Interplay of Host and Viral Genetic Variations in Modulating Antibody Responses to Genotype 3a Hepatitis C Virus: Implications for Vaccine Design

Abstract Hepatitis C virus (HCV) exhibits significant genetic diversity and is a of cause severe liver complications, including liver failure and hepatocellular carcinoma. The envelope glycoproteins E1 and E2 of HCV are the primary targets for the humoral immune response and have the highest sequence diversity in the HCV genome. The humoral immune response to HCV infection may be modulated by host and virus genetic factors. Here, using virus sequencing and host genetic data, as well as antibody binding and neutralization assays from 54 patients infected with HCV subtype 3a virus, we investigated the factors associated with antibody binding and neutralization. Genetic variation in the host IFNL4 gene were associated with antibody binding response, with the IFNλ4-P70 variant associated with reduced binding relative to IFNλ4-Null variant. Testing for association between all variable amino acids in HCV E1 and E2 glycoproteins and antibody response, we discovered two sites in or near the CD81 binding sites in E2 (sites 501 and 533) that were associated with neutralization sensitivity, along with an additional site in E2 (653) that was associated with binding. Additionally, motifs at two glycosylation sites (N476 and N234) were associated with binding and/or neutralisation. Furthermore, an increase in intra-patient hypervariable region 1 (HVR1) diversity was associated with stronger binding response. By considering the complex factors that influence antibody binding and neutralization, future vaccine strategies can be designed to elicit a robust immune response against a diverse range of HCV strains, addressing the needs of a diverse population. Competing Interest Statement The authors have declared no competing interest. Funding Statement We thank HCV Research UK (funded by the Medical Research Foundation) for their assistance in handling and coordinating the release of samples for these analyses. This work was funded by a grant from the Medical Research Council (MRC) (MR/K01532X/1; to the STOP-HCV Consortium). This work was supported by the Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Science (CIFMS), China (grant 2018-I2M-2-002). M.A.A. is supported by a Sir Henry Dale Fellowship jointly funded by the Royal Society and the Wellcome Trust (220171/Z/20/Z). PK was funded by a Wellcome Trust grant(222426/Z/21/Z). Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: This study used samples from 60 patients with HCV infection selected from BOSON clinical trial (Foster et al., 2015) (registration number: NCT01962441). The study protocol was approved by each institution's review board or ethics committee before study initiation. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Footnotes Email address zhiqing.wang{at}stcatz.ox.ac.uk (Zhiqing Wang) i.s.humphreys{at}bham.ac.uk (Isla Humphreys) jocelyn.quistrebert{at}ndm.ox.ac.uk (Jocelyn Quistrebert) haiting.chai{at}ndm.ox.ac.uk (Haiting Chai) joshdhir10{at}gmail.com (Josh Dhir) Alexandru.nisioi{at}gmail.com (Alexandru Nisioi) Paul.radford{at}nottingham.ac.uk (Paul Radford) jonathan.ball{at}nottingham.ac.uk (Jonathan K. Ball) will.irving{at}nottingham.ac.uk (William L. Irving) paul.klenerman{at}ndm.ox.ac.uk (Paul Klenerman) ellie.barnes{at}ndm.ox.ac.uk (Eleanor Barnes) jane.mckeating{at}ndm.ox.ac.uk (Jane A. McKeating) Data Availability All data produced in the present study are available upon reasonable request to the authors