Background:  HIV superinfection has been observed in high-risk individuals but the rate of superinfection in general populations and how this relates to primary HIV incidence is unclear.

Methods:  A sensitive high-throughput next-generation ultradeep sequencing technique and analysis protocol was used to test for HIV superinfection in 2 regions of the viral genome (p24 and gp41) in HIV seroconverters from the Rakai Community Cohort Study (RCCS) in Rakai District, Uganda (n = 149; 487.5 person years [PY]), with the goal of determining a rate of superinfection in these individuals. This was compared to the primary HIV incidence rate for the entire initially HIV^– RCCS heterosexual population with at least one follow-up sample over the same time period (n = 20220; 100,550 PY).

Results:  Seven cases of HIV superinfection were identified for a rate of HIV superinfection of 1.44/100 PY (95%CI 0.37 to 2.51). All superinfection events were observed in the gp41 region. There was a significant difference in total reads (p <0.05), but not in consensus sequences (p = 0.26) in the gp41 region between baseline and follow up. All 7 superinfected individuals were initially infected with HIV subtype D. Four of the superinfection events were intra-subtype; i.e., initial subtype D individuals superinfected with a new novel subtype D strain(s). The other 3 cases were inter-subtype superinfection events with new subtype A strains being found in the follow-up sample. One thousand one hundred and fifty-two HIV-seroconversion events were identified during this period in the RCCS population for an HIV incidence rate of 1.15/100 PY (95%CI 1.08 to 1.21). The rate of HIV superinfection did not differ significantly from the primary HIV incidence rate (incidence rate ratio = 1.26, 95%CI 0.50 to 2.60; p = 0.26).

Conclusions:  This is the first large-scale examination of the rate of HIV superinfection using a next-generation ultradeep sequencing technique. Although other studies have examined superinfection in small groups of high-risk individuals, this is the first study to directly compare HIV superinfection rates to HIV incidence in a general heterosexual population. The finding that HIV superinfection occurs at approximately the same rate as primary HIV incidence has multiple public health ramifications, and could have significant implications for HIV vaccine research.