The rates of HIV superinfection and primary HIV incidence in a general population in Rakai, Uganda

Background.Human immunodeficiency virus (HIV) superinfection has been documented in high-risk individuals; however, the rate of superinfection among HIV-infected individuals within a general population remains unknown.Methods.A novel next-generation ultra-deep sequencing technique was utilized to determine the rate of HIV superinfection in a heterosexual population by examining two regions of the viral genome in longitudinal samples from recent HIV seroconverters (n = 149) in Rakai District, Uganda.Results.The rate of superinfection was 1.44 per 100 person years (PYs) (95% confidence interval [CI],. 4-2.5) and consisted of both inter-and intrasubtype superinfections. This was compared to primary HIV incidence in 20 220 initially HIV-negative individuals in the general population in Rakai (1.15 per 100 PYs; 95% CI, 1.1-1.2; P =. 26). Propensity score matching (PS) was used to control for differences in sociodemographic and behavioral characteristics between the HIV-positive individuals at risk for superinfection and the HIV-negative population at baseline and follow-up. After PS matching, the estimated rate of primary incidence was 3.28 per 100 PYs (95 CI, 2.0-5.3; P =. 07) controlling for baseline differences and 2.51 per 100 PYs (95 CI, 1.5-4.3; P =. 24) controlling for follow-up differences.Conclusions.This suggests that the rate of HIV superinfection in a general population is substantial, which could have a significant impact on future public health and HIV vaccine strategies.