HIV-1 Incidence and Genetic Diversity in the Caribbean

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DESCRIPTION (provided by applicant): Two distinct but highly related research projects will be conducted to accurately determine HIV incidence and HIV molecular diversity/recombination in populations at high risk of HIV infection in five Caribbean countries (Jamaica, Trinidad, Haiti, the Dominican Republic and Puerto Rico) participating in the HIV Vaccine Trials Network (HVTN). The data generated by these studies will be critical to implementation of Phase III vaccine trials. The hypotheses to be tested are 1) that recent high HIV-1 incidence can be conveniently and reliably estimated using a modified sensitive/less sensitive (S/LS) assay on archived crosssectionally collected samples from high-risk populations, and 2) that the predominant circulating HIV subtype is clade B, with little or no evidence of recombination in the RT/protease region of the pol gene, which is the most frequent site for recombination. In addition, the data generated will provide information about common anti-retroviral resistance mutations in incident (circulating) HIV that we predict will be absent in these largely treatment naive populations. The PI, a senior scientist at the IHV/UMD, is highly experienced in conducting collaborative epidemiologic/virologic studies in the region, and will collaborate with experts in HIV molecular characterization at the Henry Jackson Foundation, as well as clinical HVTN investigators in the Caribbean. These two related projects will utilize existing characterized serum/plasma collections that will be assayed with the S/LS assay at IHV, which is a participating laboratory in the IND held by CDC, to provide incidence data. Using a two-stage algorithm to accurately characterize the incident samples, at least 50 incident samples (10 per site) will then be sequenced in the RT/protease region of the genome that commonly includes recombination breakpoints. This rapid assessment will then be confirmed using a newly developed technique in a subset of 25/50 (5 per site) full-length genomes that will be sequenced from viral RNA extracted from serum. Data generated by these studies will validate the rationale for including these five sites in vaccine and prevention testing networks and help to bolster the evidence base for programs to control the spread of HIV. Innovation is presented in the use of a modified S/LS assay algorithm to rapidly ascertain incidence estimates and accurately identify incident samples, and in the use of overlapping RT PCR for full genome sequencing of viral RNA from incident serum (cell-free) samples.