Background: Infection of an HIV-1-infected individual by a different HIV-1 strain, known as superinfection, is directly relevant to the development of vaccines and therapeutics. In addition, superinfection is likely to increase viral recombination among diverse HIV-1 strains. Identification of new HIV-1 recombinants in many geographic regions predicted the occurrence of re-infection and recombination in vivo. However, it was not known whether chronically infected, untreated individuals could be susceptible to superinfection.

Methods: We searched for evidence of superinfection in Africa, where multiple HIV-1 subtypes exist, by examining serial blood samples from women in Nairobi’s Pumwani Sex Workers Cohort. We performed serial, complete HIV-1 RNA sequence analyses and heteroduplex tracking assays of plasma viral genomes from a Kenyan long-term survivor who had never received antiretroviral therapy (ART).

Results: The first of a series of complete HIV-1 RNA sequences was derived from plasma obtained in 1986, when the woman had been HIV seropositive for at least 21 months; this sequence was determined to be subtype A. However, the sequences obtained from plasma in 1995 and 1997 were subtype-A/C recombinants. To determine whether subtype-C sequences were present as minor species in 1986, heteroduplex tracking assays were performed. The subtype-C sequences were not detectable in the 1986 sample. We documented the occurrence of superinfection by a second HIV-1 subtype and intersubtype recombination in this chronically infected, untreated Kenyan woman.

Conclusions: This finding helps to explain the rising prevalence of recombinant HIV-1 in many parts of the world. Furthermore, it illustrates that infection with one strain may not provide protection against challenge from another, suggesting that those receiving ART may be susceptible to re-infection by drug resistant HIV-1. Finally, it underscores the potential difficulties of eliciting broad immune responses necessary for an effective vaccine.