Effect of immune pressure on hepatitis C virus evolution: insights from a single-source outbreak

Abstract

The host's immune response to hepatitis C virus (HCV) can result in the selection of characteristic mutations (adaptations) that enable the virus to escape this response. The ability of the virus to mutate at these sites is dependent on the incoming virus, the fitness cost incurred by the mutation, and the benefit to the virus in escaping the response. Studies examining viral adaptation in chronic HCV infection have shown that these characteristic immune escape mutations can be observed at the population level as human leukocyte antigen (HLA)-specific viral polymorphisms. We examined 63 individuals with chronic HCV infection who were infected from a single HCV genotype 1b source. Our aim was to determine the extent to which the host's immune pressure affects HCV diversity and the ways in which the sequence of the incoming virus, including preexisting escape mutations, can influence subsequent mutations in recipients and infection outcomes.

Conclusion: HCV sequences from these individuals revealed 29 significant associations between specific HLA types within the new hosts and variations within their viruses, which likely represent new viral adaptations. These associations did not overlap with previously reported adaptations for genotypes 1a and 3a and possibly reflected a combination of constraint due to the incoming virus and genetic distance between the strains. However, these sites accounted for only a portion of the sites in which viral diversity was observed in the new hosts. Furthermore, preexisting viral adaptations in the incoming (source) virus likely influenced the outcomes in the new hosts.

Fig. 1

Highlighter plot of synonymous and nonsynonymous substitutions in NS3 and NS5B with respect to the source sequence (AF313916). The plot was created with Highlighter (available at http://www.lanl.gov). Red lines denote nonsynonymous substitutions, green lines indicate synonymous substitutions, and gray regions show unsequenced sections.

Fig. 2

Covarying sites (P < 0.001) in the HCV genome represented as coordinates. Open diamonds indicate that one or both sites fall within an epitope or at an association site, and dark diamonds indicate that the sites do not fall within either. Many covariant sites fall in close proximity to one another in the genome (illustrated by the linear trend); however, there are groupings that suggest strong covariation between residues within NS5A and residues within other proteins. Sequence coverage was not found to be a function of covariant site identification.

Fig. 3

HLA-A*03–associated viral polymorphisms at (A) positions 1087 and 1088 in NS3 and (B) position 2518 in NS5B. Sequences in regions of interest (from Table 1) are displayed for HLA-A*03⁺ and HLA-A*03⁻ subjects. The sequence identity with the source sequence is identified by a dot. Amino acid mixtures at a site are separated by a forward slash. The number of individuals with a particular sequence is shown in the count column. The lysine (K) to arginine (R) substitution at 2518 (8 of 15 HLA-A*03⁺ subjects versus 4 of 47 HLA-A*03⁻ subjects) resulted in a change in the SYFPEITHI-predicted binding score from 27 to 21. Only one HLA-A*03 individual with chronic infection did not have a polymorphism at the 1087 or 1088 site in NS3 or at the 2518 site in NS5B.