MRC PhD students

Title of Research Project: Compartmentalization, Adaptive Evolution and Therapeutic Response of HIV-1 in the Gastrointestinal Tract of African Patients Infected with Subtype C.

Based on the hypothesis that the gastrointestinal tract encodes the complete evolutionary and immunological history of HIV-1 infection, from the very onset of infection, we are proposing a comprehensive study of the GI tract in Africa patients infected with subtype C viruses. The  project will focus on the compartmentalization, genetic evolution and adaptive history of HIV-1 in different regions of the gastrointestinal tract. We expect that serial sequencing of the viruses archived in  cellular reservoirs  of the GI tract will provide the information needed to unravel the complete evolutionary history of the infection, from its inception.

The proposal is unique and innovative in that it will : 1)  use a new double balloon technique to sample along the entire GI tract; 2) systematically examine the impact of antiretroviral therapy on the containment (and clearance)  of HIV-1 throughout the entire GI tract and 3)  be conducted in a real-life African setting, where these virological  events are likely to be super-imposed on a high pre-existing burden of gastrointestinal disease.

Specific aims of the project are:

1. Conduct comprehensive analyses of HIV-1 diversity and population size in different regions of the small intestine (jejunum, duodenum, ileum), colon and cervico-vaginal mucosa in patients at different stages of disease. Studies will include an analysis of viral variants in different cellular compartments (T-cells, macrophages, dendritic cells) in patients with and without enteric co-infections. Studies will be conducted prior to, and at two time points during the first six months of antiretroviral therapy.
2. Reconstruct the phylogenetic relationships among sequences from different regions of the GI tract. Studies will use maximum likelihood and Bayesian methods under "strict" and "relaxed" conditions to identify the most common recent ancestors; determine the evolutionary rate and estimate the host selection pressures. Positive selection will be assessed using codon-based substitution ML models implemented in the CODEML programme of PAML. Population genetic estimator methods will be used to determine mutation fixation rates. Skyline plots and determinations of the posterior distribution of effective population size will be used to investigate virus population size variation in response to host selection pressure. Data-mining (WEKA, B-Course) will be used to detect the appearance and linkage of escape mutations, and protein analyses methods will be used to asses the impact of these mutations on the structure of viral proteins. 
3. Investigate the role of the different regions of the gastrointestinal tract in the archiving of resistance mutations, and in the emergence of drug resistance. 

This will be accomplished in the setting of existing  ongoing collaborative study involving the MRC Unit for Inflammation and Immunity (R. Anderson, S. Cassol), the Hepatology and GI-Research Laboratory (S. Van Der Merwe and Dr O. Mwantembe) and the MRC Pathogen Bioinformatics Unit (T. de Oliveira) in South Africa, the Evolutionary Research Group at Oxford (O. Pybus) and the AIDS Immunopathogenesis Unit, San Raffaele Scientific Institute, Milan (E. Cassol, G Poli).

This study is supervised by Prof Sharon Cassol of the MRC Unit for Inflammation and Immunity.