HIV-1 superinfection in the antiretroviral therapy era: are seroconcordant sexual partners at risk?

Abstract

Background: Acquisition of more than one strain of human immunodeficiency virus type 1 (HIV-1) has been reported to occur both during and after primary infection, but the risks and repercussions of dual and superinfection are incompletely understood. In this study, we evaluated a longitudinal cohort of chronically HIV-infected men who were sexual partners to determine if individuals acquired their partners' viral strains.

Methodology: Our cohort of HIV-positive men consisted of 8 couples that identified themselves as long-term sexual partners. Viral sequences were isolated from each subject and analyzed using phylogenetic methods. In addition, strain-specific PCR allowed us to search for partners' viruses present at low levels. Finally, we used computational algorithms to evaluate for recombination between partners' viral strains.

Principal findings/conclusions: All couples had at least one factor associated with increased risk for acquisition of new HIV strains during the study, including detectable plasma viral load, sexually transmitted infections, and unprotected sex. One subject was dually HIV-1 infected, but neither strain corresponded to that of his partner. Three couples' sequences formed monophyletic clusters at the entry visit, with phylogenetic analysis suggesting that one member of the couple had acquired an HIV strain from his identified partner or that both had acquired it from the same source outside their partnership. The 5 remaining couples initially displayed no evidence of dual infection, using phylogenetic analysis and strain-specific PCR. However, in 1 of these couples, further analysis revealed recombinant viral strains with segments of viral genomes in one subject that may have derived from the enrolled partner. Thus, chronically HIV-1 infected individuals may become superinfected with additional HIV strains from their seroconcordant sexual partners. In some cases, HIV-1 superinfection may become apparent when recombinant viral strains are detected.

Figure 1. Neighbor-joining phylogenetic tree showing PBMC-derived C2-V5 HIV envelope gene sequences from all members of the cohort with bootstrap values calculated from 1000 bootstrap replicates for each major branch.

Couples are designated by colored letters (A, B, and D–I) and correspond to the couples in Table 1. Colored bars and ovals distinguish sequences from partners in each couple.

Figure 2. Neighbor-joining tree showing PBMC- and anorectal mucosa-derived sequences from subject 1 and PBMC-derived sequences from subject 2.

Subject 1's sequences are clustered on two separate branches, signifying infection with two different HIV strains, both of which are distinct from his partner's isolates (subject 2).

Figure 3. Histogram showing the distribution of pairwise nucleotide distances within subject 1 versus those within and between the remaining subjects in the cohort.

Distances were calculated using an HKY85+I+Γ model estimated via maximum likelihood. The histogram contains two peaks for subject 1, which overlie the peaks with distances for ‘among subjects’ and ‘within subjects’ for the cohort, demonstrating the dual HIV infection in subject 1, with his two distinct sets of viral isolates.

Figure 4. RIP 3.0 analysis.

Subject 4 in Pair B had 2 sequences for which 2–3 segments were more similar to one of his partner's sequences than his own with a significance threshold of 90%, shown by parallel green horizontal lines above the curves. The areas of similarity were at positions 400–426 and 450–462 for the first sequence and 331–338, 365–407, and 412–414 in the second sequence. Subject 9 in Pair F had 2 sequences for which 3 segments were similar to his partner Subject 10, shown by purple and aqua lines above the curves. These areas of similarity did not meet the threshold for statistical significance of 90%. The areas of similarity were at positions 70–201, 204–207, and 519–552 in the first sequence and 70–211, 214–217, and 531–572 in the second sequence.

Figure 5. Alignments of phylogenetically informative sites for Pairs A, B, and F, with shading indicating shared regions.

Lavender: nucleotide in upper partner's sequences shared with lower partner's sequences. Purple: nucleotide in lower partner's sequences shared with upper partner's sequences. Yellow: gap.