Fig. 1

Highlighter plot of longitudinal 5′-half genome sequences. The single genome amplification (SGA) method was used to infer the transmitted/founder (T/F) 5′-half genome sequence from the screening sample and determine mutations in longitudinal samples. A highlighter plot denotes the location of synonymous (green tick), non-synonymous (red ticks), and deletion (grey ticks) mutations in each SGA-derived sequence from different time points compared to the T/F virus sequence. The positions of predominant and fixed mutations as well as related T cell epitopes are indicated on the bottom. Days post screening are indicated on the left