Genotype-specific acquisition, evolution and adaptation of characteristic mutations in hepatitis E virus

Abstract

Hepatitis E virus (HEV) infection is a major cause of acute hepatitis but also provokes chronic infection in immunocompromised patients. Although the pathogenesis and treatment outcome involve complex interplay between the virus and host, the nature of adaptive responses of HEV to the host immune system remain obscure at best. In this study, we used large-scale proteomic bioinformatics to profile characteristic mutations in human HEV isolates associated to ribavirin treatment failure, chronic hepatitis, hepatic failure or altered immunoreactivity. The prevalence of specific mutations was examined in a large number of protein sequences of ORF1 and ORF2 regions of the 3 major human-derived HEV genotypes (1, 3 and 4). By analyzing potential B, CD4+ and CD8+ T cell epitopes, we found that many of these mutations overlap with the predicted epitopes and are frequently present among the 3 HEV genotypes. These overlapping mutations mediate reduced antigenicity. Finally, by delineation of diversification and evolution of the underlying epitopes, we observe that most of these variants apparently evolved earlier in genotype 1 when compared with genotypes 3 and 4. These results indicate that HEV is under substantial evolutionary pressure to develop mutations enabling evasion of the host immune response and resistance to antiviral treatment. This indicates the existence of an ongoing evolutionary arms race between human immunity, antiviral medication and HEV.

Keywords: B and T cells; epitope; evolution; hepatitis E virus; mutation.

Figure 1.

(A). Identified mutations of ORF1 and ORF2 regions of HEV. The number within the box represents the amino acid position; the letter(s) above the box refer to the wild type amino acid, and the letter below the box are relevant mutations reported in previous studies. (Met: methyltransferase; Y: Y-domain; HVR: hypervariable regions; Hel: RNA helicase; RdRP: RNA-dependent RNA polymerase; C: capsid protein) (B). The prevalence of mutations within HEV genotype 1 (n = 81), 3 (n = 182) and 4 (n = 143). Amino acid diversity was measured as the proportion of sequences that varies from the consensus sequence.

Figure 2.

Antigenicity difference between wild-type and mutated T cell (MHCI and MHCII) (A) and B cell epitopes (B).

Figure 3.

The effects of mutations (P259S, L477T) on the structural stability of ORF2 region of HEV predicted by DUET web server. Mutations are shown in blue color ribbon. (A) Crystal struture without mutation of ORF2 (2ZTN-amino acid 129–606). (B). P259S; feature: distabilizing; secondary structure: loop or irregular. (C). L477T; feature: distabilizing; secondary structure: extended β-strand.

Figure 4.

A heat map showing the evolvment of mutations with years. Mutations 1 = F179S, 2 = A317T, 3 = T735I, 4 = L1110F, 5 = V1120I, 6 = V1213A, 7 = Y1320H, 8 = K1383N, 9 = D1384G, 10 = K1398N, 11 = F1439Y, 12 = V1479I, 13 = C1483W, 14 = N1530T, 15 = Y1587F, 16 = G1634R, 17 = G1634K, 18 = P259S, 19 = L477T, 20 = L613T. Each box represents the sequence of ORF 1 or ORF2, from genotype 1, 3 or 4 in a particular year. Red colored boxes represent the mutations related to hepatic failure mutations; purple to chronic hepatitis; yellow to ribavirin treatment failure; and blue to altered immunoreactivity. The year of deposition of each sequence is mentioned in the arrow below the heat map.

Figure 5.

Evolution period of overlapped mutations. Each bar represents the evolving period (years) of each mutations.

Figure 6.

Possible mechanisms of immune evasion by hepatitis E virus. Main routes by which HEV mutations may result in evasion of the host immune responses. Mutated epitopes presented by antigen presenting cells, B and T cells will results in escape recognition of the epitopes.