Fig 1 -

A and B) Highlighter plots and ML branches of single variant and multivariant infection respectively. Two distinct variants are denoted in black and blue while inter-variant recombination is denoted in red on Fig 1B. C) Average pairwise distance (APD) of HIV-1 SGA/S sequences distinguishes between single and multiple founder variants. D) Average pairwise distance (APD) plotted against days post infection showing no evidence for increased diversification and confirming that samples in this time window were close to the wild type transmitted/founder variant.