Research
Unique features of HLA-mediated HIV evolution in a Mexican cohort: a comparative study
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* Corresponding authors: Santiago Avila-Rios santiago.avila@cieni.org.mx - Gustavo Reyes-Teran reyesteran@cieni.org.mx
1 Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
2 Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
3 eScience Group, Microsoft Research, Redmond, Washington, USA
4 Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Boston, Massachusetts, USA
5 Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
6 Center for Clinical Immunology and Biomedical Statistics, Royal Perth Hospital and Murdoch University, Perth, Australia
Retrovirology 2009, 6:72 doi:10.1186/1742-4690-6-72
Published: 10 August 2009Additional files
Additional file 1:
Two additional figures and three additional tables. Figure S1 – Allelic and population frequencies for class I HLA-A, B and C genes in a cohort of HIV-infected individuals from Central/Southern Mexico. Frequencies were obtained with the HLA Frequency Analysis Tool of the Los Alamos HIV Immunology Database http://www.hiv.lanl.gov/content/immunology/tools-links.html webcite. HLA typing was carried out by SSP-PCR as described in the Methods. A total of 292 individuals (584 HLA alleles) were included; 19, 29 and 14 distinct allelic groups were observed for the HLA-A, B and C genes respectively. Figure S2 – Phylogeny of 280 HIV pol sequences from a cohort of antiretroviral treatment-naïve individuals from Central/Southern Mexico. A Neighbor-Joining tree was inferred through the analysis of 1305 bp pol sequences including the whole protease and 335 codons of the RT in MEGA 4.0. The consensus tree from 1000 bootstrap replicas is shown. Evolutionary distances were calculated with Kimura's two-parameter model and are shown in substitutions per site. Positions with missing information were eliminated by pairwise comparison. 93 reference sequences of the main HIV-1 groups, subtypes and recombinant forms, obtained from the Los Alamos HIV Sequence Database http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html webcite were included. Reference subtype B sequences are shown in blue, reference sequences of all other subtypes and recombinant forms are shown in red and Mexican sequences are shown in black. The inset shows a detail of the Mexican sequence cluster. Table S1 – HLA-A, B and C population and allelic frequencies in the Mexican cohort. Table S2 – Linkage disequilibrium for class I HLA-A, B and C genes in the Mexican cohort. Table S3 – Protease and RT HLA-HIV codon associations observed in the Mexican cohort.
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