Exploring the hepatitis C virus genome using single molecule real-time sequencing

Figure 4 Comparison of short-read and long-read sequencing for analysis of viral quasispecies. Conventional short-read sequencing, such as the IonProton sequencer, generates bulk information on viral clones. However, only fragmented information can be obtained such as the frequency of viral clones bearing the NS3-D168V or NS5A-P32del variants. By contrast, PacBio RSII sequencing can determine the contiguous genome sequence of each template, permitting analysis of linkage between several nucleotide changes through the NS3 to NS5A regions for individual viral clones. TGS: Third-generation sequencing; NGS: Next-generation sequencing; HCV: Hepatitis C virus.