Fig. 3

Diversity dynamics within selection sites and non-selection sites. a The highlighter plot (http://www.hiv.lanl.gov/content/sequence/HIGHLIGHT/highlighter_top.html) of subject CH042’s envelope gene sequences obtained 676 days after the first sample, along with the founder envelope sequence (top). Here the founder envelope sequence was inferred as the consensus sequence of subject CH042’s first sample at Fiebig stage I/II. The subsequent sequences show positions of mutations away from the founder sequence. b The mutant frequency distribution for subject CH042 in Ref. [32] (grey bars). Mutant frequency denotes the proportion of sequences from a particular time point that do not match the founder sequence nucleotide at a given site. The dotted line presents the best fit of the binomial distribution in Eq. (1) to subject CH042’s mutant frequency distribution. The threshold value of mutant frequency is determined when the tail of the fitted curve becomes less than 0.1; sites above this threshold of 0.2 were designated as putative selection sites. A total of 63 putative selection sites were identified. c The mutant frequency distribution of subject CH256 in Ref. [32] (grey bars) along with the best fit of the binomial distribution (dotted line). The threshold mutant frequency is determined as 0.2, where the tail of the binomial distribution becomes less than 0.1. The 53 sites with a mutant frequency above the threshold were regarded as putative selection sites. d The diversity dynamics of selection sites (squares) compared with those within non-selection sites (asterisks) for subject CH042. The slope of diversity at selection sites is around \(28.2 \times 10^{ - 5}\) per base per day, which is approximately 19 times greater than that of non-selection sites for the first 150 days after the first sample. The dotted line presents the neutral rate of evolution, \(2.16 \times 10^{ - 5}\) per site per day. e The diversity dynamics of selection sites (squares) compared with those of non-selection sites (asterisks) for subject CH256. The slope of diversity increase at selection sites was around 21 times greater than that at non-selection sites (\(57.3 \times 10^{ - 5}\) vs. \(2.77 \times 10^{ - 5}\) per base per day)