Diversity and mutation analyses of HCV sequences in acute infection.

a5h - 5′ half genome contains core, E1, E2, p7, NS2, and NS3; 5q1- 5′ quarter 1 genome contains core, E1, E2, p7 and partial NS2; 5q2 - 5′ quarter 2 genome contains partial NS2 and NS3.
bRate calculations were derived from sequences from each discrete transmitted/founder lineage.
cSequences from 1st sampled time point with ≥4 sequences per lineage were analyzed. If 5′ half genomes were not available, quarter genomes 1 and 2 were analyzed with each result shown.
dSequences from 2nd sampled time point were analyzed due to insufficient number of sequences or sequence diversity from 1st sampled time point.
eInsufficient numbers of sequences from each time point to calculate fit to Poisson or star-like phylogeny.
fTransmitted/founder lineage identified by this sequence in respective ML tree and Highlighter plot.
gN/A, not applicable due to multiple transmitted/founder virus genomes.
hAverages were calculated from total mutations in all transmitted/founder lineages from all subjects combined. Because of low numbers of sequences and mutations in some lineages, certain values (e.g. dN/dS for subjects 10062 v2 and 10004 v3) vary substantially from the mean.