Analysis of the Evolution and Structure of a Complex Intrahost Viral Population in Chronic Hepatitis C Virus Mapped by Ultradeep Pyrosequencing

Brendan A. Palmer, Zoya Dimitrova, Pavel Skums, Orla Crosbie, Elizabeth Kenny-Walsh, Liam J. Fanning

Hepatitis C virus (HCV) causes chronic infection in up to 50-80% of infected individuals. Hypervariable region 1 (HVR1) variability is frequently studied to gain an insight into the mechanisms of HCV adaptation during chronic infection, but the changes to and persistence of HCV subpopulations during intra-host evolution are poorly understood. In this study, we have used ultra-deep pyrosequencing (UDPS) to map viral heterogeneity of a single patient over 9.6 years of chronic HCV genotype 4a infection. Informed error correction of the raw UDPS data was performed using a temporally matched clonal data set. The resultant data set reported the detection of low frequency recombinants throughout the study period implying that recombination is an active mechanism through which HCV can explore novel sequence space. The data indicates that poly-virus infection of hepatocytes has occurred but that the fitness quotients of recombinant daughter virions are too low to compete against the parental genomes. The subpopulations of parental genomes contributing to the recombination events highlighted a dynamic virome where subpopulations of variants are in competition. In addition, we provide direct evidence that demonstrates the growth of subdominant populations to dominance in the absence of a detectable humoral response.