Human leukocyte antigen B27 selects for rare escape mutations that significantly impair hepatitis C virus replication and require compensatory mutations

Abstract

HLA-B27 is associated with spontaneous viral clearance in hepatitis C virus (HCV) infection. Viral escape within the immunodominant HLA-B27 restricted HCV-specific CD8+ T cell epitope NS5B2841-2849 (ARMILMTHF) has been shown to be limited by viral fitness costs as well as broad T cell cross-recognition, suggesting a potential mechanism of protection by HLA-B27. Here, we studied the subdominant HLA-B27 restricted epitope NS5B2936-2944 (GRAAICGKY) in order to further define the mechanisms of protection by HLA-B27. We identified a unique pattern of escape mutations within this epitope in a large cohort of HCV genotype 1a infected patients. The predominant escape mutations represented conservative substitutions at the main HLA-B27 anchor residue or a T cell receptor contact site, neither of which impaired viral replication capacity as assessed in a subgenomic HCV replicon system. In contrast, however, in a subset of HLA-B27+ subjects rare escape mutations arose at the HLA-B27 anchor residue R2937, which nearly abolished viral replication. Notably, these rare mutations only occurred in conjunction with the selection of two equally rare, and structurally proximal, upstream mutations. Co-expression of these upstream mutations with the rare escape mutations dramatically restored viral replication capacity from <5% to ≥70% of wild-type levels. Conclusion The selection of rare CTL escape mutations in this HLA-B27 restricted epitope dramatically impairs viral replicative fitness unless properly compensated. These data support a role for the targeting of highly-constrained regions by HLA-B27 in its ability to assert immune control of HCV and other highly variable pathogens.

Statistical Linkage Analysis of Substitutions in Patient-Derived Sequences of Genotype 1a Hepatitis C Virus Nonstructural Protein 3 Exposes Targets for Immunogen Design

“…Preponderance of sector 1 sites in the NS3 epitopes targeted by HCV controllers. Clinical studies of HCV-infected cohorts have shown that possession of specific HLA alleles is highly correlated with the ability to spontaneously clear HCV by immunemediated mechanisms (24,(51)(52)(53)(54)(55). In this work, we studied two classes of protective epitopes to validate our findings.…”

“…In this work, we studied two classes of protective epitopes to validate our findings. One set of epitopes was allele restricted, as some specific HLA class I and class II alleles have been linked to spontaneous clearance of HCV (24,(51)(52)(53)(54)(55). We refer to these epitopes as "allele-restricted protective epitopes."…”

“…For the allele-restricted protective epitopes, we studied the CD4 ϩ and CD8 ϩ T-cell epitopes recognized by the six specific HLA alleles (HLA-A11, HLA-B27, HLA-B57, HLA-DR1, HLA-DR4, and HLA-DR11) that were found to have a strong association with spontaneous elimination of HCV in several independent studies (24,(51)(52)(53)(54)(55). The list of NS3-specific epitopes used in this analysis is given in Table S2 in the supplemental material and was compiled using the data from the Immune Epitope Database and Analysis Resource (http://www.iedb.org/) (58).…”

CD8+ T-Cell Responses in Hepatitis B and C: The (HLA-) A, B, and C of Hepatitis B and C

“…First, several escape mutations have been shown to impact replicative capacity in subgenomic or genomic replication systems [35][36][37] . Second, it has been shown by sequence analyses that some viral escape mutations can only occur in concert with additional, compensatory mutations [38][39][40] . Third, it has been observed that viral escape mutations that evolved in one host reverted to wild-type after transmission of the virus to an individual negative for the restricting HLA class I allele [41] .…”

Emerging concepts in immunity to hepatitis C virus infection

“…The high rate of replication coupled with the lack of proofreading ability of its polymerase provides the HCV genome with a means to escape HLA-restricted immune responses (10,121). The ability of HCV to mutate at an amino acid residue is constrained, however, by fitness costs, and compensatory mutations may be required to restore HCV replicative capacity (121)(122)(123).…”