High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men

Abstract

Elucidating virus-host interactions responsible for HIV-1 transmission is important for advancing HIV-1 prevention strategies. To this end, single genome amplification (SGA) and sequencing of HIV-1 within the context of a model of random virus evolution has made possible for the first time an unambiguous identification of transmitted/founder viruses and a precise estimation of their numbers. Here, we applied this approach to HIV-1 env analyses in a cohort of acutely infected men who have sex with men (MSM) and found that a high proportion (10 of 28; 36%) had been productively infected by more than one virus. In subjects with multivariant transmission, the minimum number of transmitted viruses ranged from 2 to 10 with viral recombination leading to rapid and extensive genetic shuffling among virus lineages. A combined analysis of these results, together with recently published findings based on identical SGA methods in largely heterosexual (HSX) cohorts, revealed a significantly higher frequency of multivariant transmission in MSM than in HSX [19 of 50 subjects (38%) versus 34 of 175 subjects (19%); Fisher's exact p = 0.008]. To further evaluate the SGA strategy for identifying transmitted/founder viruses, we analyzed 239 overlapping 5′ and 3′ half genome or env-only sequences from plasma viral RNA (vRNA) and blood mononuclear cell DNA in an MSM subject who had a particularly well-documented virus exposure history 3–6 days before symptom onset and 14–17 days before peak plasma viremia (47,600,000 vRNA molecules/ml). All 239 sequences coalesced to a single transmitted/founder virus genome in a time frame consistent with the clinical history, and a molecular clone of this genome encoded replication competent virus in accord with model predictions. Higher multiplicity of HIV-1 infection in MSM compared with HSX is consistent with the demonstrably higher epidemiological risk of virus acquisition in MSM and could indicate a greater challenge for HIV-1 vaccines than previously recognized.

Phylogenetically resolving epidemiologic linkage

“…6): a common source case where two men had been infected by the same male donor resulted in an MM topology, a case from a gay couple where the recipient was recently infected by the chronically infected partner resulted in a PM topology, and a case where a known HIV-1-positive donor injured a victim in a robbery that resulted in a PP topology. Thus, the topological signal in each case was consistent with the known transmission history (33,41,42).…”

“…Furthermore, reanalyzing other published transmission pairs with known or assumed direction showed mostly PM/consistent, some PP, and a few MM phylogenies (18,33,43,44). Likewise, in known transmission chains, involving several persons with multiple sampled clones per patient, again most transmissions seemed to be PM/consistent with a few MM topologies among patients that had infected each other, whereas among patients that had not directly infected each other the topology always was MM (19,45).…”

“…We investigated in detail three real HIV-1 transmission cases that display an MM phylogeny (41), a PM phylogeny (33), and a PP phylogeny (42). The MM case consisted of two male recipients (P1 and P2) that had been infected by a common male donor on the same evening.…”

“…The PM case consisted of a chronically infected donor who recently had infected a recipient (LACU9000 and HOBR0961). It was unknown how long the donor had been infected, and based on sequence and clinical data analyses it was estimated the recipient was sampled 17 d after transmission (33). The PP case consisted of a robber who injured a victim with a knife and transmitted at least two phylogenetic lineages.…”

“…For example, donor paraphyly was suggested to indicate the source in a transmission chain (18,19,29). Several studies have shown that transmission of >1 phylogenetic lineage occurs in 20-40% of transmissions, depending on transmission route and other factors (30)(31)(32)(33). This implies that transmission histories may generate more complicated phylogenies than previously considered (i.e., involving combinations of monophyletic, paraphyletic, and polyphyletic relationships).…”