Background:  HIV-1 superinfection (HSI) has been mostly reported among untreated patients, during treatment interruption, and more recently in seroconcordant couples with poor ART suppression. Here, we report the emergence of HSI in a man successfully controlled with ART following unprotected sex with a seroconcordant partner.

Methods:  Blood samples were obtained from 2 men (M1 and M2) chronically infected with HIV-1 and sexual partners, since 2006. M1 was diagnosed in 2000 with primary HIV infection, initiated ART in 2000, and has remained on ART with undetectable viremia, normal CD4⁺ counts (mean = 883 cells/mm³), and no drug-resistance mutations through the end of 2007. In contrast, M2 has not controlled viremia (range: 3 to 4 log) despite 5 years of ART and harbored a triple class resistant virus. In February 2008, M1 presented a plasma viral load of 280 copies/mL that kept increasing and then rebounded over the following year. Therefore, a new resistant genotype assessment for both patients was performed in addition to a phylogenetic analysis of whole-genome (N = 28), env (N = 28), and gag (N = 25) sequences obtained from viral RNA collected in 2000 and in 2008. Sequence alignments were generated with clustal W or MUSCLE, and phylogenies inferred from neighbor-joining plus bootstrap re-sampling or maximum-likelihood methods.

Results:  All 86 viral sequences were assigned to Clade B. The genotypic analysis from 2008 revealed 25 new related drug resistance mutations to NRTI(6/25), NtRTI(5/25), and PI(14/25) in M1’s profile, of which 23 were also present in M2 from the same period. Additionally, M1-2008 sequences clustered within the M2-2008 branches and distinct from M1-2000 sequence clusters in all trees. No recombination between the original M1 and M2 strains was observed, rather, substantial replacement of M1 by M2 sequences was detected upon superinfection.

Conclusions:  We detected HIV-1 superinfection in a patient with continuous, efficient, long-term ART controlled infection. Initial indicators were a detectable and increasing viral load, and acquisition of drug-resistance mutations derived from the superinfecting strain. In contrast to recent reports of superinfecton among long-term known seroconcordant couples undergoing ART, this report underscores the fragile barrier exerted by ART. This evidence has important implications for ongoing HIV therapeutic vaccine strategies.