Naturally selected hepatitis C virus polymorphisms confer broad neutralizing antibody resistance
Justin R. Bailey, Lisa N. Wasilewski, Anna E. Snider, Ramy El-Diwany, William O. Osburn, Zhenyong Keck, Steven K.H. Foung, Stuart C. Ray
Justin R. Bailey, Lisa N. Wasilewski, Anna E. Snider, Ramy El-Diwany, William O. Osburn, Zhenyong Keck, Steven K.H. Foung, Stuart C. Ray
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Research Article

Naturally selected hepatitis C virus polymorphisms confer broad neutralizing antibody resistance

Abstract

For hepatitis C virus (HCV) and other highly variable viruses, broadly neutralizing mAbs are an important guide for vaccine development. The development of resistance to anti-HCV mAbs is poorly understood, in part due to a lack of neutralization testing against diverse, representative panels of HCV variants. Here, we developed a neutralization panel expressing diverse, naturally occurring HCV envelopes (E1E2s) and used this panel to characterize neutralizing breadth and resistance mechanisms of 18 previously described broadly neutralizing anti-HCV human mAbs. The observed mAb resistance could not be attributed to polymorphisms in E1E2 at known mAb-binding residues. Additionally, hierarchical clustering analysis of neutralization resistance patterns revealed relationships between mAbs that were not predicted by prior epitope mapping, identifying 3 distinct neutralization clusters. Using this clustering analysis and envelope sequence data, we identified polymorphisms in E2 that confer resistance to multiple broadly neutralizing mAbs. These polymorphisms, which are not at mAb contact residues, also conferred resistance to neutralization by plasma from HCV-infected subjects. Together, our method of neutralization clustering with sequence analysis reveals that polymorphisms at noncontact residues may be a major immune evasion mechanism for HCV, facilitating viral persistence and presenting a challenge for HCV vaccine development.

Authors

Justin R. Bailey, Lisa N. Wasilewski, Anna E. Snider, Ramy El-Diwany, William O. Osburn, Zhenyong Keck, Steven K.H. Foung, Stuart C. Ray

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Figure 8

I538V/Q546L/T563V mutations in E2 confer resistance to 6 NC1 mAbs by reducing mAb binding to E1E2.

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I538V/Q546L/T563V mutations in E2 confer resistance to 6 NC1 mAbs by red...
(A) The first bar in each graph indicates relative infection of wild-type pp1b09 in the presence of the indicated mAb, adjusted to 1. Subsequent bars indicate fold change in neutralization resistance of the indicated HCVpp relative to pp1b09. Values are the means of 2 to 6 independent experiments performed in duplicate, and error bars indicate SD. *P < 0.05, **P < 0.005 by t test. (B) Binding of mAbs CBH-2 and AR3C to E1E2 protein in an ELISA. For each mAb, binding to each of the E1E2 variants was compared at a single mAb concentration selected to produce binding within the linear range of the assay. Values are normalized for relative binding of control NC2 mAb HC33.4. Error bars indicate SD between duplicate wells. (C) Crystal structure from Kong et al. of E2 core with AR3C (34), from the Protein Data Bank, accession 4MWF, with E2 colors modified as in Figure 5. Residue 431 is purple, residue 442 is orange, and residues 538 and 563 are blue. The likely position of residue 546 is indicated with a blue asterisk. AR3C Fab is tan.