Pervasive Genomic Recombination of HIV-1 in VivoSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY496645, AY496646, AY496647, AY496648, AY496649, AY496650, AY496651, AY496652, AY496653, AY496654, AY496655, AY496656, AY496657, AY496658, AY496659, AY496660, AY496661, AY496662, AY496663, AY496664, AY496665, AY496666, AY496667, AY496668, AY496669, AY496670, AY496671, AY496672, AY496673, AY496674, AY496675, AY496676, AY496677, AY496678, AY496679, AY496680, AY496681, AY496682, AY496683, AY496684.

Author:

Shriner Daniel1,Rodrigo Allen G1,Nickle David C1,Mullins James I12

Affiliation:

1. Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195-8070

2. Departments of Medicine and Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington 98195-8070

Abstract

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.

Publisher

Oxford University Press (OUP)

Subject

Genetics

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