Introduction: HCV viral strains that establish infections are known as the transmitted/founder (T/F) viruses. Host adaptive responses against these strains during the early phase of infection are not well understood. Neutralizing antibodies (Nab) targeting structural proteins, E1 and E2, are known to block HCV entry and prevent viral replication. However, diversifying viral genomes adapt and escape these mechanisms by generating multiple mutations on the same genome that confer high fitness escape variants. Using deep sequencing data of viral genomes during early phase of primary infection we identify the evolutionary pathway of immune escape at high resolution that highlights the immune response against T/F viruses.
Methods: 19 subjects with longitudinal viraemic samples were collected and deep sequenced with Roche-454 and Illumina technology. Haplotype reconstruction has been performed on amino acids 1-800 of Core to p7 of HCV poly-protein. Mutual Information (MI) was applied to analyze the distribution of co-evolving non-synonymous mutations in the evolving viral population.
Results: Analysis of co-evolving mutations in primary infection identified novel evolutionary pathways conferring potential advantages for the viral population in terms of immune escape from antibody response. Common pathways of evolutionary change were observed amongst the 19 subjects. In particular, the establishment of chronic infection at >100 days post infection, resulted in pairs of mutations with high values of MI clustered within antibody domains. Two types of connected sites were identified. 1) Both mutated sites present potential escape variants against antibody pressure. 2) One site in domains targeted by Nab, but the co-occurrence of another mutation may provide an advantage in terms of structural conformation or in survival fitness.
Discussion: Computational analysis through MI revealed distant mutations with potential survival advantage against Nab response. Further investigation will involve experimental validation of predicted effects of connected sites in terms of structural conformational changes and fitness advantage.