ENPEP and infection: Single genome sequencing (SGS), which precludes in vitro recombination, enables linkage across amplicons, and allows proportional assessment of diverse virus populations [29,32], was used to generate sequences of gp160 env from plasma virus collected at weeks 4, 10, and 20 post-infection (total 287 sequences, median 41 per animal timepoint) (Fig 1A).