Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

TitleAdaptation to different human populations by HIV-1 revealed by codon-based analyses.
Publication TypeJournal Article
Year of Publication2006
AuthorsPond SLKosakovs, Frost SDW, Grossman Z, Gravenor MB, Richman DD, Brown AJLeigh
JournalPLoS Comput Biol
Volume2
Issue6
Paginatione62
Date Published2006 Jun 23
ISSN1553-7358
KeywordsAdaptation, Physiological, Biological Evolution, Codon, Genetic Predisposition to Disease, Genetic Variation, Genetics, Population, HIV Infections, HIV-1, Humans, Selection, Genetic, Sequence Analysis, DNA
Abstract

Several codon-based methods are available for detecting adaptive evolution in protein-coding sequences, but to date none specifically identify sites that are selected differentially in two populations, although such comparisons between populations have been historically useful in identifying the action of natural selection. We have developed two fixed effects maximum likelihood methods: one for identifying codon positions showing selection patterns that persist in a population and another for detecting whether selection is operating differentially on individual codons of a gene sampled from two different populations. Applying these methods to two HIV populations infecting genetically distinct human hosts, we have found that few of the positively selected amino acid sites persist in the population; the other changes are detected only at the tips of the phylogenetic tree and appear deleterious in the long term. Additionally, we have identified seven amino acid sites in protease and reverse transcriptase that are selected differentially in the two samples, demonstrating specific population-level adaptation of HIV to human populations.

DOI10.1371/journal.pcbi.0020062
Alternate JournalPLoS Comput. Biol.
PubMed ID16789820
PubMed Central IDPMC1480537
Grant ListAI27670 / AI / NIAID NIH HHS / United States
AI29164 / AI / NIAID NIH HHS / United States
AI36214 / AI / NIAID NIH HHS / United States
AI38858 / AI / NIAID NIH HHS / United States
AI43638 / AI / NIAID NIH HHS / United States
AI47745 / AI / NIAID NIH HHS / United States
AI57167 / AI / NIAID NIH HHS / United States