Genome-to-genome analysis highlights the impact of the human innate and adaptive immune systems on the hepatitis C virus

Outcomes of hepatitis C virus (HCV) infection and treatment depend on viral and host genetic factors. We use human genome-wide genotyping arrays and new whole-genome HCV viral sequencing technologies to perform a systematic genome-to-genome study of 542 individuals chronically infected with HCV, predominately genotype 3. We show that both HLA alleles and interferon lambda innate immune system genes drive viral genome polymorphism, and that IFNL4 genotypes determine HCV viral load through a mechanism that is dependent on a specific polymorphism in the HCV polyprotein. We highlight the interplay between innate immune responses and the viral genome in HCV control.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 3 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00010001202	Human genotyping data for patients infected by hepatitis C virus	Affymetrix UKBiobank Array	563

Publications	Citations
Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus. Ansari MA, Pedergnana V, L C Ip C, Magri A, Von Delft A, Bonsall D, Chaturvedi N, Bartha I, Smith D, Nicholson G, McVean G, Trebes A, Piazza P, Fellay J, Cooke G, Foster GR, STOP-HCV Consortium, Hudson E, McLauchlan J, Simmonds P, Bowden R, Klenerman P, Barnes E, Spencer CCA. Nat Genet 49: 2017 666-673	72
Interferon lambda 4 impacts the genetic diversity of hepatitis C virus. Ansari MA, Aranday-Cortes E, Ip CL, da Silva Filipe A, Lau SH, Bamford C, Bonsall D, Trebes A, Piazza P, Sreenu V, Cowton VM, STOP-HCV Consortium, Hudson E, Bowden R, Patel AH, Foster GR, Irving WL, Irving WL, Agarwal K, Thomson EC, Simmonds P, Klenerman P, Holmes C, Barnes E, Spencer CC, McLauchlan J, Pedergnana V. Elife 8: 2019 e42463	22
Using host genetics to infer the global spread and evolutionary history of HCV subtype 3a. Lin SK, De Maio N, Pedergnana V, Wu CH, Thézé J, Wilson DJ, Barnes E, Ansari MA. Virus Evol 7: 2021 veab065	0