Molecular Biology

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Globally circulating strains of HIV-1 are extraordinarily variable, and this diversity poses a major obstacle to AIDS vaccine development. This HIVRAD team will test whether immunogens derived from HIV-1 consensus and/or ancestral sequences are capable of eliciting more broadly cross-reactive immune responses than immunogens derived from contemporary HIV-1 strains. In this context, an important objective is to generate full-length genome sequences as well as functional env/rev expression cassettes from acute/early HIV-1 infections representative of multiple different subtypes. These reagents will be used to examine whether recently transmitted HIV-1 strains exhibit unique sequence signatures and/or biological properties that should be incorporated into AIDS vaccine design. Recently transmitted, contemporary HIV-1 strains are also the most appropriate viruses against which to test the potency and breadth of vaccine elicited neutralizing antibody responses. Functional env clones from acute/early HIV-1 infections will be used to generate such virus panels. The Molecular Biology Core will support this HIVRAD effort by molecularly characterizing 30 to 40 acute/early HIV-1 infections per year. Specific aims include: 1. To PCR amplify, clone and sequence full-length gp160 (env/rev) quasispecies from patients with acute or early HIV-1 infection representing a broad range of group M subtypes. 2. To derive full-length genome sequences of recently transmitted HIV-1 from these same patients. 3. To generate functional env clones from acute/early HIV-1 infections for the generation of contemporary subtype specific control genes and pseudovirus panels for neutralization studies. 4. To provide general molecular biology services to the entire HIVRAD team. The resulting sequences and reagents will be critical for the success of all other HIVRAD projects since they will facilitate the generation of (i) an acute/early HIV-1 database (Project #1); (ii) functional contemporary env control genes (Projects #2, #3 and #4), and (iii) a panel of subtype specific, contemporary acute/early HIV-1 strains to test the breadth and potency of neutralizing antibody responses elicited by centralized immunogens (Project #2 and Neutralization Core C).