Background:   Anecdotal reports of HIV superinfection coupled with systematic investigations of chronically infected individuals who could not identify cases of superinfection prompted our investigation in a cohort of newly infected individuals.

Methods:   We retrospectively analyzed plasma samples from 54 subjects enrolled in the San Diego and Los Angeles Acute HIV Infection and Early Disease Research Programs who deferred ARV treatment for 6 months or longer (46 subject-years of follow-up). Population-based sequencing of the pol gene was performed (Viroseq, Celera Diagnostics) from RNA extracted from plasma at 2 times (mean 313, range 177 to 597 days apart). Superinfection was suspected when phylogenetic analysis showed that the 2 sequences clustered independently. Superinfection was confirmed by clonal (V3) and dye-primer (pol) sequencing and length polymorphism analysis (V1-2 and V4-5) (GeneScan, Applied Biosystems).

Results:   We identified 3 cases of superinfection, representing a rate of 6.5% per year. Superinfection occurred 5 to 13 months after the estimated date of initial infection. All 3 subjects were male whose risk factor was sexual exposure; each superinfecting HIV strain was associated with a change in ARV susceptibility. Two were initially infected with drug-resistant HIV and then became superinfected with a wild-type strain, while the other was initially infected with a wild-type strain and then was superinfected with a drug-resistant strain. Within 6 months of acquiring the superinfecting strain, plasma viral loads increased (mean 1.6 log) and CD4 counts decreased (mean 132 cells/µL).

Conclusions: While initial co-infection cannot be ruled out, 4 independent lines of molecular investigation provide compelling evidence that these are cases of HIV-1 clade-B superinfection. Since population-based pol sequencing is a conservative screening method, this may underestimate the true superinfection rate. Other cases may have been missed if the superinfecting strain was a minor variant below the level of detection, or if the superinfecting strain replaced its original pol gene with the initial HIV strain’s pol gene through recombination. Harm reduction counseling with patients is essential even if their risk exposures are with other HIV-infected people, as superinfection could have detrimental clinical consequences by accelerating disease progression and limiting future treatment options.

Keywords: HIV; Incidence; Superinfection