Viral Sequencing Core

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Describe the interactions between Core J and site investigators and others within CHAVI to explain the goals and the ways in which these various groups might work synergistically. Results generated by Core J investigators are discussed on a regular basis at the weekly CHAVI conference calls. Thus, clinical site and other CHAVI investigators are acutely aware of pertinent data, questions and issues, and are consulted with respect to moving forward. Examples of such interactions in the past year included: (i) selection of samples from chronically infected patients by clinical investigators as controls for the acute infection analysis, (ii) selection of a first set of functional env clones for further biological characterization, (iii) selection of a subset of acute infection samples for more detailed longitudinal quasispecies analyses, and (iv) selection of acute infection samples for full-length genome analysis for CTL studies. How are the different sequencing sites monitoring performance metrics (UAB and South Africa)? Who is doing what between these two sites? In the past budget period, the South African site has focused on the genetic characterization of acute and chronic subtype C infections, while UAB, Duke and UNC sites have completed the first comprehensive analysis of acute subtype B infections. In the coming year, South Africa and UNC sites will be responsible for the completion of the genetic characterization of acute subtype C infections in South Africa and Malawi, while UAB and Duke will focus on longitudinal analyses of acute infection samples, full length genome sequence analysis, and generation of functional clones. Priorities and workload are discussed on a quarterly basis. Progress at individual sites is reviewed by the CHAVI SLG and budgetary adjustments are made when necessary.