High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease

Hedegaard, Ditte L.; Tully, Damien C.; Rowe, Ian A.; Reynolds, Gary M.; Bean, David J.; Hu, Ke; Davis, Christopher; Wilhelm, Annika; Ogilvie, Colin B.; Power, Karen A.; Tarr, Alexander W.; Kelly, Deirdre; Allen, Todd M.; Balfe, Peter; McKeating, Jane A.

Abstract

Background & Aims

The high replication and mutation rate of hepatitis C virus (HCV) results in a heterogeneous population of viral sequences in vivo. HCV replicates in the liver and infected hepatocytes occur as foci surrounded by uninfected cells that may promote compartmentalization of viral variants. Given recent reports showing interferon stimulated gene (ISG) expression in chronic hepatitis C, we hypothesized that local interferon responses may limit HCV replication and evolution.
Methods

To investigate the spatial influence of liver architecture on viral replication we measured HCV RNA and ISG mRNA from each of the 8 Couinaud segments of the liver from 21 patients undergoing liver transplant.
Results

HCV RNA and ISG mRNA levels were comparable across all sites from an individual liver but showed up to 500-fold difference between patients. Importantly, there was no association between ISG and HCV RNA expression across all sites in the liver or plasma. Deep sequencing of HCV RNA isolated from the 8 hepatic sites from two subjects showed a similar distribution of viral quasispecies across the liver and uniform sequence diversity. Single genome amplification of HCV E1E2-envelope clones from 6 selected patients at 2 hepatic sites supported these data and showed no evidence for HCV compartmentalization.
Conclusions

We found no differences between the hepatic and plasma viral quasispecies in all patients sampled. We conclude that in end-stage liver disease HCV RNA levels and the genetic pool of HCV envelope sequences are indistinguishable between distant sites in the liver and plasma, arguing against viral compartmentalization.

Citation

Hedegaard, D. L., Tully, D. C., Rowe, I. A., Reynolds, G. M., Bean, D. J., Hu, K., Davis, C., Wilhelm, A., Ogilvie, C. B., Power, K. A., Tarr, A. W., Kelly, D., Allen, T. M., Balfe, P., & McKeating, J. A. (2017). High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease. Journal of Hepatology, 66(1), 28-38. https://doi.org/10.1016/j.jhep.2016.07.048

• Journal Article Type: Article
• Acceptance Date: Jul 29, 2016
• Online Publication Date: Aug 13, 2016
• Publication Date: Jan 1, 2017
• Deposit Date: Feb 13, 2017
• Publicly Available Date: Feb 13, 2017
• Journal: Journal of Hepatology
• Print ISSN: 0168-8278
• Electronic ISSN: 1600-0641
• Publisher: Elsevier
• Peer Reviewed: Peer Reviewed
• Volume: 66
• Issue: 1
• Pages: 28-38
• DOI: https://doi.org/10.1016/j.jhep.2016.07.048
• Keywords: Hepatitis C; ESLD; Evolution; Compartmentalization; Innate immunity
• Public URL: https://nottingham-repository.worktribe.com/output/970968
• Publisher URL: http://www.sciencedirect.com/science/article/pii/S016882781630424X
• Additional Information: This article is maintained by: Elsevier; Article Title: High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease; Journal Title: Journal of Hepatology; CrossRef DOI link to publisher maintained version: https://doi.org/10.1016/j.jhep.2016.07.048; Content Type: article; Copyright: © 2016 European Association for the Study of the Liver. Published by Elsevier B.V.
• Contract Date: Feb 13, 2017