Mechanisms of Hepatitis C Virus Escape from Vaccine-Relevant Neutralizing Antibodies

Abstract

Hepatitis C virus (HCV) is a major causative agent of acute and chronic hepatitis. It is estimated that 400,000 people die every year from chronic HCV infection, mostly from severe liver-related diseases such as cirrhosis and liver cancer. Although HCV was discovered more than 30 years ago, an efficient prophylactic vaccine is still missing. The HCV glycoprotein complex, E1/E2, is the principal target of neutralizing antibodies (NAbs) and, thus, is an attractive antigen for B-cell vaccine design. However, the high genetic variability of the virus necessitates the identification of conserved epitopes. Moreover, the high intrinsic mutational capacity of HCV allows the virus to continually escape broadly NAbs (bNAbs), which is likely to cause issues with vaccine-resistant variants. Several studies have assessed the barrier-to-resistance of vaccine-relevant bNAbs in vivo and in vitro. Interestingly, recent studies have suggested that escape substitutions can confer antibody resistance not only by direct modification of the epitope but indirectly through allosteric effects, which can be grouped based on the breadth of these effects on antibody susceptibility. In this review, we summarize the current understanding of HCV-specific NAbs, with a special focus on vaccine-relevant bNAbs and their targets. We highlight antibody escape studies pointing out the different methodologies and the escape mutations identified thus far. Finally, we analyze the antibody escape mechanisms of envelope protein escape substitutions and polymorphisms according to the most recent evidence in the HCV field. The accumulated knowledge in identifying bNAb epitopes as well as assessing barriers to resistance and elucidating relevant escape mechanisms may prove critical in the successful development of an HCV B-cell vaccine.

Keywords: B-cell vaccine; antibody escape; hepatitis C virus; virus neutralization.

Figure 2

Structural mapping of E1/E2 CD81bs, epitope clusters, and escape mutations. (A) Residues participating or affecting the binding to CD81 according to Gopal et al. 2017 [47] are represented in purple. The CD81bs originally defined by competition assays, mutagenesis, and electron microscopy is indicated as a dashed line in all structures. (B) Depicts antigenic sites AS412, AS434, and AS523. (C) Solved crystal structures of AS412 peptide in complex with AP33 (PDB ID: 4GAG), HC33.1 (PDB ID: 4XVJ), and 3/11 (PDB ID: 4WHY). Yellow arrows depict β-sheet secondary structures. (D) Depicts antigenic regions 1–5. (E) Depicts antigenic domains A–E. Epitopes are consistently depicted in green, position of described escape mutations in AS412 (412, 413, 415, 417, 419, 434, 610, 665), AR3A (431, 438, 442), AR4A (696), AR5A (665 and 680), domain B (438, 439), and domain E (412, 413, 415, 417, 419, 434, 610, 665) are shown in red (see Table 1 for escape mutation overview). All epitope clusters are mapped on the E1/E2 ectodomain structural model described in Castelli et al. 2017 [76]. Escape mutations in E1 (A349D for AR5A and M345T for AR3A) are not shown as these were not included in the model.

Figure 1

Schematic representation of the primary E1/E2 sequence, including functional regions and epitope clusters. Domain legends not defined in the main text: NTD (N-terminal domain), pFP (putative fusion peptide), CR (conserved region), CD81bs (CD81 binding site). CD81bs and conformational epitopes defined as in Gopal et al. 2017 [47]. Residues comprising each epitope are reported in red, residues involved in the interaction with CD81 in green. N- and O-glycosylation sites are depicted as black and red branched forks, respectively.

Figure 3

Mechanisms of direct HCV escape from neutralizing antibodies. (A) Contact residue change. Substitutions that directly alter a contact residue, whereby antibody–antigen affinity is reduced. (B) Glycan shift. Altered glycosylation can lead to HCV resistance to NAbs. The glycan masks the broadly neutralizing epitope on the viral glycoproteins, thus preventing neutralization of the viral particle. (C) Local allosteric change. Substitutions at positions not directly within the epitope can alter HCV sensitivity to a specific NAb by inducing local allosteric changes that alter specific NAb epitope accessibility. (D) Global allosteric change. Substitutions at positions not directly within the epitope can alter HCV sensitivity to a wide range of NAbs by inducing global allosteric changes that alter NAb epitope accessibility.

Figure 4

Indirect HCV neutralizing antibody escape by increased viral fitness, cell-to-cell spread, and speed of entry. HCV mutations can lead to (A) increased production of viral particles, thus increasing the number of infectious particles at any given concentration of antibody; (B) increased cell-to-cell spread, resulting in an increase in viral particles avoiding NAbs present in the extracellular environment; and (C) increased speed of entry, affording NAbs in shorter time to interact with their epitopes on the viral particles in the extracellular environment.