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Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation

Evolutionary changes in the hepatitis B virus (HBV) genome could reflect its adaptation to host-induced selective pressure. Leveraging paired human exome and ultra-deep HBV genome-sequencing data from 567 affected individuals with chronic hepatitis B, we comprehensively searched for the signatures o...

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Main Authors: Xu, Zhi Ming (Author) , Gnouamozi, Gnimah Eva (Author) , Rüeger, Sina (Author) , Shea, Patrick R. (Author) , Buti, Maria (Author) , Chan, Henry Ly (Author) , Marcellin, Patrick (Author) , Lawless, Dylan (Author) , Naret, Olivier (Author) , Zeller, Matthias (Author) , Schneuing, Arne (Author) , Scheck, Andreas (Author) , Junier, Thomas (Author) , Moradpour, Darius (Author) , Podlaha, Ondrej (Author) , Suri, Vithika (Author) , Gaggar, Anuj (Author) , Subramanian, Mani (Author) , Correia, Bruno (Author) , Gfeller, David (Author) , Urban, Stephan (Author) , Fellay, Jacques (Author)
Format: Article (Journal)
Language:English
Published: 14 May 2024
In: The American journal of human genetics
Year: 2024, Volume: 111, Issue: 6, Pages: 1018-1034
ISSN:1537-6605
DOI:10.1016/j.ajhg.2024.04.013
Online Access:Verlag, kostenfrei, Volltext: https://doi.org/10.1016/j.ajhg.2024.04.013
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Author Notes:Zhi Ming Xu, Gnimah Eva Gnouamozi, Sina Rüeger, Patrick R. Shea, Maria Buti, Henry Ly Chan, Patrick Marcellin, Dylan Lawless, Olivier Naret, Matthias Zeller, Arne Schneuing, Andreas Scheck, Thomas Junier, Darius Moradpour, Ondrej Podlaha, Vithika Suri, Anuj Gaggar, Mani Subramanian, Bruno Correia, David Gfeller, Stephan Urban, and Jacques Fellay
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Summary:Evolutionary changes in the hepatitis B virus (HBV) genome could reflect its adaptation to host-induced selective pressure. Leveraging paired human exome and ultra-deep HBV genome-sequencing data from 567 affected individuals with chronic hepatitis B, we comprehensively searched for the signatures of this evolutionary process by conducting "genome-to-genome" association tests between all human genetic variants and viral mutations. We identified significant associations between an East Asian-specific missense variant in the gene encoding the HBV entry receptor NTCP (rs2296651, NTCP S267F) and mutations within the receptor-binding region of HBV preS1. Through in silico modeling and in vitro preS1-NTCP binding assays, we observed that the associated HBV mutations are in proximity to the NTCP variant when bound and together partially increase binding affinity to NTCP S267F. Furthermore, we identified significant associations between HLA-A variation and viral mutations in HLA-A-restricted T cell epitopes. We used in silico binding prediction tools to evaluate the impact of the associated HBV mutations on HLA presentation and observed that mutations that result in weaker binding affinities to their cognate HLA alleles were enriched. Overall, our results suggest the emergence of HBV escape mutations that might alter the interaction between HBV PreS1 and its cellular receptor NTCP during viral entry into hepatocytes and confirm the role of HLA class I restriction in inducing HBV epitope variations.
Item Description:Gesehen am 21.02.2025
Physical Description:Online Resource
ISSN:1537-6605
DOI:10.1016/j.ajhg.2024.04.013

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