Basic Science Programme / Molecular epidemiology of HIV infection

Lead Research Organisation: MRC/UVRI Uganda Research Unit on AIDS


One of the unique features of HIV-1 is its genetic diversity. No two HIV-1 viruses will be exactly the same. For that reason HIV has been grouped into subtypes. In Uganda the major subtypes are A and D. It has also been found that an individual can be infected with more than one HIV subtype, called dual infection in case of infection with two different HIV subtypes or multiple infection in case of more than two HIV subtypes. When different viruses enter the same cell they can recombine to form recombinant viruses. We conduct studies to look at the trends in the distribution of these viruses in our population and relate different HIV subtypes and recombinant viruses to disease outcome. We also study the distribution of virus subtypes across sexual networks especially in high risk populations such as commercial sex workers and fishing communities. Such information will help us understand better the epidemiology of HIV-1 infection and how we can control this epidemic more effectively. In order to perform these studies, we use technology that allows us to analyse the genetic composition of different viruses. We are also using assays that allow us to identify individuals infected with more than one HIV subtype. The information obtained is important as we prepare for HIV vaccine trials and as we roll out anti-retroviral therapy in our populations.

Technical Summary

Overall aim: To provide information on the HIV-1 subtypes circulating in Uganda including those in high risk populations such as commercial sex workers and fishing communities. Specific objectives are 1) to describe the circulating HIV-1 subtypes in different cohorts, 2) to determine the frequency of dual infections in these populations and 3) to relate molecular epidemiology with sexual networks. We have previously reported that individuals infected with HIV subtype D progress faster than those infected with subtype A. Similarly there are reports that HIV subtype A is more transmissible than D. The above, combined with reports of superinfection and viral recombination especially in high risk populations means that the HIV epidemic will evolve in terms of circulating HIV subtypes. We are therefore following the trends of subtype patterns, especially in incident cases. This information has relevance to future interventions such as vaccines and HIV care with ART. The molecular epidemiology of HIV infection within sexual networks (especially among the fishing population with its high rate of migration and demographic mixing with nearby trading towns and the rural hinterland) could provide additional useful information on risk factors, and facilitate a more effcetive control of HIV infection in these populations. In areas where multiple HIV-1 subtypes and their recombinants co-circulate, there is a risk of super-infection and co-infection with diverse viruses which presents a substantial challenge to vaccine development. Furthermore, inter-subtype and intra-subtype multiple HIV-1 infections enable rapid viral evolution through recombination. We study the frequency of dual infection, its relationship with disease progression and viral and host factors that determine their existence. Methods used: molecular epidemiology is performed in different cohorts of MRC/UVRI, including the Rural Clinical Cohort, the female high risk and the fisherfolk cohorts, with a focus on incident HIV infections. Viral RNA is extracted from cryo-preserved serum using QIAamp Viral RNA Mini Kit. Reverse transcription and first round PCR is performed using QIAGEN OneStep RT-PCR. Env-C2V3 and gag-p24 genes and other regions of interest are amplified using universal primers. PCR products are cleaned and in-house sequencing done using either a Beckman capillary sequencer or an ABI capillary sequencer. We align the generated sequences using ClustalX. The MEGA version 4.0 software package is used to perform phylogenetic analysis and the pairwise evolutionary distances estimated using the HKY85 model. Phylogenetic trees are constructed by neighbour joining, and the reliability of tree topologies estimated by bootstrap analysis. Subtype reference sequences of HIV-1 group M available from the Los Alamos sequence database are used. To determine dual infections we perform Heteroduplex mobility assays, Single Genome Amplification Assay (SGA) and cloning into pGEM-T Easy Vector Systems, and plasmids are transformed into High Efficiency Competent cells. Between 10 and 20 positive clones are selected for each sample. This work is supported from the MRC/UVRI Unit core budget, and co-funded from other projects.


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Ssemwanga D (2012) Transmitted antiretroviral drug resistance among drug-naive female sex workers with recent infection in Kampala, Uganda. in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

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Hemelaar J (2011) Global trends in molecular epidemiology of HIV-1 during 2000-2007. in AIDS (London, England)

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Yebra G (2015) Analysis of the history and spread of HIV-1 in Uganda using phylodynamics. in The Journal of general virology

Description EDCTP
Amount € 3,000,000 (EUR)
Organisation European Union 
Sector Public
Country European Union (EU)
Start 04/2017 
End 03/2020
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 Ministry of Health 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Primary Audience Policymakers/politicians
Results and Impact We have presented information on the development of drug resistance to the Ministry of Health officials

In the context of Dart the ministry of health is aware of the efficacy of the drug regimens The ministry is aware of the prevalence of mutations in drug naice patients and in recently infected people
Year(s) Of Engagement Activity 2008