PMC

Infection with a single variant is determined by generating sequences during acute infection and comparing all sequences to themselves. In panel A, of the 21 sequences shown in the tree (left) and in the highlighter alignment (center) over half (62%) are identical to themselves and identical to the consensus over the entire env gene. The remaining sequences differ from this consensus sequence by one (33%) or two (5%) mutations. The differences between all sequences are compared to a Poisson distribution and deviations are identified by a goodness of fit test. When two sequences are transmitted (B), variant 1 (black) can be distinguished from variant 2 (grey) and the consensus of each lineage represents a unique transmitted/founder viral sequences. When all sequences from both lineages are compared, the Poisson distribution does not fit, but is restored when each lineage is analyzed independently.