Genetic Diversity of Near Genome-Wide Hepatitis C Virus Sequences during Chronic Infection: Evidence for Protein Structural Conservation Over Time

Abstract

Infection with hepatitis C virus (HCV) is one of the leading causes of chronic hepatitis, liver cirrhosis and end-stage liver disease worldwide. The genetics of HCV infection in humans and the disease course of chronic hepatitis C are both remarkably variable. Although the response to interferon treatment is largely dependent on HCV genotypes, whether or not a relationship exists between HCV genome variability and clinical course of hepatitis C disease still remains unknown. To more thoroughly understand HCV genome evolution over time in association with disease course, near genome-wide HCV genomes present in 9 chronically infected participants over 83 total study years were sequenced. Overall, within HCV genomes, the number of synonymous substitutions per synonymous site (dS) significantly exceeded the number of non-synonymous substitutions per site (dN). Although both dS and dN significantly increased with duration of chronic infection, there was a highly significant decrease in dN/dS ratio in HCV genomes over time. These results indicate that purifying selection acted to conserve viral protein structure despite persistence of high level of nucleotide mutagenesis inherent to HCV replication. Based on liver biopsy fibrosis scores, HCV genomes from participants with advanced fibrosis had significantly greater dS values and lower dN/dS ratios compared to participants with mild liver disease. Over time, viral genomes from participants with mild disease had significantly greater annual changes in dN, along with higher dN/dS ratios, compared to participants with advanced fibrosis. Yearly amino acid variations in the HCV p7, NS2, NS3 and NS5B genes were all significantly lower in participants with severe versus mild disease, suggesting possible pathogenic importance of protein structural conservation for these viral gene products.

Antigenic cooperation among intrahost HCV variants organized into a complex network of cross-immunoreactivity

“…Surprisingly, a similar temporal pattern of diversity and diversion was observed for intrahost HCV populations (9,10). Furthermore, for HCV, the consistent increase in negative selection during chronic infection was observed (9)(10)(11)(12)(13). The late-stage HCV populations were shown to remain constant and homogeneous under the strong negative selection for years, indicating a high level of intrahost adaptation (9).…”

“…Whereas other models of host-viral interaction predict a constant increase in genetic heterogeneity of the intrahost viral population as a result of continuous immune escape (22)(23)(24)(25), the AC model predicts a different outcome of the intrahost HCV evolution: reduction in heterogeneity of the persistent viral population. This prediction is strongly supported by experimental observations of increasing negative selection during intrahost HCV evolution, long-term persistence of viral variants, and substantial heterogeneity loss associated with a strong negative selection after years of infection (9)(10)(11)(12)(13)(14).…”

“…Thus, in-hub variants can be viewed as playing an altruistic role in AC because they improve fitness of adjacent variants at their own fitness cost, whereas adjacent variants are selfish because they gain fitness at the expense of in-hub variants. These selfish variants remain in existence without eliciting strong specific immune responses and are predicted to persist under negative selection as was recently observed (9,(11)(12)(13)(14)(15). In contrast, altruistic variants are efficiently eliminated from the viral population while their immune responses are being continuously sustained.…”

“…Analysis of effects of replication rates and initial conditions on solutions [11] suggests that small replication rate and initial population size may be beneficial for a variant with an advantageous position in the CRN (SI Text, section S1.2).…”

Network Analysis of the Chronic Hepatitis C Virome Defines Hypervariable Region 1 Evolutionary Phenotypes in the Context of Humoral Immune Responses

“…Rapid mutational change of HVR1 has been documented over weeks during the acute phase of infection, where HVR1 evolution is governed predominantly by strong selective pressures, with fixation of beneficial mutations (11,18,19). Reports examining samples collected over years to decades have documented the emergence of convergent HVR1 quasispecies variant pools under purifying selection pressures in established chronic infections (20)(21)(22)(23)(24). In selected instances, the maintenance of the dominant HVR1 epitope extended over years and in the absence of an associated antibody response (22).…”