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Updated: Jun 28, 2026

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
Published on: December 28, 2010
Estimating selection pressures on HIV-1 using phylogenetic likelihood models
S L Kosakovsky Pond1, A F Y Poon, S Zárate
1Department of Pathology, University of California, San Diego, CA 92093, USA.
None:
Human immunodeficiency virus (HIV-1) can rapidly evolve due to selection pressures exerted by HIV-specific immune responses, antiviral agents, and to allow the virus to establish infection in different compartments in the body. Statistical models applied to HIV-1 sequence data can help to elucidate the nature of these selection pressures through comparisons of non-synonymous (or amino acid changing) and synonymous (or amino acid preserving) substitution rates. These models also need to take into account the non-independence of sequences due to their shared evolutionary history. We review how we have developed these methods and have applied them to characterize the evolution of HIV-1 in vivo. To illustrate our methods, we present an analysis of compartment-specific evolution of HIV-1 env in blood and cerebrospinal fluid and of site-to-site variation in the gag gene of subtype C HIV-1.
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