High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease
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 vira...
| Main Authors: | , , , , , , , , , , , , , , |
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Elsevier
2017
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| Online Access: | https://eprints.nottingham.ac.uk/40558/ |
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| author | 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. |
| author_facet | 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. |
| author_sort | Hedegaard, Ditte L. |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-14T19:42:23Z |
| format | Article |
| id | nottingham-40558 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T19:42:23Z |
| publishDate | 2017 |
| publisher | Elsevier |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-405582020-05-04T19:59:03Z https://eprints.nottingham.ac.uk/40558/ 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. 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. Elsevier 2017-01 Article PeerReviewed 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 and McKeating, Jane A. (2017) High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease. Journal of Hepatology, 66 (1). pp. 28-38. ISSN 1600-0641 Hepatitis C; ESLD; Evolution; Compartmentalization; Innate immunity http://www.sciencedirect.com/science/article/pii/S016882781630424X 10.1016/j.jhep.2016.07.048 10.1016/j.jhep.2016.07.048 10.1016/j.jhep.2016.07.048 |
| spellingShingle | Hepatitis C; ESLD; Evolution; Compartmentalization; Innate immunity 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. High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease |
| title | High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease |
| title_full | High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease |
| title_fullStr | High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease |
| title_full_unstemmed | High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease |
| title_short | High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease |
| title_sort | high resolution sequencing of hepatitis c virus reveals limited intra-hepatic compartmentalization in end-stage liver disease |
| topic | Hepatitis C; ESLD; Evolution; Compartmentalization; Innate immunity |
| url | https://eprints.nottingham.ac.uk/40558/ https://eprints.nottingham.ac.uk/40558/ https://eprints.nottingham.ac.uk/40558/ |