Figure 6. SGA analysis of virus diversity and co-evolution.
(A) Neighbor-joining (NJ) phylogenetic tree of 111 non-redundant HIV-1 Env sequences isolated from donor DRVI01 by single genome amplification (SGA). These Env sequences, shown as phylogenetic branches, are color-coded by the time point at which the sample was collected. 14 Env sequences selected for experimental validation are labeled as color-coded dots on the tree. (B) NJ tree of non-redundant Env sequences for each individual time point, namely 2005, 2006, 2008, and 2009. The four NJ trees have been rescaled to use the same unit of genetic distance. (C) Trimer models of SGA-derived consensus Env sequences with mutational hotspots labeled on the surface. Top view is shown in panel 1 and side view is shown in panel 2. Molecular surfaces are colored according to sequence conservation. Root-mean-square fluctuation (RSMF) relative to the consensus sequence at each time point is calculated as a diversity score for gp120, gp41, and gp140 and labeled beneath the structural model. (D) The gp120 core models of SGA-derived consensus sequences with CD4bs and mutational hotspots labeled on the molecular surface, which is colored as in (C). The diversity score for gp120 core is labeled beneath each structural model. (E) ELISA binding of VRC01, DRVIA7, and DRVIA7 variants to selected Env trimers at the four time points studied.