wang_hcv
HCV transmission bottlenecks analyzed by deep sequencing
Hepatitis C virus (HCV) replication in infected patients produces large and diverse viral populations, which give rise to drug resistant and immune escape variants. Here we analyzed HCV populations during transmission and diversification in longitudinal and cross sectional samples using 454/Roche pyrosequencing, in total analyzing 174,185 sequence reads. To sample diversity, four locations in the HCV genome were analyzed, ranging from high diversity (the envelope HVR1 region) to almost no diversity (the 5' UTR). For three longitudinal samples for which early time points were available, we found that only 1-4 viral variants were present, suggesting that productive infection was initiated by a very low number of HCV particles. Sequence diversity accumulated subsequently, with the 5' untranslated region showing almost no diversification while the envelope hypervariable region HVR1 showed >100 variants in some subjects. Calculation of the transmission probability for only a single variant, taking in to account the measured population structure within patients, confirmed initial infection by one or a few viral particles. These findings provide the most detailed sequence-based analysis of HCV transmission bottlenecks to date. The analytical methods described here are broadly applicable to studies of viral diversity using deep sequencing.)