Department | Centre for Tropical Medicine and Global Health |
| Country | United Kingdom |
| Sector | Hospitals |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | University of Oxford |
| Department | Department of Zoology |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |
| Start Year | 2014 |
| Description | The Global Consortium for H5N8 and Related Influenza Viruses |
| Organisation | Utrecht University |
| Department | Department of Farm Animal Health |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the 2016/2017 outbreaks and investigating the generation of reassortments by phylodynamic (computational) methods. This work has now been submitted to a journal and we are doing the revisions (Feb 2020). Following on from this, many of the partners (including Roslin) are now in a recently (2020) funded European collaborative grant (details reported separately). |
| Collaborator Contribution | The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute. |
| Impact | Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852 |