Journal
VIROLOGY
Volume 396, Issue 2, Pages 213-225Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.virol.2009.10.002
Keywords
HIV; Subtype C; Primary infection; Immune escape; Reversion
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Funding
- National Institute of Allergy and infectious Disease (NIAID)
- National Institutes of Health (NIH)
- US Department of Health and Human Services (DHHS) [AI51794]
- National Research Foundation [67385]
- Fogarty AITRP [TWO-02]
- Wellcome Trust
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It is unresolved whether recently transmitted human immunodeficiency viruses (HIV) have genetic features that specifically favour their transmissibility. To identify potential transmission signatures, we compared 20 full-length HIV-1 subtype C genomes from primary infections, with 66 sampled from ethnically and geographically matched individuals with chronic infections. Controlling for recombination and phylogenetic relatedness, we identified 39 sites at which amino acid frequency spectra differed significantly between groups. These sites were predominantly located within Env, Pol and Gag (14/39, 9/39 and 6/39 respectively) and were significantly clustered (33/39) within known immunoreactive peptides. Within 6 months of infection, we detected reversion-to-consensus mutations at 14 sites and potential CTL escape mutations at seven. Here we provide evidence that frequent reversion mutations probably allows the virus to recover replicative fitness which, together with immune escape driven by the HLA alleles of the new hosts. differentiate sequences from chronic infections from those sampled shortly after transmission. (C) 2009 Elsevier Inc. All rights reserved.
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