Human immunodeficiency virus type 1 (HIV-1) diversity at time of infection is not restricted to certain risk groups or specific HIV-1 subtypes

Abstract

African women frequently acquire several genetically distinct human immunodeficiency virus type 1 (HIV-1) variants from a heterosexual partner, whereas the acquisition of multiple variants appears to be rare in men. To determine whether newly infected individuals in other risk groups acquire genetically diverse viruses, we examined the viral envelope sequences in plasma samples from 13 women and 4 men from the United States infected with subtype B viruses and 10 men from Kenya infected with non-subtype B viruses. HIV-1 envelope sequences differed by more than 2% in three U.S. women, one U.S. man, and one Kenyan man near the time of seroconversion. These findings suggest that early HIV-1 genetic diversity is not exclusive to women from Africa or to infection with any particular HIV-1 subtype.

FIG. 1.

Examples of the HMA of the V1-through-V5 envelope region in cases in which there were detectable heteroduplexes. A subject's identification number is shown above each lane of the gel and is followed by a “P” or a “C.” P lanes show the combination of two PCR amplifications of 10 HIV-1 genomes from the original plasma sample. C lanes show the combination of the PCR products from envelope inserts. These inserts were those with sequence data from the cloned variants from the subject. (A) Examples of HMA in which the combination of all of the variants with sequence data matched the HMA pattern of the original plasma sample. (B) Examples of HMA in which new heteroduplexes were detected in the combination of the individual clones when this combination was compared to the original plasma sample.

FIG. 2.

Phylogram of the two most divergent V1-through-V5 envelope gene sequences from each subject. The two most divergent sequences were selected based on pairwise differences. The sequence designation includes the subject identification number followed by a letter designating the clone. Sequences were aligned by using ClustalX with manual adjustment by use of MacClade (version 4.01). A phylogenetic tree was generated by using a distance-based method, neighbor joining, in the software package Phylogenetic Analysis Using Parsimony and Other Methods (PAUP 4.02b2a) (28). For these analyses, a two-parameter distance matrix, the Kimura two-parameter distance correction, was applied. H.BE.93.VI was selected as an outgroup to root the tree because it was likely to be the least related to the other sequences. Numbers at the nodes represent the bootstrap values for those nodes from 100 bootstrap resamplings. The results of this analysis were confirmed by using parsimony and maximum-likelihood methods.