Identification of HIV Superinfection in Seroconcordant Couples in Rakai, Uganda, by Use of Next-Generation Deep Sequencing

Johns Hopkins University School of Medicine, Rangos Building, Room 530, 855 N Wolfe St, Baltimore, MD 21205, USA.
Journal of clinical microbiology (Impact Factor: 3.99). 06/2011; 49(8):2859-67. DOI: 10.1128/JCM.00804-11
Source: PubMed


HIV superinfection, which occurs when a previously infected individual acquires a new distinct HIV strain, has been described in a number of populations. Previous methods to detect superinfection have involved a combination of labor-intensive assays with various rates of success. We designed and tested a next-generation sequencing (NGS) protocol to identify HIV superinfection by targeting two regions of the HIV viral genome, p24 and gp41. The method was validated by mixing control samples infected with HIV subtype A or D at different ratios to determine the inter- and intrasubtype sensitivity by NGS. This amplicon-based NGS protocol was able to consistently identify distinct intersubtype strains at ratios of 1% and intrasubtype variants at ratios of 5%. By using stored samples from the Rakai Community Cohort Study (RCCS) in Uganda, 11 individuals who were HIV seroconcordant but virally unlinked from their spouses were then tested by this method to detect superinfection between 2002 and 2005. Two female cases of HIV intersubtype superinfection (18.2%) were identified. These results are consistent with other African studies and support the hypothesis that HIV superinfection occurs at a relatively high rate. Our results indicate that NGS can be used for detection of HIV superinfection within large cohorts, which could assist in determining the incidence and the epidemiologic, virologic, and immunological correlates of this phenomenon.

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    • "Pyrosequencing using the Roche/454 platform has been used to study HIV-1 transmission [1,2], emergence of drug resistance [3-5], and superinfection [6,7]. Pyrosequencing allows many relatively long DNA templates to be sequenced in parallel (~350nt with product literature promising >600bp), generating more than 1 million sequences in a single run. "
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    PLoS ONE 10/2013; 8(10):e76502. DOI:10.1371/journal.pone.0076502 · 3.23 Impact Factor
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    • "Moreover, with an adult seroprevalence rate of ~20% in Zambia, extramarital exposures should in a majority of instances be with seronegative individuals and therefore present less of a risk of potential superinfection than with the known seropositive partner. Interestingly, a similar lack of intra-couple superinfection has been observed in a recent study of 11 seroconcordant couples infected with disparate viruses in Uganda [48]. "
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