Pervasive genomic recombination of HIV-1 in vivo

Daniel Shriner*, Alien G. Rodrigo, David C. Nickle, James I. Mullins

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

133 Citations (Scopus)

Abstract

Recombinants of preexisting human immunodeficiency virus type 1 (HIV-1) strains are now circulating globally. To increase our understanding of the importance of these recombinants, we assessed recombination within an individual infected from a single source by studying the linkage patterns of the auxiliary genes of HIV-1 subtype B. Maximum-likelihood phylogenetic techniques revealed evidence for recombination from topological incongruence among adjacent genes. Coalescent methods were then used to estimate the in vivo recombination rate. The estimated mean rate of 1.38 × 10-4 recombination events/adjacent sites/generation is ∼5.5-fold greater than the reported point mutation rate of 2.5 × 10-5/site/generation. Recombination was found to be frequent enough to mask evidence for purifying selection by Tajima's D test. Thus, recombination is a major evolutionary force affecting genetic variation within an HIV-1-infected individual, of the same order of magnitude as point mutational change.

Original languageEnglish
Pages (from-to)1573-1583
Number of pages11
JournalGenetics
Volume167
Issue number4
DOIs
Publication statusPublished - Aug 2004
Externally publishedYes

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