Ultra-deep pyrosequencing analysis of hepatitis C virus populations passaged in the absence or presence of ribavirina.

aThe populations analyzed correspond to the infections at an initial MOI of 1 to 2 TCID50/cell described in Fig. 3a.bThe HCV genome residue numbering corresponds to the JFH-1 genome (accession number #AB047639). Amplicon (A) length ranged between 216 and 339 nucleotides. The number of nucleotides sequenced was 2.1×106 to 3.3×106, and the number of reads on which the parameters were calculated was 10,000 for each amplicon. Procedures are described in Materials and Methods.cIn parenthesis the number of haplotypes with one and two mutations is given.dIn parenthesis the two terms of the ratio are given. Mutation types are summarized in Fig. 4c and their position in the HCV genome and deduced amino acid substitutions are given in Table S5.