Pathogen Genomics, Phenotype and Immunity (PGPI) & Basic Sciences Programme
Lead Research Organisation:
London School of Hygiene & Tropical Medicine
Department Name: UNLISTED
Abstract
This programme aims to conduct research that will lead to better understanding of pathogen genomics in order to characterise diseases and epidemics for better control and to investigate virological, immunological and genetic factors required for the development of effective interventions against HIV-1 and other infections. Advantage will be taken of a) well characterised cohorts and biobanks b) Unit track record in intervention trials c) investment in new technologies in genomics, immunological assays and bioinformatics and d) established collaborations.
We propose to monitor the HIV epidemic by characterising the circulating HIV-1 subtypes especially in recent infections and use full length genome sequencing to understand better the increasing recombinant viruses using better bioinformatics tools. We will use molecular in combination with social-epidemiological and modelling approaches to provide novel avenues to monitor epidemic trends and transmission dynamics, and to contribute to targeted interventions through the identification of transmission clusters and hotspots. HIV drug resistance (HIVDR) is emerging as one of the most important challenges to ART roll out for both care and prevention, more so in resource limited areas characterized by the use of limited ARV regimens, stock outs, regimen change based on available supply and often limited use of viral load (VL) testing to monitor treatment outcomes. We will expand our drug resistance studies to contribute to improved interventions.
HIV superinfection (SI) investigations will utilise a large collection of specimens from high risk populations to study host and viral factors associated with SI.
We propose to monitor the HIV epidemic by characterising the circulating HIV-1 subtypes especially in recent infections and use full length genome sequencing to understand better the increasing recombinant viruses using better bioinformatics tools. We will use molecular in combination with social-epidemiological and modelling approaches to provide novel avenues to monitor epidemic trends and transmission dynamics, and to contribute to targeted interventions through the identification of transmission clusters and hotspots. HIV drug resistance (HIVDR) is emerging as one of the most important challenges to ART roll out for both care and prevention, more so in resource limited areas characterized by the use of limited ARV regimens, stock outs, regimen change based on available supply and often limited use of viral load (VL) testing to monitor treatment outcomes. We will expand our drug resistance studies to contribute to improved interventions.
HIV superinfection (SI) investigations will utilise a large collection of specimens from high risk populations to study host and viral factors associated with SI.
Technical Summary
We propose to monitor the HIV epidemic by characterising the circulating HIV-1 subtypes especially in recent infections and use full length genome sequencing to understand better the increasing recombinant viruses using better bioinformatics tools. We will use molecular in combination with social-epidemiological and modelling approaches to provide novel avenues to monitor epidemic trends and transmission dynamics, and to contribute to targeted interventions through the identification of transmission clusters and hotspots. We will expand our drug resistance (DR) studies to contribute to improved interventions. We are well positioned to provide such data being a National and Regional Reference laboratory for HIV DR and active participants in related national activities. We propose to undertake a comprehensive and systematic analysis of HIV-1 viruses representing the subtypes and recombinant forms circulating in Uganda to elucidate if transmitted/early HIV-1 viruses have recurrent patterns (signatures) that distinguish them from chronic viruses.
We will contribute to the studies aimed at understanding whether Zika virus exists among humans, primates and mosquitos in Uganda and conduct studies to molecularly characterize the Zika genome. There is renewed global interest in understanding events surrounding HIV superinfection (SI). However, due to the introduction of test and treat, opportunities to study this phenomenon are very limited. We are uniquely positioned to address this subject, we have a large collection of specimens from high risk populations and hence propose to investigate the host and viral factors associated with SI. This information will contribute to knowledge on protective immune responses. We recently won an NIH RO1 to address this topic and have set up an international collaborative network to address specific questions. The best vaccine induced protection achieved to date against SIV in macaques has been a live attenuated SIV. We propose to study the potential protective immune responses against HIV through PrEP in highly exposed populations. This is in order to explore whether exposure to HIV under PrEP cover could induce immunity equivalent to that afforded by a live attenuated vaccine. This is a proof of the concept that immunity to HIV might be achieved if the initial infections are hampered by chemoprophylaxis, simulating vaccination with a live attenuated virus strain. Gilead has provided the drugs for this study. We will participate in other studies to contribute to HIV Vaccine research and development
We will contribute to the studies aimed at understanding whether Zika virus exists among humans, primates and mosquitos in Uganda and conduct studies to molecularly characterize the Zika genome. There is renewed global interest in understanding events surrounding HIV superinfection (SI). However, due to the introduction of test and treat, opportunities to study this phenomenon are very limited. We are uniquely positioned to address this subject, we have a large collection of specimens from high risk populations and hence propose to investigate the host and viral factors associated with SI. This information will contribute to knowledge on protective immune responses. We recently won an NIH RO1 to address this topic and have set up an international collaborative network to address specific questions. The best vaccine induced protection achieved to date against SIV in macaques has been a live attenuated SIV. We propose to study the potential protective immune responses against HIV through PrEP in highly exposed populations. This is in order to explore whether exposure to HIV under PrEP cover could induce immunity equivalent to that afforded by a live attenuated vaccine. This is a proof of the concept that immunity to HIV might be achieved if the initial infections are hampered by chemoprophylaxis, simulating vaccination with a live attenuated virus strain. Gilead has provided the drugs for this study. We will participate in other studies to contribute to HIV Vaccine research and development
Organisations
- London School of Hygiene & Tropical Medicine (Lead Research Organisation)
- University College London (Collaboration)
- University of Alabama at Birmingham (Collaboration)
- National Institute of Virology Johannesburg (Collaboration)
- The Wellcome Trust Sanger Institute (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- Ministry of Health, Uganda (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- UNIVERSITY OF GLASGOW (Collaboration)
- PharmAccess Foundation (Collaboration)
- Johns Hopkins University (Collaboration)
- Uganda Virus Research Institute (Collaboration)
- University of Cape Town (Collaboration)
Publications
Abeler-Dörner L
(2019)
PANGEA-HIV 2: Phylogenetics And Networks for Generalised Epidemics in Africa.
in Current opinion in HIV and AIDS
Aceng J
(2020)
Uganda's experience in Ebola virus disease outbreak preparedness, 2018-2019
in Globalization and Health
Anywaine Z
(2019)
Safety and Immunogenicity of a 2-Dose Heterologous Vaccination Regimen With Ad26.ZEBOV and MVA-BN-Filo Ebola Vaccines: 12-Month Data From a Phase 1 Randomized Clinical Trial in Uganda and Tanzania.
in The Journal of infectious diseases
Atim SA
(2022)
Risk factors for Crimean-Congo Haemorrhagic Fever (CCHF) virus exposure in farming communities in Uganda.
in The Journal of infection
Baker OR
(2021)
Differential Performance of CoronaCHEK SARS-CoV-2 Lateral Flow Antibody Assay by Geographic Origin of Samples.
in Journal of clinical microbiology
Bareng OT
(2022)
HIV-1 drug resistance mutations among individuals with low-level viraemia while taking combination ART in Botswana.
in The Journal of antimicrobial chemotherapy
Bbosa N
(2020)
Short Communication: Choosing the Right Program for the Identification of HIV-1 Transmission Networks from Nucleotide Sequences Sampled from Different Populations.
in AIDS research and human retroviruses
Bbosa N
(2019)
HIV subtype diversity worldwide.
in Current opinion in HIV and AIDS
Bbosa N
(2019)
Phylogeography of HIV-1 suggests that Ugandan fishing communities are a sink for, not a source of, virus from general populations
in Scientific Reports
Bbosa N
(2022)
Rapid Replacement of SARS-CoV-2 Variants by Delta and Subsequent Arrival of Omicron, Uganda, 2021
in Emerging Infectious Diseases
Bekker LG
(2020)
The complex challenges of HIV vaccine development require renewed and expanded global commitment.
in Lancet (London, England)
Bugembe DL
(2021)
Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda.
in Nature microbiology
Bugembe DL
(2020)
Computational MHC-I epitope predictor identifies 95% of experimentally mapped HIV-1 clade A and D epitopes in a Ugandan cohort.
in BMC infectious diseases
Bugembe DL
(2020)
Main Routes of Entry and Genomic Diversity of SARS-CoV-2, Uganda.
in Emerging infectious diseases
Capoferri AA
(2020)
Recombination Analysis of Near Full-Length HIV-1 Sequences and the Identification of a Potential New Circulating Recombinant Form from Rakai, Uganda.
in AIDS research and human retroviruses
Chen J
(2021)
The trans-ancestral genomic architecture of glycemic traits.
in Nature genetics
Cotten M
(2021)
Alternate primers for whole-genome SARS-CoV-2 sequencing
in Virus Evolution
Davis C
(2019)
Highly Diverse Hepatitis C Strains Detected in Sub-Saharan Africa Have Unknown Susceptibility to Direct-Acting Antiviral Treatments.
in Hepatology (Baltimore, Md.)
Debebe BJ
(2020)
Identifying the immune interactions underlying HLA class I disease associations.
in eLife
Dunn D
(2021)
New Insights on Long-Term Hepatitis B Virus Responses in HIV-Hepatitis B virus Co-infected Patients: Implications for Antiretroviral Management in Hepatitis B virus-Endemic Settings
in JAIDS Journal of Acquired Immune Deficiency Syndromes
Elangovan R
(2021)
Global and Regional Estimates for Subtype-Specific Therapeutic and Prophylactic HIV-1 Vaccines: A Modeling Study.
in Frontiers in microbiology
Fatumo S
(2019)
Complimentary Methods for Multivariate Genome-Wide Association Study Identify New Susceptibility Genes for Blood Cell Traits.
in Frontiers in genetics
Fily F
(2018)
HIV-1 drug resistance testing at second-line regimen failure in Arua, Uganda: avoiding unnecessary switch to an empiric third-line.
in Tropical medicine & international health : TM & IH
Galiwango RM
(2021)
Short Communication: Validation of the Asante HIV-1 Rapid Recency Assay for Detection of Recent HIV-1 Infections in Uganda.
in AIDS research and human retroviruses
Gossez M
(2019)
Virological remission after antiretroviral therapy interruption in female African HIV seroconverters.
in AIDS (London, England)
Granger LA
(2021)
Broadly neutralizing antibody responses in the longitudinal primary HIV-1 infection Short Pulse Anti-Retroviral Therapy at Seroconversion cohort.
in AIDS (London, England)
Gupta RK
(2018)
HIV-1 drug resistance before initiation or re-initiation of first-line antiretroviral therapy in low-income and middle-income countries: a systematic review and meta-regression analysis.
in The Lancet. Infectious diseases
Gurdasani D
(2019)
Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa.
in Cell
Hassan AS
(2021)
A Stronger Innate Immune Response During Hyperacute Human Immunodeficiency Virus Type 1 (HIV-1) Infection Is Associated With Acute Retroviral Syndrome.
in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
Hemelaar J
(2019)
Global and regional molecular epidemiology of HIV-1, 1990-2015: a systematic review, global survey, and trend analysis.
in The Lancet. Infectious diseases
Hemelaar J
(2020)
Global and regional epidemiology of HIV-1 recombinants in 1990-2015: a systematic review and global survey.
in The lancet. HIV
Inzaule SC
(2019)
Increasing levels of pretreatment HIV drug resistance and safety concerns for dolutegravir use in women of reproductive age.
in AIDS (London, England)
Inzaule SC
(2020)
High levels of resistance to nucleoside/nucleotide reverse transcriptase inhibitors in newly diagnosed antiretroviral treatment-naive children in sub-Saharan Africa.
in AIDS (London, England)
Jenkin D
(2023)
Safety and immunogenicity of a ChAdOx1 vaccine against Rift Valley fever in UK adults: an open-label, non-randomised, first-in-human phase 1 clinical trial.
in The Lancet. Infectious diseases
Kaleebu P
(2018)
Evaluation of HIV-1 rapid tests and identification of alternative testing algorithms for use in Uganda.
in BMC infectious diseases
Kalungi A
(2019)
Internalizing Mental Disorders and Accelerated Cellular Aging Among Perinatally HIV-Infected Youth in Uganda
in Frontiers in Genetics
Kamacooko O
(2021)
Knowledge, Attitudes, and Practices Regarding COVID-19 among Healthcare Workers in Uganda: A Cross-Sectional Survey.
in International journal of environmental research and public health
Related Projects
Project Reference | Relationship | Related To | Start | End | Award Value |
---|---|---|---|---|---|
MC_UU_00027/1 | 01/02/2018 | 30/03/2023 | £2,855,127 | ||
MC_UU_00027/2 | Transfer | MC_UU_00027/1 | 01/02/2018 | 30/03/2023 | £1,326,187 |
MC_UU_00027/3 | Transfer | MC_UU_00027/2 | 01/02/2018 | 30/03/2023 | £1,829,053 |
MC_UU_00027/4 | Transfer | MC_UU_00027/3 | 01/02/2018 | 30/03/2023 | £959,532 |
MC_UU_00027/5 | Transfer | MC_UU_00027/4 | 01/02/2018 | 30/03/2023 | £932,836 |
Description | Guidance on HIV hot spots and direction of transmission |
Geographic Reach | National |
Policy Influence Type | Participation in a guidance/advisory committee |
Impact | This has helped in understanding which are the hot spots for HIV, for example we showed that though fishing communities have high HIV prevalence they are not the main source of HIV transmissions in the general population. This has influenced on how prevention is done to spread beyond concentrating on the fishing communities. This has led to better HIV prevention in Uganda |
Description | Guidance to Ministry on which COVID-19 antigen, antibody and PCR kits to use |
Geographic Reach | National |
Policy Influence Type | Citation in other policy documents |
Impact | This has guided on the tests to use during the COVID-19 pandemic and guided private sector which kits to import |
Guideline Title | HIV testing algorithm for Uganda |
Description | Provided guidance on the testing algorithm for HIV |
Geographic Reach | National |
Policy Influence Type | Citation in clinical guidelines |
Impact | Provided guidance to best kits for testing for HIV |
Description | SARSCoV2 variants in Uganda for proper vaccination planning |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
Impact | This work has guided on the selection of vaccines for SARSCoV2 |
Description | Understanding the cirsulating HIV strains in Uganda |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
Impact | By describing and providing information on the circulating HIV subtypes in Uganda, this information is used in HIV vaccine design and treatment. The vaccine, monoclonal antibodies and drugs developed have to be relevant in terns of the HIV strains they target. We are seeing an increase in the proportion of HIV recombinant viruses in Uganda. |
Guideline Title | The revised 2018 HIV treatment guidelines |
Description | Use of Integrase strand inhibitors (Dolutegravir) as first line due to high Pre-Treatment HIVDR to NNRTIs in the country. |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Citation in clinical guidelines |
Impact | Uganda and other countries where HIV pre-treatment drug resistance is above 10%, have adopted Dolutegragir ased regimens as the preferred first line ART regimen in women >50 years, adolescent and adult men; and as an alternative second line in the above eligible groups. |
Guideline Title | The revised 2018 HIV treatment guidelines |
Description | Use of PI based regimens as first line for HIV infected infants especially with prior PMTCT exposure. |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Citation in clinical guidelines |
Impact | Due to the high prevalence of pre-treatment drug resistance especiallt to NNRTIs and to some extent NRTIs, the ministry rolled out use of Lopinavir pellets as first line for HIV positive infants <3 years country -wide in 2016 |
Guideline Title | The revised 2018 HIV treatment guidelines |
Description | Viral Load monitoring at 6 and 12 months after ART initiation instead of 18 months. |
Geographic Reach | National |
Policy Influence Type | Citation in clinical guidelines |
Impact | We are not able to get viral load data at 6 and 12 months which is used as an early warning sign for the development of HIV drug resistance |
Description | A combination efficacy study in Africa of two DNA-MVA & DNA-protein/adjuvant HIV-1 vaccine regimens with pre-exposure prophylaxis (PrEP); "PrEPVacc |
Amount | € 15,000,000 (EUR) |
Funding ID | S-RIALoI2015-555 |
Organisation | Sixth Framework Programme (FP6) |
Department | European and Developing Countries Clinical Trials Partnership |
Sector | Public |
Country | Netherlands |
Start | 07/2018 |
End | 07/2024 |
Description | Accelerate the Development of Vaccines and New Technologies to Combat the AIDS Epidemic (ADVANCE) |
Amount | $90,000,000 (USD) |
Funding ID | SOL-OAA-16-000026 |
Organisation | United States Agency for International Development |
Sector | Public |
Country | United States |
Start | 01/2017 |
End | 12/2022 |
Description | An open-label, single arm study to provide additional information on immunogenicity and safety of Ad26.ZEBOV/MVA-BN®-Filo |
Amount | $2,789,182 (USD) |
Organisation | Coalition for Epidemic Preparedness Innovations |
Sector | Learned Society |
Country | Norway |
Start | 02/2019 |
End | 12/2022 |
Description | Combined HIV African Prevention Study: On demand Truvada and F/TAF Pre-exposure and Post exposure prophylaxis to protect adolescents from HIV |
Amount | € 2,999,999 (EUR) |
Funding ID | RIA2016MC-1616 |
Organisation | Sixth Framework Programme (FP6) |
Department | European and Developing Countries Clinical Trials Partnership |
Sector | Public |
Country | Netherlands |
Start | 03/2018 |
End | 03/2022 |
Description | DH EPSRC Future Vaccines Manufacturing Research Hub |
Amount | £10,000,000 (GBP) |
Funding ID | Grant No-EP/R013764/1 |
Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
Sector | Public |
Country | United Kingdom |
Start | 04/2017 |
End | 11/2022 |
Description | Global Immunology and Immune Sequencing for Epidemic Response (GIISER) |
Amount | $299,997 (USD) |
Organisation | Bill and Melinda Gates Foundation |
Sector | Charity/Non Profit |
Country | United States |
Start | 08/2021 |
End | 08/2024 |
Description | Globally Relevant AIDS Vaccine Europe-Africa Trials Partnership (GREAT) |
Amount | € 6,000,000 (EUR) |
Funding ID | SRIA2015-1066 |
Organisation | Sixth Framework Programme (FP6) |
Department | European and Developing Countries Clinical Trials Partnership |
Sector | Public |
Country | Netherlands |
Start | 06/2017 |
End | 06/2023 |
Description | IAVI funded through USAID |
Amount | $100,000,000 (USD) |
Organisation | International AIDS Vaccine Initiative (IAVI) |
Sector | Charity/Non Profit |
Country | Global |
Start | 06/2016 |
End | 06/2021 |
Description | INTEGRATIVE OMICS OF HEPB VACCINE RESPONSE IN CO-INFECTION WITH PARASITES |
Amount | $6,246,562 (USD) |
Funding ID | U19AI128910 |
Organisation | National Institute of Allergy and Infectious Diseases (NIAID) |
Sector | Public |
Country | United States |
Start | 07/2017 |
End | 07/2022 |
Description | MRC Informatics |
Amount | £2,860,000 (GBP) |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 06/2014 |
End | 06/2019 |
Description | NIH RO1 |
Amount | $650,000 (USD) |
Organisation | National Institutes of Health (NIH) |
Sector | Public |
Country | United States |
Start | 02/2015 |
End | 01/2020 |
Description | Phase I studies of a novel chimpanzee adenovirus Rift Valley Fever vaccine |
Amount | £2,183,221 (GBP) |
Funding ID | GHR Project:16/107/02 |
Organisation | National Institute for Health Research |
Sector | Public |
Country | United Kingdom |
Start | 05/2016 |
End | 08/2022 |
Description | Phylogenetics Networks to Address Transmission of HIV (PANGEA) |
Amount | $300,000 (USD) |
Organisation | Bill and Melinda Gates Foundation |
Sector | Charity/Non Profit |
Country | United States |
Start | 09/2014 |
End | 02/2017 |
Description | Use of Point of Care HIV Viral Load Monitoring to improve Viral Load Suppression among Children and Adolescents Living with HIV in East Africa. |
Amount | € 5,000,000 (EUR) |
Funding ID | EDCTP RIA2019IR-2873 |
Organisation | Sixth Framework Programme (FP6) |
Department | European and Developing Countries Clinical Trials Partnership |
Sector | Public |
Country | Netherlands |
Start | 05/2020 |
End | 05/2023 |
Description | Viral Surveillance and Discovery in Uganda. Abbott Diagnostics |
Amount | $821,733 (USD) |
Organisation | Abbott |
Sector | Private |
Country | United States |
Start | 03/2022 |
End | 03/2024 |
Description | Collaboration with Ministry of Health |
Organisation | Ministry of Health, Uganda |
Country | Uganda |
Sector | Public |
PI Contribution | Generation of SARS CoV2 sequence data, policy on vaccine usage |
Collaborator Contribution | Generation of SARS CoV2 sequence data, policy on vaccine usage |
Impact | Publications, policy |
Start Year | 2023 |
Description | Collaborationwith the Ministry of Health on Research on emerging and re-emeging infections |
Organisation | Ministry of Health, Uganda |
Country | Uganda |
Sector | Public |
PI Contribution | We are conducting surveillance studies for new and re-ermerging viruses. We look for funding, collaborations and conduct some of the studies locally |
Collaborator Contribution | The Ministry of Health Departments offer the environment to work in different surveillance sites and some epidemiological expertise |
Impact | Publications, policies, and valuable samples |
Start Year | 2016 |
Description | Dual and superinfection studies |
Organisation | University of Alabama at Birmingham |
Department | School of Medicine |
Country | United States |
Sector | Academic/University |
PI Contribution | Generation of ideas and Proposal writting Looking for external funding Supervision |
Collaborator Contribution | Training Supervision of studentsTraining Supervision of students Paper manuscripts |
Impact | Training Supervision External funding |
Start Year | 2008 |
Description | Dual and superinfection studies |
Organisation | University of Cape Town |
Country | South Africa |
Sector | Academic/University |
PI Contribution | Generation of ideas and Proposal writting Looking for external funding Supervision |
Collaborator Contribution | Training Supervision of studentsTraining Supervision of students Paper manuscripts |
Impact | Training Supervision External funding |
Start Year | 2008 |
Description | HIV Drug resistance surveillance |
Organisation | PharmAccess Foundation |
Country | Netherlands |
Sector | Private |
PI Contribution | We have conducted molecular virology experiments |
Collaborator Contribution | Training and network |
Impact | Information of transmitted HIV drug resistance and publications |
Start Year | 2008 |
Description | HIV molecular epidemiology |
Organisation | University College London |
Department | MRC Centre for Medical Molecular Virology |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Generation of research ideas, training, supervision and looking for additional external funding |
Collaborator Contribution | Training and supervision |
Impact | Training, supervision and looking for additional external funding |
Start Year | 2014 |
Description | HIV transmission network studies |
Organisation | University College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have together worked on a grant proposal to the Gates Foundation which has been funded and due to start in 2014 |
Collaborator Contribution | We have together written grant application, and in the future will contribute to training |
Impact | Proposal writing New funding |
Start Year | 2014 |
Description | HIV transmission network studies |
Organisation | University of Edinburgh |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have together worked on a grant proposal to the Gates Foundation which has been funded and due to start in 2014 |
Collaborator Contribution | We have together written grant application, and in the future will contribute to training |
Impact | Proposal writing New funding |
Start Year | 2014 |
Description | Imperial College on development of Rift Valley Fever, COVID-19 and HIV Vaccines |
Organisation | Imperial College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have provided samples, cohorts and some of the assays performed by the Unit. We also have students |
Collaborator Contribution | Raising of funds, capacity building and linking to other partners |
Impact | Publications, collection of valuable specimens, training |
Start Year | 2023 |
Description | Medical Informatics |
Organisation | The Wellcome Trust Sanger Institute |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Training, publications, networking and additional funding |
Collaborator Contribution | Training, publications, networking and additional funding |
Impact | Training, publications, additional funding and networks |
Start Year | 2014 |
Description | Metagenomics analyses with Glasgow University |
Organisation | University of Glasgow |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have provided specimens. We have received sequences generated at Glasgow for analysis at UVRI. We have participated in writing of new research grants. We have worked with the team to present data to the research community and to the local communities in West Nile where a new virus was isolated |
Collaborator Contribution | They have trained our staff in metagenomics, and contributed to the transfer of technology. Three of our staff have visited Glasgow and a team led by Dr Emma Thompson has also visited us. We are together writing other research grants |
Impact | In the process of looking for Zika virus, we have also identified other viruses including Le Dantec Rhabdovirus. Metagenomic analysis of the acute plasma RNA revealed a contiguous sequence of 11,423 nucleotides that had a 94% identity with a 1965 LDV strain isolated from a Senegalese girl (DakHD763 strain, KM205006) by phylogenetic analysis. The metagenomics sequence was confirmed by PCR and Sanger sequencing of a 5'-half genome fragment. We have also identified a new virus named Adumi virus, from a girl in West Nile region |
Start Year | 2015 |
Description | Partnership with UVRI on Zika virus studies |
Organisation | Uganda Virus Research Institute |
Department | Department of Arbovirology, Emerging and Re-emerging Infections |
Country | Uganda |
Sector | Public |
PI Contribution | We provide sequencing expertise and its analyses. We have provided facilities to analyse more samples. We have provided training opportunities to UVRI staff including those studying for MSc and PhD |
Collaborator Contribution | UVRI provides mosquito and human specimens to analyse. They also perform some other analyses such as the plaque neutralization reduction assays, and characterization of the mosquitoes from which we are looking for viruses. |
Impact | We have analysed a number of samples, this has led to more collaboration with other partners such as USA CDC and University of Glasgow. In the process of this work we have identified Le Dantec virus, only previously identified in two people in West Africa and in UK |
Start Year | 2015 |
Description | Partnership with UVRI on Zika virus studies |
Organisation | Uganda Virus Research Institute |
Department | Department of Arbovirology, Emerging and Re-emerging Infections |
Country | Uganda |
Sector | Public |
PI Contribution | We provide sequencing expertise and its analyses. We have provided facilities to analyse more samples. We have provided training opportunities to UVRI staff including those studying for MSc and PhD |
Collaborator Contribution | UVRI provides mosquito and human specimens to analyse. They also perform some other analyses such as the plaque neutralization reduction assays, and characterization of the mosquitoes from which we are looking for viruses. |
Impact | We have analysed a number of samples, this has led to more collaboration with other partners such as USA CDC and University of Glasgow. In the process of this work we have identified Le Dantec virus, only previously identified in two people in West Africa and in UK |
Start Year | 2015 |
Description | Research in Hepatitis B |
Organisation | University College London |
Department | MRC Centre for Medical Molecular Virology |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Our laboratory performed viral loads and some genotyping |
Collaborator Contribution | Training Capacity in Hepatitis research |
Impact | Training Increased capacity to conduct research in hepatitis |
Start Year | 2008 |
Description | Superinfection studies |
Organisation | Johns Hopkins University |
Department | School of Medicine Johns Hopkins |
Country | United States |
Sector | Academic/University |
PI Contribution | Provision of samples Clinical and epidemiological data |
Collaborator Contribution | Training in neutralization and screening for neutralization |
Impact | Training of staff and generation of results |
Start Year | 2015 |
Description | Superinfection studies |
Organisation | Johns Hopkins University |
Country | United States |
Sector | Academic/University |
PI Contribution | Provision of specimens for testing of our samples for superinfection. Provision of other clinical and epidemiological data |
Collaborator Contribution | Testing of samples for superinfection using the 454 deep sequencing |
Impact | Data has been generated on the frequency of HIV superinfection in one of our high risk cohorts. Training of our in data analyses |
Start Year | 2014 |
Description | Superinfection studies |
Organisation | National Institute of Virology Johannesburg |
Country | South Africa |
Sector | Academic/University |
PI Contribution | Provision of samples Clinical and epidemiological data |
Collaborator Contribution | Training in neutralization and screening for neutralization |
Impact | Training of staff and generation of results |
Start Year | 2015 |
Description | University of Edinburgh Phylogenetics and Phylogeograghy of HIV |
Organisation | University of Edinburgh |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Provision of samples and sequences |
Collaborator Contribution | Training including PhD supervision, opportunities for attachments, transfer of sequence analysis capacity, contribution to publications |
Impact | Publications, Training and attachments |
Start Year | 2015 |
Description | Use of HIV full length sequencing to characterise HIV epidemics and evaluate interventions |
Organisation | University College London |
Department | UCL Genomics |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We provide specimens including clinical and epidemiological data. We also participate in the analysis of data |
Collaborator Contribution | They provide funds, sequencing of the samples and training in the analyses of large sequence data |
Impact | Conference Abstracts, paper manuscripts, we have also started analysing of near full length sequencing of HIV sequences within our Uganda Medical Informatics Centre |
Start Year | 2014 |
Title | SARSCoV2 vaccine |
Description | Self amplifying RNA vaccine for SARS CoV2 being developed at Imperial College |
Type | Preventative Intervention - Nutrition and Chemoprevention |
Current Stage Of Development | Early clinical assessment |
Year Development Stage Completed | 2021 |
Development Status | Under active development/distribution |
Clinical Trial? | Yes |
Impact | This trial is planned and the protocol is about to be submitted for ethics review |