Novitsky, VladimirWang, RuiBaca, JeannieMargolin, LaurenMcLane, Mary F.Moyo, SikhulileWidenfelt, Erik vanMakhema, JosephEssex, M.2019-10-152011Novitsky, Vladimir, Rui Wang, Jeannie Baca, Lauren Margolin, Mary F. McLane, Sikhulile Moyo, Erik van Widenfelt, Joseph Makhema, and M. Essex. 2011. “Evolutionary Gamut of in Vivo Gag Substitutions during Early HIV-1 Subtype C Infection.” Virology 421 (2): 119–28. https://doi.org/10.1016/j.virol.2011.09.020.1178-122Xhttp://nrs.harvard.edu/urn-3:HUL.InstRepos:41552036Two analyses of HIV-1 subtype C Gag quasispecies were performed in a prospective cohort of 42 acutely and recently infected individuals by SGA on viral RNA/proviral DNA templates. First, in vivo Gag substitutions were assessed in relation to the HIV-1C consensus sequence, which revealed that 29.3% of detected amino acid substitutions can be classified as reversions to subtype consensus, 61.3% as forward substitutions from subtype consensus, and 9.3% as polymorphisms not associated with the subtype consensus sequence. Second, the proportion, dynamics, and relationships within individual pools of viral quasispecies were analyzed. Among reverse substitutions, 16.1% were minor, 11.0% transient, 13.6% dominant, and 59.2% fixed. In contrast, 31.6% of forward substitutions were minor, 59.3% transient, 3.8% dominant, and 5.3% fixed. The distinct patterns in the spectrum and dynamics of reverse and forward Gag substitutions suggest that these differences should be considered in HIV-1 evolutionary studies and analyses of viral mutational pathways.en-USJournal Article2019-10-1510.1016/j.virol.2011.09.020