Pathogen diversity, host specificity and virulence

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

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.

Organisations

People

ORCID iD

David Lawrence Gally (Principal Investigator)
Sarah Mills Brown (Co-Investigator)
Samantha Lycett (Co-Investigator) orcid http://orcid.org/0000-0003-3159-596X
Tanja Opriessnig (Co-Investigator) orcid http://orcid.org/0000-0001-9642-0904
Nikki Smith (Co-Investigator)
Adrian Muwonge (Co-Investigator) orcid http://orcid.org/0000-0002-8579-0384
Gerry McLachlan (Co-Investigator) orcid http://orcid.org/0000-0001-5362-9804
Mark Bronsvoort (Co-Investigator)
Philippa Beard (Co-Investigator)
Eleanor Fiona Houston (Co-Investigator) orcid http://orcid.org/0000-0002-4082-2274
Neil Andrew Mabbott (Co-Investigator) orcid http://orcid.org/0000-0001-7395-1796
Tom Freeman (Co-Investigator)
Ross Fitzgerald (Co-Investigator)
Abigail Diack (Co-Investigator) orcid http://orcid.org/0000-0002-4293-3437
Liam James Morrison (Co-Investigator) orcid http://orcid.org/0000-0002-8304-9066
Christine Tait-Burkard (Co-Investigator) orcid http://orcid.org/0000-0002-0471-3230
TAHAR AIT-ALI (Co-Investigator)
Elizabeth Glass (Co-Investigator) orcid http://orcid.org/0000-0002-6183-0185
Robert Dalziel (Co-Investigator)
Michael T Cheeseman (Co-Investigator)
Finn Grey (Co-Investigator)
Michael Bryan Watson (Co-Investigator)
K Salamat (Co-Investigator)
Rowland Raymond Kao (Co-Investigator) orcid http://orcid.org/0000-0003-0919-6401
Nick Sparks (Co-Investigator) orcid http://orcid.org/0000-0002-2879-2762
Musa A Hassan (Co-Investigator) orcid http://orcid.org/0000-0002-0371-3300
Rona Barron (Co-Investigator)
Andrew Christopher Gill (Co-Investigator) orcid http://orcid.org/0000-0001-5201-9473
Lonneke Vervelde (Co-Investigator)
Tim Regan (Co-Investigator) orcid http://orcid.org/0000-0002-0979-7875
Helen Sang (Co-Investigator) orcid http://orcid.org/0000-0002-6427-6853
Wilfred Goldmann (Co-Investigator)
Andrea Beate Doeschl-Wilson (Co-Investigator)
Joanne Marie Stevens (Co-Investigator)
Jacqueline Smith (Co-Investigator) orcid http://orcid.org/0000-0002-2813-7872
Clare Pridans (Co-Investigator)
Bernadette Mary Dutia (Co-Investigator)
Deborah Hoyle (Co-Investigator)
Jean Manson (Co-Investigator)
Mark Paul Stevens (Co-Investigator)
David Arthur Hume (Co-Investigator)
Paul Digard (Co-Investigator)

Publications

10 25 50

publication icon
Alber A (2021) The bird's immune response to avian pathogenic Escherichia coli. in Avian pathology : journal of the W.V.P.A

 
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 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.
Repurposing of funds for Covid-19 research:
1. Roslin is central to the UoE's effort in fundamental molecular SARS-CoV2 biology as we have the only currently functional CL3 suites in the University that can work with the virus. We have our own active research programmes into the molecular virology of COVID and support many others across the University through provision of these BBSRC-supported facilities (an exhaustive list can be supplied on request). The work of Dr Christine Tait-Burkard deserves particular highlighting - as an early career researcher supported by an Institute tenure track fellowship who trained as a coronavirologist before joining us and has been absolutely central to the UoE effort, through her detailed knowledge of these types of viruses, through managing one of the CL3 suites and through training a cohort of other researchers to safely handle the pandemic virus. Her own COVID research is largely focussed on repurposing existing licensed drugs that may have clinical benefit in treating COVID-19, through her membership in a very large IMI2 consortium grant. Immediate impact has come however from her input into to the development of a highly sensitive, multiplexed RT-qPCR assay at a vastly reduced price compared to commercially available products that is being used by one of the local NHS hub testing facilities for diagnosis. 2. Roslin's diverse epidemiological modelling teams play a central role in providing the Scottish and UK government with data-informed model predictions to underpin Covid-19 policy decisions. Including: (i) An individual-based computer model of Covid-19 transmission in Scotland to help Health Protection Scotland better understand regional differences in risks and to plan for changes in control. (ii) A dashboard for tracking the progress of Covid-19 in Scotland (https://smazeri.shinyapps.io/Covid19_Scotland). (iii) Working with the COG-UK consortium (https://www.cogconsortium.uk), for which the massive sequencing effort has resulted in approximately 50% of the global publicly available SARS-CoV-2 sequences. We help track the spread of the virus in Scotland by looking at its genetic makeup in different areas of Scotland, (iv) Provision of key computational inference software for the models of The Scottish COVID-19 Response Consortium (SCRC), which is a major contributor to the Royal Society's RAMP scheme as part of the national COVID-19 response. (v) Development of waste water sampling to detect SARS-CoV-2 genome in sewage as a surveillance technique and now rolled out to cover 80% of the Scottish population and will be used to examine vaccine efficacy.
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. Major direct contributions to the UK Covid response: Our website lists past and current activity here: https://www.ed.ac.uk/roslin/news-events/roslin-covid-19-research
4. 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. 5. Covid-19 response. We have repurposed some of our ISP funds to study the basic biology of SARS-CoV2, develop diagnostic tests, map the evolution of variants and model transmission and interventions (as defined in key findings). For examples also see: https://www.ed.ac.uk/roslin/news-events/roslin-covid-19-research.
Sector Agriculture, Food and Drink,Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Economic,Policy & public services

 
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 Member of Defra's Science Advisory Council
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
Impact As a member of Defra's Science Advisory Council, I provide comments on a wide variety of Defra science-related policies and draw upon both my personal research experience, but also the broader research community at the Roslin Institute
URL https://www.gov.uk/government/organisations/science-advisory-council/about/our-governance#members
 
Description Member of Defra's Science Advisory Council
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a 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 the Defra bovine Tuberculosis partnership
Geographic Reach National 
Policy Influence Type Participation in a 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 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 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 £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 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 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 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 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 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 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 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 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 Environmental and Economic Impacts of Improved Antibiotics Stewardship in Poultry Systems
Amount £647,418 (GBP)
Funding ID BB/T004436/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2019 
End 05/2022
 
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 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 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 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 04/2021 
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 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 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 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 09/2018 
End 09/2021
 
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 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 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 05/2020
 
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 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 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 £414,291 (GBP)
Funding ID BB/W000296/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2021 
End 09/2024
 
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 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 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 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 £471,476 (GBP)
Funding ID MR/V034952/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 11/2020 
End 05/2022
 
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 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 08/2021 
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 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 07/2019 
End 08/2023
 
Description [YY-EEID US-UK XXXX] Predictive phylogenetics for evolutionary and transmission dynamics of newly emerging avian influenza viruses
Amount £1,091,366 (GBP)
Funding ID BB/V011286/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2021 
End 12/2023
 
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 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 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 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 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 COVID-19 Genomics UK (COG-UK) Consortium 
Organisation NHS Greater Glasgow and Clyde (NHSGGC)
Department West of Scotland Specialist Virology Centre
Country United Kingdom 
Sector Hospitals 
PI Contribution Member of COG-UK and developing computational methods and performing phylodynamic analysis on SARS-CoV-2 sequences, with particular focus on Scotland.
Collaborator Contribution The COVID-19 Genomics UK (COG-UK) consortium was created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government. Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and twelve academic partners providing sequencing and analysis capacity. A full list of collaborators can be found here: https://www.cogconsortium.uk/about/. Professor Peacock is also on a part-time secondment to PHE as Director of Science, where she focuses on the development of pathogen sequencing through COG-UK. COG-UK was established in March 2020 supported by £20 million funding from the UK Department of Health and Social Care (DHSC), UK Research and Innovation (UKRI) and the Wellcome Sanger Institute, administered by UK Research and Innovation. I collaborated particularly with the other Scottish partners of COG-UK for this work (about Scottish SARS-CoV-2), and these are listed in the collaborators section. The list of authors on the Scotland report (Dec 2020) include: Samantha Lycett, Joseph Hughes, Martin McHugh, Ana da Silva Filipe, Lu Lu, Thomas Doherty, Amy Shepherd, Rhys Inward, Gianluigi Rossi, Daniel Balaz, Rowland Kao, James Shepherd, Matthew T.G. Holden, Kate Templeton, Emma C Thomson, Mark Woolhouse, Rambaut A, David L Robertson
Impact Report on Scotland sequences sent to SAGE (recorded under policy influence) - here is the link to the report - there are a large number of authors, Samantha Lycett (myself) is the first author. https://www.cogconsortium.uk/wp-content/uploads/2020/12/9th-December-2020-COG-UK-Report-Scotland-SARS-CoV-2-a-genomics-perspective-SAGE.pdf
Start Year 2020
 
Description COVID-19 Genomics UK (COG-UK) Consortium 
Organisation NHS Health Scotland
Department Public Health Science NHS Scotland
Country United Kingdom 
Sector Public 
PI Contribution Member of COG-UK and developing computational methods and performing phylodynamic analysis on SARS-CoV-2 sequences, with particular focus on Scotland.
Collaborator Contribution The COVID-19 Genomics UK (COG-UK) consortium was created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government. Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and twelve academic partners providing sequencing and analysis capacity. A full list of collaborators can be found here: https://www.cogconsortium.uk/about/. Professor Peacock is also on a part-time secondment to PHE as Director of Science, where she focuses on the development of pathogen sequencing through COG-UK. COG-UK was established in March 2020 supported by £20 million funding from the UK Department of Health and Social Care (DHSC), UK Research and Innovation (UKRI) and the Wellcome Sanger Institute, administered by UK Research and Innovation. I collaborated particularly with the other Scottish partners of COG-UK for this work (about Scottish SARS-CoV-2), and these are listed in the collaborators section. The list of authors on the Scotland report (Dec 2020) include: Samantha Lycett, Joseph Hughes, Martin McHugh, Ana da Silva Filipe, Lu Lu, Thomas Doherty, Amy Shepherd, Rhys Inward, Gianluigi Rossi, Daniel Balaz, Rowland Kao, James Shepherd, Matthew T.G. Holden, Kate Templeton, Emma C Thomson, Mark Woolhouse, Rambaut A, David L Robertson
Impact Report on Scotland sequences sent to SAGE (recorded under policy influence) - here is the link to the report - there are a large number of authors, Samantha Lycett (myself) is the first author. https://www.cogconsortium.uk/wp-content/uploads/2020/12/9th-December-2020-COG-UK-Report-Scotland-SARS-CoV-2-a-genomics-perspective-SAGE.pdf
Start Year 2020
 
Description COVID-19 Genomics UK (COG-UK) Consortium 
Organisation Royal Infirmary of Edinburgh
Country United Kingdom 
Sector Hospitals 
PI Contribution Member of COG-UK and developing computational methods and performing phylodynamic analysis on SARS-CoV-2 sequences, with particular focus on Scotland.
Collaborator Contribution The COVID-19 Genomics UK (COG-UK) consortium was created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government. Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and twelve academic partners providing sequencing and analysis capacity. A full list of collaborators can be found here: https://www.cogconsortium.uk/about/. Professor Peacock is also on a part-time secondment to PHE as Director of Science, where she focuses on the development of pathogen sequencing through COG-UK. COG-UK was established in March 2020 supported by £20 million funding from the UK Department of Health and Social Care (DHSC), UK Research and Innovation (UKRI) and the Wellcome Sanger Institute, administered by UK Research and Innovation. I collaborated particularly with the other Scottish partners of COG-UK for this work (about Scottish SARS-CoV-2), and these are listed in the collaborators section. The list of authors on the Scotland report (Dec 2020) include: Samantha Lycett, Joseph Hughes, Martin McHugh, Ana da Silva Filipe, Lu Lu, Thomas Doherty, Amy Shepherd, Rhys Inward, Gianluigi Rossi, Daniel Balaz, Rowland Kao, James Shepherd, Matthew T.G. Holden, Kate Templeton, Emma C Thomson, Mark Woolhouse, Rambaut A, David L Robertson
Impact Report on Scotland sequences sent to SAGE (recorded under policy influence) - here is the link to the report - there are a large number of authors, Samantha Lycett (myself) is the first author. https://www.cogconsortium.uk/wp-content/uploads/2020/12/9th-December-2020-COG-UK-Report-Scotland-SARS-CoV-2-a-genomics-perspective-SAGE.pdf
Start Year 2020
 
Description COVID-19 Genomics UK (COG-UK) Consortium 
Organisation University of Glasgow
Department Institute of Biodiversity, Animal Health and Comparative Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution Member of COG-UK and developing computational methods and performing phylodynamic analysis on SARS-CoV-2 sequences, with particular focus on Scotland.
Collaborator Contribution The COVID-19 Genomics UK (COG-UK) consortium was created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government. Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and twelve academic partners providing sequencing and analysis capacity. A full list of collaborators can be found here: https://www.cogconsortium.uk/about/. Professor Peacock is also on a part-time secondment to PHE as Director of Science, where she focuses on the development of pathogen sequencing through COG-UK. COG-UK was established in March 2020 supported by £20 million funding from the UK Department of Health and Social Care (DHSC), UK Research and Innovation (UKRI) and the Wellcome Sanger Institute, administered by UK Research and Innovation. I collaborated particularly with the other Scottish partners of COG-UK for this work (about Scottish SARS-CoV-2), and these are listed in the collaborators section. The list of authors on the Scotland report (Dec 2020) include: Samantha Lycett, Joseph Hughes, Martin McHugh, Ana da Silva Filipe, Lu Lu, Thomas Doherty, Amy Shepherd, Rhys Inward, Gianluigi Rossi, Daniel Balaz, Rowland Kao, James Shepherd, Matthew T.G. Holden, Kate Templeton, Emma C Thomson, Mark Woolhouse, Rambaut A, David L Robertson
Impact Report on Scotland sequences sent to SAGE (recorded under policy influence) - here is the link to the report - there are a large number of authors, Samantha Lycett (myself) is the first author. https://www.cogconsortium.uk/wp-content/uploads/2020/12/9th-December-2020-COG-UK-Report-Scotland-SARS-CoV-2-a-genomics-perspective-SAGE.pdf
Start Year 2020
 
Description COVID-19 Genomics UK (COG-UK) Consortium 
Organisation University of Glasgow
Department MRC - University of Glasgow Centre for Virus Research
Country United Kingdom 
Sector Academic/University 
PI Contribution Member of COG-UK and developing computational methods and performing phylodynamic analysis on SARS-CoV-2 sequences, with particular focus on Scotland.
Collaborator Contribution The COVID-19 Genomics UK (COG-UK) consortium was created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government. Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and twelve academic partners providing sequencing and analysis capacity. A full list of collaborators can be found here: https://www.cogconsortium.uk/about/. Professor Peacock is also on a part-time secondment to PHE as Director of Science, where she focuses on the development of pathogen sequencing through COG-UK. COG-UK was established in March 2020 supported by £20 million funding from the UK Department of Health and Social Care (DHSC), UK Research and Innovation (UKRI) and the Wellcome Sanger Institute, administered by UK Research and Innovation. I collaborated particularly with the other Scottish partners of COG-UK for this work (about Scottish SARS-CoV-2), and these are listed in the collaborators section. The list of authors on the Scotland report (Dec 2020) include: Samantha Lycett, Joseph Hughes, Martin McHugh, Ana da Silva Filipe, Lu Lu, Thomas Doherty, Amy Shepherd, Rhys Inward, Gianluigi Rossi, Daniel Balaz, Rowland Kao, James Shepherd, Matthew T.G. Holden, Kate Templeton, Emma C Thomson, Mark Woolhouse, Rambaut A, David L Robertson
Impact Report on Scotland sequences sent to SAGE (recorded under policy influence) - here is the link to the report - there are a large number of authors, Samantha Lycett (myself) is the first author. https://www.cogconsortium.uk/wp-content/uploads/2020/12/9th-December-2020-COG-UK-Report-Scotland-SARS-CoV-2-a-genomics-perspective-SAGE.pdf
Start Year 2020
 
Description COVID-19 Genomics UK (COG-UK) Consortium 
Organisation University of St Andrews
Department School of Medicine St Andrews
Country United Kingdom 
Sector Academic/University 
PI Contribution Member of COG-UK and developing computational methods and performing phylodynamic analysis on SARS-CoV-2 sequences, with particular focus on Scotland.
Collaborator Contribution The COVID-19 Genomics UK (COG-UK) consortium was created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government. Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and twelve academic partners providing sequencing and analysis capacity. A full list of collaborators can be found here: https://www.cogconsortium.uk/about/. Professor Peacock is also on a part-time secondment to PHE as Director of Science, where she focuses on the development of pathogen sequencing through COG-UK. COG-UK was established in March 2020 supported by £20 million funding from the UK Department of Health and Social Care (DHSC), UK Research and Innovation (UKRI) and the Wellcome Sanger Institute, administered by UK Research and Innovation. I collaborated particularly with the other Scottish partners of COG-UK for this work (about Scottish SARS-CoV-2), and these are listed in the collaborators section. The list of authors on the Scotland report (Dec 2020) include: Samantha Lycett, Joseph Hughes, Martin McHugh, Ana da Silva Filipe, Lu Lu, Thomas Doherty, Amy Shepherd, Rhys Inward, Gianluigi Rossi, Daniel Balaz, Rowland Kao, James Shepherd, Matthew T.G. Holden, Kate Templeton, Emma C Thomson, Mark Woolhouse, Rambaut A, David L Robertson
Impact Report on Scotland sequences sent to SAGE (recorded under policy influence) - here is the link to the report - there are a large number of authors, Samantha Lycett (myself) is the first author. https://www.cogconsortium.uk/wp-content/uploads/2020/12/9th-December-2020-COG-UK-Report-Scotland-SARS-CoV-2-a-genomics-perspective-SAGE.pdf
Start Year 2020
 
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 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 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 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 None as yet
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 None as yet
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 None as yet
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 None as yet
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 None as yet
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
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Wageningen University & Research
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 Wellcome Trust
Department Wellcome Trust Major Overseas Programme in Ho Chi Minh City Vietnam
Country Viet Nam 
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 Tracking Haulage in East Africa to support COVID-19 surveillace 
Organisation Makerere University
Country Uganda 
Sector Academic/University 
PI Contribution I am the Principal investigator
Collaborator Contribution Co- Principal Investigator
Impact Still early staged of the project
Start Year 2020
 
Description Tracking Haulage in East Africa to support COVID-19 surveillace 
Organisation University of Edinburgh
Department School of Informatics Edinburgh
Country United Kingdom 
Sector Academic/University 
PI Contribution I am the Principal investigator
Collaborator Contribution Co- Principal Investigator
Impact Still early staged of the project
Start Year 2020
 
Description USDA-SEPRL 
Organisation U.S. Department of Agriculture USDA
Department Agricultural Research Service
Country United States 
Sector Public 
PI Contribution This partnership started with a joint grant from the USDA and the BBSRC to our collaborators and ourselves and continues through a second such joint award.
Collaborator Contribution As above, the USDA contributes direct funding to the partner laboratory (PIs Dr Darrell Kapcyzinski and Mary Pantin-Jackwood). Their laboratory also benefits from core funding that provides further in kind benefits to the project.
Impact Major outputs are: a patent awarded, and further funding. US Patent No. 11,214,799 B2 (Jan 4th 2022) entitled 'HA-specific influenza virus attenuated vaccine comprising mutations in segment 7 and uses therefor'; D.R. Kapczynski, , P. Digard, L. Vervelde and D. Suarez. BBSRC US-UK-China Collaborative grant: Predictive phylogenetics for evolutionary and transmission dynamics of newly emerging avian influenza viruses (BB/V011286/1).
Start Year 2015
 
Description University of Nottingham - genome-wide RNA interference applied to Trypanosoma congolense 
Organisation University of Nottingham
Country United Kingdom 
Sector Academic/University 
PI Contribution This is a new collaboration within this project, applying a novel genome wide RNA interference screen to identifying drug mode of action and mechanisms of resistance. The project team provided input into experimental design and analysis.
Collaborator Contribution The partners have developed the screen, and facilitated access to apply the screen to our biological problem of interest. Collaborators have also provided significant input into analysis and interpretation of results.
Impact Identification of candidate genes in Trypanosome congolense involved in drug mode of action or drug resistance. Analysis, validation and further experiments are ongoing.
Start Year 2019
 
Description Vaccine development for EHEC in cattle with Roslin Technologies Ltd 
Organisation Roslin Technologies
Country United Kingdom 
Sector Private 
PI Contribution We have provided expertise on the selection of antigen for the vaccine, published trial vaccine data and IP contributions
Collaborator Contribution RTL are funding are now licensing the IP, funding production production of antigens in the USA, a small scale safety and efficacy trial of the antigens produced at MRI, consultancy for a submission to CVB (USA) to allow cattle that have received the experimental vaccine to be returned to the food chain. If successful RTL will then fund a trial of the vaccine in a commercial feedlot with collaboration from ARS-USDA
Impact not applicable yet
Start Year 2019
 
Title IMMUNOGENIC OMPOSITIONS CONTAINING ESCHERICHIA COLI H7 FLAGELLA AND METHODS OF USE THEREOF 
Description Immunogenic compositions containing Escherichia coli O157:H7 flagella including fusion proteins and methods using the immunogenic compositions are disclosed. Inducing an immune response in an animal to Escherichia coli O157:H7 flagella will result in prevention of colonization by Escherichia coli O157:H7 in the animal or a reduction in the amount of Escherichia coli O157:H7 infecting the animal. The immune composition will prevent or reduce the attachment of Escherichia coli O157:H7 to cells within the animal. 
IP Reference WO2009050474 
Protection Patent granted
Year Protection Granted 2009
Licensed No
Impact A commercial partner (Roslin Technologies Ltd) has now licensed the patents associated with this potential cattle vaccine and the wider possibilities for the mucosal adjutancy of H7 flagella. They are currently supporting manufacture of the antigens as well as some safety and efficacy testing towards a trial of the vaccine in a commercial feedlot.
 
Title Covid-19 track and trace system tailored for haulage in East Africa 
Description Project-THEA aims to deliver an open access mobile application to support track and trace tailored to the haulage industry. The tool is designed to combine anonymized time-stamped geo-location information relative to the road infrastructure with COVID-19 test results, to not only support public health efforts to limit transmission but also the safe reopening of economies. Critically the efficiency in track and trace enhances the flow of the regional supply chain as well as strategic allocation of public health surveillance resources. NB: The tool is open access but the data access is limited to public health institutions. This way its use is not limited to East Africa. 
Type Of Technology Webtool/Application 
Year Produced 2021 
Open Source License? Yes  
Impact The technology is still under implementation. 
URL https://project-thea.org
 
Title PULpy 
Description Polysaccharide utilisation loci (PUL) are regions within bacterial genomes that encode all the necessary machinery for the cleavage of particular carbohydrates. For the Bacteroidetes phylum, prediction of PUL from genomic data alone involves the identification of carbohydrate-active enzymes (CAZymes) co-localised with susCD gene pairs. Here we present the open prediction of PUL in 5414 public Bacteroidetes genomes, and an open-source pipeline to reproduce or extend the results. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact We use this software in our metagenomics and microbiome research 
URL https://github.com/WatsonLab/PULpy
 
Title PorkMartAgent- A data driven Market intelligence to support the pig industry in Uganda 
Description PorkMart aims to deliver real-time market intelligence on the pork value chain for Uganda. It leverages stakeholder inputs, market research and state of the art data science to deliver actionable end user information 
Type Of Technology Webtool/Application 
Year Produced 2021 
Impact We have just started processing the data, to allow for realtime mark intelligence, the impact of this on the should be in the next 6-12 months 
URL https://www.pork-mart.com
 
Title THEA-trucker 
Description This is a mobile application for digital contact tracing tailored to haulage in East Africa https://play.google.com/store/apps/details?id=com.theatrucker 
Type Of Technology Software 
Year Produced 2021 
Open Source License? Yes  
Impact This is the second version of the software, with the final version due in May 2022. The publication relating to this tool is under review in BMJ protocol 
 
Description Speaker at an International Conference on One Health Antimicrobial Resistance - Leiden 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I presented a talk on 'alternative approaches to tackling antimicrobial resistance'. A number of scientists at RI have now contributed to a review in this area to be published in 2020.
Year(s) Of Engagement Activity 2019
URL http://www.icohar2019.org/icohar2019/organization.html
 
Description Campus Open Day- Midlothian Science Festival 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact The Roslin Institute and Easter Bush Campus Open Day was an event undertaken within the Midlothian Science Festivals. Hands on public activities lead by scientists under "Pathogen diversity, host specificity and virulence" included Science is for Everyone
Year(s) Of Engagement Activity 2018
URL https://www.ed.ac.uk/easter-bush-campus/science-outreach-centre
 
Description "Covid-19 research" Science Insights Online Webinar 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact Webinar for all applicants to the Science Insights Online programme, about UoE research on Covid-19
Year(s) Of Engagement Activity 2020
 
Description "Freedom Fear and Quest for Vaccine" Just Festival 2020 online 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Online panel event for the Just Festival (Edinburgh) featuring Rowland Kao
Year(s) Of Engagement Activity 2020
 
Description "Investigating the Antimicrobial Effects of Scottis Honey" online workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Project launch online workshop for teacher and beekeeper citizen scientists, and project team - Emily Clark, Mark Barnett, Tim Regan & Nicola Stock (Roslin) and Patrick Pollock (R(D)SVS). Research talks, information about planned project activities and a practical demonstration of lab honey testing for contamination.
Year(s) Of Engagement Activity 2020
 
Description 15 interviews on ITV/STV News 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Discuss coronavirus pandemic
Year(s) Of Engagement Activity 2021,2022
 
Description 2 snippets for Newsbeat on BBC Radio 1 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Pre-recorded snippet on coronavirus pandemic
Year(s) Of Engagement Activity 2020,2021,2022
 
Description 20 commissioned articles for iNews 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Opinion pieces on covid, 600-700 words
Year(s) Of Engagement Activity 2020,2021,2022
URL https://inews.co.uk/opinion/virologist-spending-christmas-without-self-isolating-10-days-795255
 
Description 24 interviews on BBC Radio 5 Live 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact I have been interviewed on BBC Radio 5 Live relating to various aspects of the covid-19 pandemic several times.
Year(s) Of Engagement Activity 2020,2021,2022
 
Description 24 interviews on BBC Scotland 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Discuss new variant of coronavirus
Year(s) Of Engagement Activity 2021,2022
 
Description 35 interviews on BBC Radio Scotland 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact I have been on BBC Radio Scotland several times to discuss various aspects of the covid-19 pandemic.
Year(s) Of Engagement Activity 2020,2021,2022
 
Description 7 interviews on BBC News (TV) 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact I was interviewed on BBC News to discuss coronavirus testing and vaccination progress.
Year(s) Of Engagement Activity 2021,2022
 
Description Annual Roslin Institute Open Doors Day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact The annual Roslin Institute Open Doors day was held on 14 October 2017 and was attended by 491 people. It involved 81 members of staff and students and showcased a wide range of research arising from BBSRC strategic investment, including (but not limited to), food safety, influenza, genetic improvement, DNA, imaging and the ethical treatment of animals in research.
Year(s) Of Engagement Activity 2017
 
Description Annual Roslin Institute Open Doors Day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact The annual Roslin Institute Open Doors day was held on 14 October 2017 and was attended by 491 people. It involved 81 members of staff and students and showcased a wide range of research arising from BBSRC strategic investment, including (but not limited to), food safety, influenza, genetic improvement, DNA, imaging and the ethical treatment of animals in research.
Year(s) Of Engagement Activity 2017
 
Description Article for British Deer Society journal 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Supporters
Results and Impact Co-authored an article with Silvia Perez-Espona (lecturer in Conservation Science at the R(D)SVS) summarizing several recent scientific papers reporting transmission of SARS-CoV-2 to white tailed deer in North America. This generated some questions from members on the likelihood of similar transmission events in the UK, and what might be done to prevent this.
Year(s) Of Engagement Activity 2021
 
Description Artificial Intelligence (AI) workshop at Earlham 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Inter-institute workshop that discussed main applications of AI in their fields and potential for further research collaboration
Year(s) Of Engagement Activity 2018
 
Description Aviagen / CP workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact I presented our work on functional microbiome analysis during a one-day workshop which I set up and organised at The Roslin Institute. In attendance were employees of CP (a large Asian conglomerate) and Aviagen (one of the world's largest chicken breeding companies). The focus of the workshop was animal genetics and microbiome.
Year(s) Of Engagement Activity 2010,2017
 
Description BBC Countryfile film related to the work of the Centre for Tropical Livestock Genetics & Health at Roslin 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Bill Gates was interviewed by BBC Countryfile on 26 January 2018 in relation to work funded by the Gates Foundation involving Roslin Institute scientists towards the genetic improvement of farmed animals in low- and middle-income countries. The programme aired on 11 February 2018 and reached an estimated audience in excess of 5 million. The interview took place on the same day as the launch of the Global Academy of Agriculture & Food Security, which was attended by the Secretary of State for the Department for International Development the Rt Hon Penny Mordaunt (see separate activity) and generated significant press interest, featuring on BBC Scotland news. Particular emphasis was placed on the work of Roslin scientists to understand the genetic make-up of African diary cattle and chickens and to understand how this relates to performance traits in order to guide breeding decisions.
Year(s) Of Engagement Activity 2018
 
Description BBC One Scotland COVID Update 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interview / comments on COVID-19 Pandemic and situation in Scotland, UK and globally. Roughly 10 appearances.
Year(s) Of Engagement Activity 2020,2021,2022
 
Description BBC Radio 4 programme - Beyond the Buzzwords - 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact An interview on a podcast on the buzzword "Big Data" (or buzz phrase :) ). Discussed the role of big data in particular in mobility tracking and how it is used to help us understand and control infectious diseases, including COVID-19.
Year(s) Of Engagement Activity 2020
URL https://www.bbc.co.uk/programmes/m000lghg
 
Description BBC Radio Scotland - Debate night extra 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interview / comments on COVID-19 Pandemic and situation in Scotland, UK and globally. Roughly 10 appearances
Year(s) Of Engagement Activity 2020,2021,2022
 
Description BBC Radio Scotland - Mornings Programme 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interview / comments on COVID-19 Pandemic and situation in Scotland, UK and globally. Roughly 20 appearances.
Year(s) Of Engagement Activity 2020,2021,2022
 
Description BBC Radio Scotland Lunchtime Live 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interview / comments on COVID-19 Pandemic and situation in Scotland, UK and globally. Roughly 15 appearances
Year(s) Of Engagement Activity 2020,2021,2022
 
Description BBC Radio Wales 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interview / comments on COVID-19 Pandemic and situation in Scotland, UK and globally. 3 appearances
Year(s) Of Engagement Activity 2020,2021,2022
 
Description BBC Three Counties Radio 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Interview / comments on COVID-19 Pandemic and situation in Scotland, UK and globally. Roughly 5 engagements.
Year(s) Of Engagement Activity 2020,2021,2022
 
Description BBSRC Animal Health Research Club Final Dissemination Event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact A final presentation was given on the BBSRC Animal Health Research Club project on "Genetics of host responses to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) was given followed by discussion of the results. There was also a wider discussion on the challenges of studying the genetics of host responses to infection in pigs - challenge experiments in animal research facilities lack the power as the numbers that can be studied are too small on the one hand, but field data from natural exposure to disease can be noisy and logistically challenge to acquire.
Year(s) Of Engagement Activity 2018
 
Description BBSRC workshop & briefing at Science Media Centre plus associated news coverage 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact BBSRC workshop & briefing at Science Media Centre plus associated news coverage in The Guardian, Sky, The Telegraph, Hereford Times, Yahoo, Daily Mail, The Sun, Mail on Sunday, The Times, Aol, BT, Sky News, The Irish Sun, Scotsman Food and Drink, The Herald, The National, Breaking News.ie, The Irish News, Irish Examiner, Classic FM, Eagle Radio, Spirit FM, Capital FM, Heart, Gazette and Herald, Farm Week, Gazette, Evening Express, Border Telegraph, Times and Star, TalkTalk, Wales Farmer, Evening Telegraph, South West Farmer
Year(s) Of Engagement Activity 2019
URL https://www.ed.ac.uk/roslin/news-events/latest-news/livestock-research-focus-at-international-event
 
Description Bacteria insights could advance dog infection treatments 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact report around 'Bacteria insights could advance dog infection treatments'
Year(s) Of Engagement Activity 2021
 
Description Bacterial gene has key role in Legionnaires' disease 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact reporting that Bacterial gene has a key role in Legionnaires' disease
Year(s) Of Engagement Activity 2021,2022
 
Description British Science Festival Hull 2018: "From lab to farmyard: genome editing our livestock" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact A talk on genome editing and it's potential impact on livestock breeding was presented to the general public at the British Science Festival in Hull in 2018. Around 50-100 people attended the talk. Publicity around the event, including blogging, press releases etc. reached a much larger public.
Year(s) Of Engagement Activity 2018
URL https://www.britishsciencefestival.org/event/from-lab-to-farmyard-genome-editing-our-livestock/
 
Description CLSU "Updates on Swine Diagnostics" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact A presentation on the benefits of new pen-side diagnostics and how they could help decision making by farmers and veterinary professionals. The audience were Veterinary students from Central Luzon State University (The Philippines).
Year(s) Of Engagement Activity 2018
 
Description Careers event for S4 secondary pupils 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Opportunity for S4 pupils to interact with professionals across a range of areas including STEM. Aim was to give pupils information on careers in biological research prior to choosing final year subjects and University degrees.
Year(s) Of Engagement Activity 2015,2016,2017
 
Description Changing World Conversations - The future of food. Live online panel session plus prerecorded researcher interviews. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Changing World Conversations - The future of food. Live online panel session plus prerecorded researcher interviews.
Year(s) Of Engagement Activity 2021
 
Description Cited in print or broadcasting media 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Interview / News on COVID-19 pandemic.
Total number of article citations
from Dec 2020 - 11/03/22: 1,145

Total reach: 16,973,830,000

Online news mentions: 891
Broadcast news mentions: 145
Print mentions: 105
Blogs: 4

Breakdown by location:
UK: 1,039
US: 31
New Zealand: 8
Ireland: 7
Canada: 6
Year(s) Of Engagement Activity 2020,2021,2022
 
Description Connections: COVID 19 One Year On 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact A panel discussion held online but organised by Lucy Cavendish College, University of Cambridge, where experts in the broad area of public health discussed the COVID-19 pandemic and the UK response to it.
Year(s) Of Engagement Activity 2021
URL https://youtu.be/sAayZH9WHEc
 
Description Covid early warning system could avert lockdowns 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact article around 'Covid early warning system could avert lockdowns' in The Press and Journal, The Herald, Edinburgh Live, Evening Express, Medical Xpress, Edinburgh Evening News, Midlothian Advertiser
Year(s) Of Engagement Activity 2021
 
Description Covid-19 dashboard tracks spread across Scotland 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact report around 'Covid-19 dashboard tracks spread across Scotland'
Year(s) Of Engagement Activity 2021
 
Description Development of new public engagement activity 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Development of outreach activity on theme of bacterial host-adaptation funded by Wellcome Trust
HostBusters! Highschool activity. Midlothian Science Festival 2019. Midlothian, UK. 7-11 October 2019
Year(s) Of Engagement Activity 2019,2020
 
Description EASTBio student symposium invited speaker and panel member 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact EASTBio supported PhD students attended a two day symposium in Dundee, and I was invited as a speaker. I gave a talk about my experiences as a PhD student and how they have impacted me throughout my career. I had several messages from students after the event thanking me for sharing personal information and saying how they found my story so relatable. After the talks the invited speakers held a panel Q&A session.
Year(s) Of Engagement Activity 2019
 
Description EBSOC Led Engagement Activities- Talks/Discussions 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact The Easter Bush Science Outreach Centre (EBSOC) which opened in January 2018 is the first of its kind in Scotland. EBSOC is a unique, purpose-built laboratory space where visitors, including primary and secondary pupils and their teachers, engage with real-life science. Supported by scientists from "Pathogen diversity, host specificity and virulence", EBSOC's schools workshops enable pupils to meet scientists from The Roslin Institute. As well as supporting scientist-lead workshops both to National and International audiences, scientists undertaking research within "Pathogen diversity, host specificity and virulence"undertake discussions and talks within these activities on research undertaken within this theme for example antimicrobial resistance
Year(s) Of Engagement Activity 2018
URL https://www.ed.ac.uk/easter-bush-campus/science-outreach-centre
 
Description EBSOC Newsletter 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Regular communications from EBSOC about our resources, activities and workshops are communicated to all contacts. These contacts are working in or closely with Scottish education settings.
Year(s) Of Engagement Activity 2021,2022
 
Description EBSOC PCR Masterclass: A Question of Taste 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Regional high school pupils (25) attended a full day PCR workshop to learn about the PCR techniques we can use in the lab to explore genetic differences between individuals and how these impact on characteristics such as ability to taste certain flavours. There was opportunity for discussion about careers in science and I discussed my own area of research into Shiga toxin-producing Escherichia coli. Pupils reported increased interest in the subject area afterwards and felt their perception of science accessibility had improved.
Year(s) Of Engagement Activity 2018
URL https://www.ed.ac.uk/easter-bush-campus/science-outreach-centre
 
Description FAO expert consultation ('Parasite control in livestock for enhanced food security') 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact This was an FAO workship with an invited audience of stakeholders invested in Animal Trypanosomiasis; ranging from academic scientists, representatives of pharmaceutical industry s, non-governmental organisations, funders, and national control programmes, to FAO senior personnel. The workshop aimed at assessing the current knowledge with respect to prevalence and extent of drug resistance in animal trypanosomiasis across Africa, the current understanding of drug resistance mechanisms and markers in the clinically relevant trypanosome species, and the outputs included identification of agreed knowledge gaps and priorities for future research focus and investment.
Year(s) Of Engagement Activity 2021
 
Description Farm detectives 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Pupils attended for a school visit to carry out hands-on science workshops. This led to questions and awareness of what jobs are available in science and what they entail
Year(s) Of Engagement Activity 2018
 
Description Fellows Debate at the Royal Society for Edinburgh, 5/11/19 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Invited to lead a Fellows Debate at the Royal Society of Edinburgh on the subject of "Should we care any more about BSE and other prion diseasea?
Year(s) Of Engagement Activity 2019
 
Description Gel Electrophoresis Wall Tank 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact A classroom resource developed by EBSOC to support teachers to explore how gel electrophoresis works with their pupils.
Year(s) Of Engagement Activity 2021,2022
 
Description Gel Electrophoresis in Action 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact This video has been designed to support Higher Biology and Higher Human Biology learners to develop their knowledge and understanding of gel electrophoresis.
Year(s) Of Engagement Activity 2020,2021
URL https://www.ed.ac.uk/easter-bush-campus/science-outreach-centre/teacher-zone/home-classroom-educatio...
 
Description Genetic changes alter risk of food bug 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact article in Pig World, The Pig Site, MRCVSonline, VNonline, Food Safety News, Farming UK, Bioscience Today around 'Genetic changes alter risk of food bug'
Year(s) Of Engagement Activity 2021
 
Description Genetic contact tracing could help curb TB outbreaks 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact article in Vet Times, That's Farming, Phys.org around "Genetic contact tracing could help curb TB outbreaks"
Year(s) Of Engagement Activity 2021
 
Description Genetic engineering of viruses - benefits and controversies 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact An evening public talk to members of the Institution of Engineering & Technology
Year(s) Of Engagement Activity 2020
URL https://www.theiet.org/
 
Description Global network formed to investigate coronaviruses 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact journal article in Cambridge Network, Mirage around 'Global network formed to investigate coronaviruses'
Year(s) Of Engagement Activity 2021
 
Description Great Science Share (online) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact In 2018 the Easter Bush Science Outreach Centre became the Great Science Share's Edinburgh Satellite and in 2020 the Roslin Institute's Education & Engagement Officer (Jayne Quoiani) became Regional Champion for Scotland. Supported by scientists and technicians from The Roslin Institute we offered Edinburgh and Midlothian participating schools our Big Balloon Blow Up Investigation kits, which included all the experimental materials, teacher CPD session, classroom resources and the creation of a celebration video for the pupils doing their investigations in school which was shared on the day in June 2021.
Year(s) Of Engagement Activity 2021
 
Description Great Science Share for Schools in Scotland Webinar 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact In partnership with the Scottish Schools Research Center (SSERC) we will run a national information session for Scottish primary school practioners on the 2022 Great Science Share for Schools Campaign. Our Education & Engagement Officer is a Regional Champion of this global programme.
Year(s) Of Engagement Activity 2022
 
Description Great Science Share | Penicuik Beeslack Cluster Project 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact In 2018 the Easter Bush Science Outreach Centre became the Great Science Share's Edinburgh Satellite and in 2020 the Roslin Institute's Education & Engagement Officer (Jayne Quoiani) became Regional Champion for Scotland. Supported by scientists and technicians from The Roslin Institute we offerred our local participating schools to use our Science @Home Investigation packs and submit photos and vides of their pupils at home doing the investigations (first lockdown) so that we could create a video to be shared on the Great Science Share day in June 2020.
Year(s) Of Engagement Activity 2020
URL https://www.ed.ac.uk/easter-bush-campus/science-outreach-centre/teacher-zone/great-science-share-202...
 
Description Guardian Opinion Article - "England's bungled response to Covid-19 leaves it vulnerable to more outbreaks" 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact This opinion piece was written around the low point of COVID-19 infections in the UK illustrating some of the dangers that could be foreseen as leading to a potential second wave of infection in the autumn winter of 2020. The Guardian newspaper is one of the most trusted in the world. This piece received considerable attention on social media.
Year(s) Of Engagement Activity 2020
URL https://www.theguardian.com/commentisfree/2020/aug/03/england-bungled-covid-19-outbreaks-scotland
 
Description Guardian Opinion Article - "How has Cummings harmed the fight against coronavirus? Here's the scientific answer" 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact This article was an opinion piece written in response to evidence that the Govt. advisor had 'broken lockdown' - the piece used the science of behavioural game theory and epidemic spread to show how individual actions influence the broader community. The Guardian is one of the leading, most trusted newspapers in the world - the piece received substantial attention on social media.
Year(s) Of Engagement Activity 2020
URL https://www.theguardian.com/commentisfree/2020/may/26/dominic-cummings-coronavirus-scientific-boris-...
 
Description Guardian Opinion Article - "To prevent a second coronavirus wave, we need to look beyond the R number" 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact I wrote an opinion piece for the Guardian newspaper on the various factors influencing the spread of infectious diseases between people and how they relate to COVID-19 control. The Guardian is one of the most highly regarded and well read newspapers in the world. This piece received considerable attention in social media.
Year(s) Of Engagement Activity 2020
URL https://www.theguardian.com/commentisfree/2020/may/19/second-coronavirus-wave-r-number-uk-test-and-t...
 
Description Guardian Podcast - Covid-19: does more testing always mean more cases? 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact A podcast to explain the importance of tracking COVID-19 test positivity, and highlighting how it could be used incorrectly to either over or under estimate the severity of an infectious disease's impact.
Year(s) Of Engagement Activity 2020
URL https://www.theguardian.com/science/audio/2020/aug/04/covid-19-does-more-testing-always-mean-more-ca...
 
Description Health care access could curb drug resistance in Africa 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact report in Medical Xpress around 'Health care access could curb drug resistance in Africa'
Year(s) Of Engagement Activity 2021
 
Description Host and convenor of the joint SAPHIR and VET-VAC workshop, Roslin, UK, May 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact The Roslin Institute hosted the 2nd International Veterinary Vaccinology workshop with the goal to provide scientists and practicioners integrated and up-to-date knowledge on the challenges facing the development of effective veterinary vaccines
Year(s) Of Engagement Activity 2018
URL http://www.vetvaccnet.ac.uk/events/european-veterinary-vaccinology-workshop-2018
 
Description Hosted a PRRS eradication workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact The purpose of the 1 day meeting was to determine how research in Roslin could contribute to eradicating PRRS in Scotland and the UK, and to map out future collaborations.
Outcomes of the day include highlighting the need to consider pig genetics and other risk factors (e.g. transportation) in current and future studies, and has instigated regular dialogue with the pig farming community.
Year(s) Of Engagement Activity 2019
 
Description ITV Borders - News Pieces on COVID-19 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Interview / comments on COVID-19 Pandemic and situation in Scotland, UK and globally. Roughly 15 appearances
Year(s) Of Engagement Activity 2020,2021,2022
 
Description In the shadow of the coronavirus: China records bird flu outbreak 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Online article, produced via an interview with the Brazilian Society for Tropical Medicine
Year(s) Of Engagement Activity 2020
URL https://tinyurl.com/ycosj8gz
 
Description Inside-out mini-guts aid research into poultry 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact online report on Inside-out mini-guts aid research into poultry in VNonline
Year(s) Of Engagement Activity 2021
 
Description Instagram Live: Coronavirus 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact 15 minute online Q&A on Covid-19 with Neil Mabbott, available online via Instagram stories
Year(s) Of Engagement Activity 2021
 
Description Instagram Live: Viral mutation 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact 15 minute online Q&A on Covid-19 mutations with Christine Tait-Burkard, available online via Instagram stories
Year(s) Of Engagement Activity 2020
 
Description International PRRSV symposium - South Korea 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact 60-100 practitioners met to learn about advances in PRRSV including control and diagnostics.
Year(s) Of Engagement Activity 2018
 
Description International workshop on Shiga toxin-producing Escherichia coli at The Roslin Institute 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact A two-day international workshop was held at The Roslin Institute on Shiga toxin-producing Escherichia coli (STEC), funded partly by this award (for travel of US collaborators) and partly by the Food Standards Agency of Scotland via a £2m award for collaborative research by a consortium led by Professor Gally. The workshop attracted leading academics working on E. coli O157 and other STEC from the US (Jim Bono, Guy Loneragan, Tom Edrington), Canada (Tim McAllister, Kim Stanford), Germany (Christian Menge), Belgium (Eric Cox), Sweden (Erik Eriksson, Lena-Mari Tamminen, Robert Soderlund) and the United Kingdom (Claire Jenkins, Tim Dallman, Dominic Mellor, Norval Strachan [Chief Scientific Advisor for FSA Scotland]). The workshop shared the latest advances in understanding of the biology of E. coli O157 and other STEC, including epidemiology, genomics, virulence, super-shedding and control strategies.
Year(s) Of Engagement Activity 2017
 
Description Interview for BBC Radio Stoke 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Discuss new variant of coronavirus
Year(s) Of Engagement Activity 2020
 
Description Interview for US coronavirus blog 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact I was interviewd by a Minnesotan journalist to provide insights into the impact of the new coronavirus variant
Year(s) Of Engagement Activity 2021
URL https://www.npr.org/sections/goatsandsoda/2021/01/08/954967079/coronavirus-faq-how-do-i-protect-myse...
 
Description Interview on BBC Radio 4 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Discuss coronavirus pandemic
Year(s) Of Engagement Activity 2021
 
Description Interview on BBC Radio Wiltshire 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Discuss the new variant of coronavirus
Year(s) Of Engagement Activity 2020
 
Description Interview on Channel 5 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Discussing coronavirus pandemic
Year(s) Of Engagement Activity 2022
 
Description Interview on RT TV 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Discussing coronavirus pandemic
Year(s) Of Engagement Activity 2022
 
Description Interview on national Canadian TV about COVID variants 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact An interview on the current state of COVID-19, broadcast on national Canadian television; the programme included broad discussion of COVID-19 variants and the role that viral sequencing has in controlling the COVID-19 pandemic.
Year(s) Of Engagement Activity 2021
URL https://globalnews.ca/news/7567835/covid-19-variant-research/
 
Description Interview with Harvard Crimson magazine 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact An interview with the Harvard Crimson magazine (a student-run magazine at Harvard University) over attempts to date the start of the COVID-19 pandemic
Year(s) Of Engagement Activity 2021
URL https://www.thecrimson.com/article/2021/4/22/lack-transparency-covid-wuhan-study/
 
Description Interviews on various regional radio stations 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Discussing coronavirus pandemic on various local radio stations including BBC radio London, Shetland, Stoke, Ulster, Wales, Wiltshire
Year(s) Of Engagement Activity 2020,2021,2022
 
Description Introduction to the Research of the Roslin Institute - Royal Society of Biology Scottish Branch Annual Symposium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Professor Stevens provided an overview of the research of The Roslin Institute to members of the public and the Royal Society of Biology, who convened for the annual symposium of the RSB Scottish Branch on 14 October 2017 at Roslin. The event coincided with the annual Roslin 'Open Doors' day and featured BBSRC-funded research.
Year(s) Of Engagement Activity 2017
 
Description Invited lecture at MSD-Animal Health 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Invited lecture at MSD-Animal Health in Boxmeer the Netherlands, with WebEx connection to all other location o MSD -AH around the world.
Year(s) Of Engagement Activity 2019
 
Description Invited speaker - Avian Genetics and Immunity Symposium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Research on Avian Genetics and Immunity (RAGI) has been established to strengthen global partnerships and links between academic researchers, students and the poultry professionals working on the genetics of avian immunity. The purpose of the symposium was to provide a forum for discussion and exchange of ideas around the single theme of exploiting available opportunities in ultimately dealing emerging and existing infectious avian diseases in poultry production systems and to safeguard food supplies and human health.
The purpose of KW talk was to overview the current situation in industry for breeding for disease resistance and introduce the NARF. The overview of NARF included a review of facilities, lines available and current work being carried out using NARF avian lines. The presentation stimulated significant discussion.
Year(s) Of Engagement Activity 2017
URL http://geneticsandimmunity.com/
 
Description Invited speaker at Genome Science 2019 Edinburgh 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Presentation on the genomics of zoonotic E. coli O157
Year(s) Of Engagement Activity 2019
URL https://www.ed.ac.uk/edinburgh-infectious-diseases/news/events-archive/genome-science-2019-edinburgh
 
Description Invited speaker at the 'Women in Science' career day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact I gave a talk about my career progression and how I thought being a woman had impacted that through my career so far.
Year(s) Of Engagement Activity 2018
 
Description Invited speaker: Wellcome Trust - Hosts, Pathogens & Global Health (HPGH) PhD retreat. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Presentation of scientific studies to PhD students. Discussion and questions.
Year(s) Of Engagement Activity 2019
 
Description Invited speaker: • The University of Edinburgh AWERB 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Presentation of scientific background pertaining to animal use to AWERB (members include scientists, lay members, animal unit staff, vets)
Year(s) Of Engagement Activity 2019
 
Description Invited talk European Veterinary Vaccinology Workshop 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Talk on career opportunities in academia for young scientists
Year(s) Of Engagement Activity 2018
URL https://www.youtube.com/watch?v=hTujbImUCcI
 
Description Joint organiser of the Gordon Lawson Memorial Symposium 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We organised the first International conference on Lawsonia intracellularis in association with Boehringer Ingelheim. The conference was in memory of Dr Gordon Lawson to honour his pioneering work on the important pig pathogen that bears his name. ~100 people attended, mainly veterinary practitioners dealing with the disease and companies trying to detect and prevent it. The symposium was held over two days at the Roslin Institute and RDSVS
Year(s) Of Engagement Activity 2019
URL https://www.ed.ac.uk/roslin/news-events/scientific-events/archive/gordon-lawson-memorial-symposium
 
Description Just Festival - freedom fear and quest for vaccine 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact In this online event run as part of the Edinburgh Fringe Festival, I discussed with a well known author/journalist the potential issues around people who are likely to be hesitant or refusing to be vaccinated against COVID-19. the event was attended by an online audience of about 30 to 40 people and posted later on youtube.
Year(s) Of Engagement Activity 2020
URL https://www.just-festival.org/eventbrite-event/vaccine-nation/
 
Description Kick Start Summer Widening Participation- DNA profiling The Great Escape Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No