Genetics, Vol. 167, 1573-1583, August 2004, Copyright © 2004
doi:10.1534/genetics.103.023382

Pervasive Genomic Recombination of HIV-1 in Vivo

Daniel Shriner^*,1, Allen G. Rodrigo^*,2, David C. Nickle^* and James I. Mullins^*,

^* Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195-8070
Departments of Medicine and Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington 98195-8070

¹ Corresponding author: Department of Microbiology, Rosen Bldg., University of Washington School of Medicine, Box 358070, Seattle, WA 98195-8070.
E-mail: dshriner{at}u.washington.edu

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 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.

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