UC San Diego

HIV-1 dual infection occurs when the same individual is infected by two different strains of HIV-1. Although the high prevalence of circulating and unique recombinant forms of HIV-1, which can only be generated in the setting of dual infection, indicates that dual infection is not rare, relatively few cases of it have been documented. Hypothesizing that existing methods to detect dual infection were insufficiently sensitive, we developed and validated a novel technique utilizing 454 ultra-deep sequencing to detect low minority viral populations. We then applied this method to determine the prevalence of dual infection in a well-characterized study cohort and investigated the identified dual infection cases for clinical, virologic, and immunologic correlates of dual infection. At approximately 40% of the cost and 20% of the laboratory and analysis time of previous methods, ultra- deep sequencing identified three times more dual infection cases than previously documented in this study cohort. Dually infected participants had significantly faster viral load increases than monoinfected controls and displayed multiple patterns of viral recombination and CTL escape