Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation
Copyright policy )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 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.
- German Center for Infection Research Germany
- École Polytechnique Fédérale de Lausanne EPFL Switzerland
- Chinese University of Hong Kong China (People's Republic of)
- King’s University United States
- Deutsche Zentren der Gesundheitsforschung Germany
Hepatitis B virus, Other subheadings::Other subheadings::Other subheadings::/genetics, FENÓMENOS Y PROCESOS::fenómenos genéticos::estructuras genéticas::genoma::genoma microbiano::genoma viral, PHENOMENA AND PROCESSES::Microbiological Phenomena::Host-Pathogen Interactions, Virus de l'hepatitis B - Aspectes genètics, Epitopes, T-Lymphocyte, Organic Anion Transporters, Sodium-Dependent, Genome, Viral, Article, Hepatitis B, Chronic, Microorganismes patògens, ORGANISMOS::virus::virus ADN::Hepadnaviridae::Orthohepadnavirus::virus de la hepatitis B, Otros calificadores::Otros calificadores::Otros calificadores::/genética, Humans, Humans; Hepatitis B virus/genetics; Organic Anion Transporters, Sodium-Dependent/genetics; Organic Anion Transporters, Sodium-Dependent/metabolism; Symporters/genetics; Symporters/metabolism; Mutation; Host-Pathogen Interactions/genetics; Host-Pathogen Interactions/immunology; Hepatitis B, Chronic/virology; Hepatitis B, Chronic/genetics; Genome, Viral; Hepatitis B Surface Antigens/genetics; Epitopes, T-Lymphocyte/genetics; Epitopes, T-Lymphocyte/immunology; Genomics/methods; Histocompatibility Antigens Class I/genetics; Histocompatibility Antigens Class I/metabolism; HBV entry; escape variants; evolutionary genomics; hepatitis B virus; host-pathogen genomics; immunogenetics; selection; viral restriction, ORGANISMS::Viruses::DNA Viruses::Hepadnaviridae::Orthohepadnavirus::Hepatitis B virus, FENÓMENOS Y PROCESOS::fenómenos genéticos::variación genética::mutación, Hepatitis B Surface Antigens, Symporters, Histocompatibility Antigens Class I, Genomes bacterians, Genomics, PHENOMENA AND PROCESSES::Genetic Phenomena::Genetic Structures::Genome::Genome, Microbial::Genome, Viral, Anomalies cromosòmiques, PHENOMENA AND PROCESSES::Genetic Phenomena::Genetic Variation::Mutation, FENÓMENOS Y PROCESOS::fenómenos microbiológicos::interacciones huésped-patógeno, Host-Pathogen Interactions, Mutation
Hepatitis B virus, Other subheadings::Other subheadings::Other subheadings::/genetics, FENÓMENOS Y PROCESOS::fenómenos genéticos::estructuras genéticas::genoma::genoma microbiano::genoma viral, PHENOMENA AND PROCESSES::Microbiological Phenomena::Host-Pathogen Interactions, Virus de l'hepatitis B - Aspectes genètics, Epitopes, T-Lymphocyte, Organic Anion Transporters, Sodium-Dependent, Genome, Viral, Article, Hepatitis B, Chronic, Microorganismes patògens, ORGANISMOS::virus::virus ADN::Hepadnaviridae::Orthohepadnavirus::virus de la hepatitis B, Otros calificadores::Otros calificadores::Otros calificadores::/genética, Humans, Humans; Hepatitis B virus/genetics; Organic Anion Transporters, Sodium-Dependent/genetics; Organic Anion Transporters, Sodium-Dependent/metabolism; Symporters/genetics; Symporters/metabolism; Mutation; Host-Pathogen Interactions/genetics; Host-Pathogen Interactions/immunology; Hepatitis B, Chronic/virology; Hepatitis B, Chronic/genetics; Genome, Viral; Hepatitis B Surface Antigens/genetics; Epitopes, T-Lymphocyte/genetics; Epitopes, T-Lymphocyte/immunology; Genomics/methods; Histocompatibility Antigens Class I/genetics; Histocompatibility Antigens Class I/metabolism; HBV entry; escape variants; evolutionary genomics; hepatitis B virus; host-pathogen genomics; immunogenetics; selection; viral restriction, ORGANISMS::Viruses::DNA Viruses::Hepadnaviridae::Orthohepadnavirus::Hepatitis B virus, FENÓMENOS Y PROCESOS::fenómenos genéticos::variación genética::mutación, Hepatitis B Surface Antigens, Symporters, Histocompatibility Antigens Class I, Genomes bacterians, Genomics, PHENOMENA AND PROCESSES::Genetic Phenomena::Genetic Structures::Genome::Genome, Microbial::Genome, Viral, Anomalies cromosòmiques, PHENOMENA AND PROCESSES::Genetic Phenomena::Genetic Variation::Mutation, FENÓMENOS Y PROCESOS::fenómenos microbiológicos::interacciones huésped-patógeno, Host-Pathogen Interactions, Mutation
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