Fig. 3
From: Effective treatment of SIVcpz-induced immunodeficiency in a captive western chimpanzee
SIVcpzANT env gene evolution over time. A maximum likelihood tree depicting the phylogenetic relationships of full-length env nucleotide sequences generated from Cotton’s plasma using SGA approaches is shown for a 16-year time period. Samples are colored by time point (11/30/2000, purple; 7/19/2004, green; 11/01/2006, brown; 9/25/2012, magenta; 11/25/2014, blue; 9/25/2015, red; 3/16/2016, black), with sequences from 2015 and 2016 representing rebound virus after insufficient suppression of viral replication due to low drug concentrations. Sequences were analyzed using PhyML [47] based on an evolutionary substitution model (TVM+I+G) selected by jModelTest [55]. The tree is rooted using the original SIVcpzANT sequence (U42720). Bootstrap values (of 1000 replicates) ≥80% are shown for major clades. The scale bar indicates 0.01 substitutions per site