Comparisons of Human Immunodeficiency Virus Type 1 Envelope Variants in Blood and Genital Fluids near the Time of Male-to-Female Transmission

Abstract

To better understand the transmission of human immunodeficiency virus type 1 (HIV-1), the genetic characteristics of blood and genital viruses from males were compared to those of the imputed founding virus population in their female partners. Initially serodiscordant heterosexual African couples with sequence-confirmed male-to-female HIV-1 transmission and blood and genital specimens collected near the time of transmission were studied. Single viral templates from blood plasma and genital tract RNA and DNA were sequenced across HIV-1 env gp160. Eight of 29 couples examined yielded viral sequences from both tissues. Analysis of these couples' sequences demonstrated, with one exception, that the women's founding viral populations arose from a single viral variant and were CCR5 tropic, even though CXCR4 variants were detected within four males. The median genetic distance of the imputed most recent common ancestor of the women's founder viruses showed that they were closer to the semen viruses than to the blood viruses of their transmitting male partner, but this finding was biased by detection of a greater number of viral clades in the blood. Using multiple assays, the blood and genital viruses were consistently found to be compartmentalized in only two of eight men. No distinct amino acid signatures in the men's viruses were found to link to the women's founders, nor did the women's env sequences have shorter variable loops or fewer N-linked glycosylation sites. The lack of selective factors, except for coreceptor tropism, is consistent with others' findings in male-to-female and high-risk transmissions. The infrequent compartmentalization between the transmitters' blood and semen viruses suggests that cell-free blood virus likely includes HIV-1 sequences representative of those of viruses in semen.IMPORTANCE Mucosal transmissions account for the majority of HIV-1 infections. Identification of the viral characteristics associated with transmission would facilitate vaccine design. This study of HIV strains from transmitting males and their seroconverting female partners found that the males' genital tract viruses were rarely distinct from the blood variants. The imputed founder viruses in women were genetically similar to both the blood and genital tract variants of their male partners, indicating a lack of evidence for genital tract-specific lineages. These findings suggest that targeting vaccine responses to variants found in blood are likely to also protect from genital tract variants.

Keywords: HIV; N-linked glycosylation; coreceptor usage; genetic bottleneck; heterosexual transmission; viral compartmentalization.

FIG 1

Maximum likelihood phylogenetic analyses of HIV-1 gp160 sequences from all male-to-female transmission pairs. Unaligned, hypervariable regions were removed from the alignment. Generalized time-reversible phylogenetic maximum likelihood trees of the transmitting male’s blood plasma RNA, semen RNA, and semen DNA (■) and the seroconverting female’s blood plasma RNA and cervical sequences (○), derived by single-genome sequencing, are shown. The scale bar indicates the horizontal branch length, corresponding to 1 substitution per 100 sites. Teal, partner pair 1; blue, partner pair 2; red, partner pair 3; orange, partner pair 4; magenta, partner pair 5; brown, partner pair 6; green, partner pair 7; black, partner pair 8.

FIG 2

Maximum likelihood phylogenetic analyses of HIV-1 env gp160 sequences from male-to-female transmission pairs. Generalized time-reversible phylogenetic maximum likelihood trees of HIV env sequences derived from each of the eight partner pairs are shown, with pairs labeled A to H, respectively. Hypervariable regions were included in the alignments. See the key for symbol designations. Phylograms were rooted using subtypes A (GenBank accession number AF484509.1), B (GenBank accession number K03455.1), C (GenBank accession number AY772699.1), and D (GenBank accession number U88824.1) sequences from GenBank (not shown). Bootstrap proportions of ≥75% are labeled with an asterisk. The scale bar indicates the horizontal branch length, corresponding to 1 substitution per 100 sites.

FIG 2

Maximum likelihood phylogenetic analyses of HIV-1 env gp160 sequences from male-to-female transmission pairs. Generalized time-reversible phylogenetic maximum likelihood trees of HIV env sequences derived from each of the eight partner pairs are shown, with pairs labeled A to H, respectively. Hypervariable regions were included in the alignments. See the key for symbol designations. Phylograms were rooted using subtypes A (GenBank accession number AF484509.1), B (GenBank accession number K03455.1), C (GenBank accession number AY772699.1), and D (GenBank accession number U88824.1) sequences from GenBank (not shown). Bootstrap proportions of ≥75% are labeled with an asterisk. The scale bar indicates the horizontal branch length, corresponding to 1 substitution per 100 sites.

FIG 3

Genetic distances of male partner sequences to the imputed founder of infection in the female seroconverters. Pairwise genetic distances from each male-derived HIV env gp160-coding sequence relative to the imputed founder sequence in their female partners are shown. The founder was taken to be the calculated most recent common ancestor (MRCA) of infection. Male-derived sequences corresponded to plasma RNA (pR), semen RNA (sR), and semen DNA (sD).