Identification of HIV superinfection in seroconcordant couples in Rakai, Uganda, by use of next-generation deep sequencing.

ABSTRACT: 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 Rak

SUBMITTER: Redd AD 

PROVIDER: S-EPMC3147722 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature