Pervasive genomic recombination of HIV-1 in vivo.


Journal Article

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 x 10(-4) recombination events/adjacent sites/generation is approximately 5.5-fold greater than the reported point mutation rate of 2.5 x 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.

Full Text

Cited Authors

  • Shriner, D; Rodrigo, AG; Nickle, DC; Mullins, JI

Published Date

  • August 2004

Published In

Volume / Issue

  • 167 / 4

Start / End Page

  • 1573 - 1583

PubMed ID

  • 15342499

Pubmed Central ID

  • 15342499

Electronic International Standard Serial Number (EISSN)

  • 1943-2631

International Standard Serial Number (ISSN)

  • 0016-6731

Digital Object Identifier (DOI)

  • 10.1534/genetics.103.023382


  • eng