Naturally selected hepatitis C virus polymorphisms confer broad neutralizing antibody resistance
Justin R. Bailey, … , Steven K.H. Foung, Stuart C. Ray
Justin R. Bailey, … , Steven K.H. Foung, Stuart C. Ray
Published December 15, 2014
Citation Information: J Clin Invest. 2015;125(1):437-447. https://doi.org/10.1172/JCI78794.
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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 3

Sequence analysis reveals polymorphisms associated with neutralization resistance.

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Sequence analysis reveals polymorphisms associated with neutralization r...
(A) Representative E1E2 sequence analysis to identify mAb HC84.22 resistance-associated polymorphisms. Similar analyses for the remaining NC1 mAbs are shown in Supplemental Figure 4. E1E2 clones are ranked by increasing resistance to HC84.22. Clones are grouped into the 5 most sensitive, 7 with intermediate resistance, and 7 with greatest resistance, separated by horizontal black lines. Gray vertical bars indicate positions with a substitution in any resistant E1E2 clone but in none of the 5 most sensitive E1E2 clones. Black vertical bars indicate CD81-binding sites in E2 determined by alanine scanning. Blue vertical bars indicate critical binding residues for HC84.22 determined by alanine scanning. Sites with substitutions in at least 2 resistant clones but in no sensitive clones are included in the summary panel in the bottom row. (A–C) Sites marked with red are predominantly polymorphic in the 7 most resistant clones. Orange indicates sites that are polymorphic in an equal number of highly resistant and intermediate resistant clones. Green indicates sites that are predominantly polymorphic in the 7 clones with intermediate resistance. (B) Compiled results for all NC1 mAbs. (C) Resistance-associated polymorphisms, with the more commonly observed polymorphism listed first. The amino acid found at each position in the 5 most neutralization-sensitive E1E2 clones is indicated in the top row. Black boxes indicate positions at which results from this analysis are concordant with alanine scanning mutagenesis results with the same mAb.