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Holmes JA, Congiu M, Bonanzinga S, Sandhu MK, Kia YH, Bell SJ, Nguyen T, Iser DM, Visvanathan K, Sievert W, Bowden DS, Desmond PV, Thompson AJ. The relationships between IFNL4 genotype, intrahepatic interferon-stimulated gene expression and interferon treatment response differs in HCV-1 compared with HCV-3. Aliment Pharmacol Ther 2015; 42:296-306. [PMID: 26032235 DOI: 10.1111/apt.13263] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/02/2015] [Accepted: 05/09/2015] [Indexed: 12/19/2022]
Abstract
BACKGROUND The biological mechanism underlying the association between IFNL4/IFNL3 polymorphism and peginterferon/ribavirin (PR) response in HCV-1 is thought to involve differential intrahepatic interferon-stimulated gene expression. HCV-3 is more sensitive to PR, but there are no studies of the association between IFNL4 polymorphism, PR treatment response and liver interferon-stimulated gene expression in HCV-3. AIM We evaluated the association between IFNL4/IFNL3 genotypes, PR treatment outcomes and intrahepatic interferon-stimulated gene expression, according to HCV genotype. METHODS HCV-1 and HCV-3 patients who received PR therapy were identified. IFNL3 (rs12979860) and IFNL4 genotype (rs368234815) were determined. A second cohort with stored liver specimens was identified. Expression of ISGs was measured by rt-PCR. RESULTS Two hundred and fifty-nine patients were identified: 55% HCV-1, 45% HCV-3. IFNL4 genotype frequency was TT/TT 44%, TT/ΔG 42% andΔG/ΔG 14%. Linkage disequilibrium with IFNL3 genotype was high (r(2) = 0.98). The association between IFNL4 genotype and PR response was attenuated in HCV-3 vs. HCV-1 (HCV-3: SVR 89% vs. 76% vs. 72% for TT/TT vs. TT/ΔG vs. ΔG/ΔG, P = 0.09; HCV-1: SVR: 82% vs. 29% vs. 24%, P < 0.001). Intrahepatic ISG expression was evaluated in 92 patients; 61% HCV-1. The association between IFNL4 genotype and liver ISG expression was significantly different for HCV-3 vs. HCV-1 (P-value for interaction = 0.046), with levels of interferon-stimulated gene expression being highest in HCV-1 patients who carried a poor-response IFNL4 genotype. CONCLUSIONS The relationship between IFNL4 genotype and PR treatment response as well as intrahepatic interferon-stimulated gene expression differs between HCV-1 and HCV-3. These data suggest fundamental differences in host-virus interactions according to HCV genotype.
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Affiliation(s)
- J A Holmes
- Department of Gastroenterology, St Vincent's Hospital, The University of Melbourne, Fitzroy, Vic., Australia
| | - M Congiu
- Department of Gastroenterology, St Vincent's Hospital, The University of Melbourne, Fitzroy, Vic., Australia
| | - S Bonanzinga
- Victorian Infectious Diseases Reference Laboratory, The Doherty Institute, Melbourne, Vic., Australia
| | - M K Sandhu
- Department of Gastroenterology, St Vincent's Hospital, The University of Melbourne, Fitzroy, Vic., Australia
| | - Y H Kia
- Department of Gastroenterology, St Vincent's Hospital, The University of Melbourne, Fitzroy, Vic., Australia
| | - S J Bell
- Department of Gastroenterology, St Vincent's Hospital, The University of Melbourne, Fitzroy, Vic., Australia
| | - T Nguyen
- Department of Gastroenterology, St Vincent's Hospital, The University of Melbourne, Fitzroy, Vic., Australia
| | - D M Iser
- Department of Gastroenterology, St Vincent's Hospital, The University of Melbourne, Fitzroy, Vic., Australia
| | - K Visvanathan
- Immunology Research Centre, St Vincent's Hospital, The University of Melbourne, Fitzroy, Vic., Australia
| | - W Sievert
- Department of Gastroenterology, Monash Medical Centre, Monash University, Clayton, Vic., Australia
| | - D S Bowden
- Victorian Infectious Diseases Reference Laboratory, The Doherty Institute, Melbourne, Vic., Australia
| | - P V Desmond
- Department of Gastroenterology, St Vincent's Hospital, The University of Melbourne, Fitzroy, Vic., Australia
| | - A J Thompson
- Department of Gastroenterology, St Vincent's Hospital, The University of Melbourne, Fitzroy, Vic., Australia
- Victorian Infectious Diseases Reference Laboratory, The Doherty Institute, Melbourne, Vic., Australia
- Department of Gastroenterology, Duke University Medical Centre, Duke Clinical Research Institute, Durham, NC, USA
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Smith DB, Bukh J, Kuiken C, Muerhoff AS, Rice CM, Stapleton JT, Simmonds P. Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource. Hepatology 2014; 59:318-27. [PMID: 24115039 PMCID: PMC4063340 DOI: 10.1002/hep.26744] [Citation(s) in RCA: 924] [Impact Index Per Article: 92.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 08/29/2013] [Indexed: 12/11/2022]
Abstract
UNLABELLED The 2005 consensus proposal for the classification of hepatitis C virus (HCV) presented an agreed and uniform nomenclature for HCV variants and the criteria for their assignment into genotypes and subtypes. Since its publication, the available dataset of HCV sequences has vastly expanded through advancement in nucleotide sequencing technologies and an increasing focus on the role of HCV genetic variation in disease and treatment outcomes. The current study represents a major update to the previous consensus HCV classification, incorporating additional sequence information derived from over 1,300 (near-)complete genome sequences of HCV available on public databases in May 2013. Analysis resolved several nomenclature conflicts between genotype designations and using consensus criteria created a classification of HCV into seven confirmed genotypes and 67 subtypes. There are 21 additional complete coding region sequences of unassigned subtype. The study additionally describes the development of a Web resource hosted by the International Committee for Taxonomy of Viruses (ICTV) that maintains and regularly updates tables of reference isolates, accession numbers, and annotated alignments (http://talk.ictvonline.org/links/hcv/hcv-classification.htm). The Flaviviridae Study Group urges those who need to check or propose new genotypes or subtypes of HCV to contact the Study Group in advance of publication to avoid nomenclature conflicts appearing in the literature. While the criteria for assigning genotypes and subtypes remain unchanged from previous consensus proposals, changes are proposed in the assignment of provisional subtypes, subtype numbering beyond "w," and the nomenclature of intergenotypic recombinant. CONCLUSION This study represents an important reference point for the consensus classification of HCV variants that will be of value to researchers working in clinical and basic science fields.
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Affiliation(s)
- Donald B Smith
- Centre for Immunity, Infection and Evolution, University of EdinburghScotland, UK
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, and Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of CopenhagenDenmark
| | - Carla Kuiken
- Theoretical Biology and Biophysics group, Los Alamos National LaboratoryLos Alamos, NM, USA
| | | | - Charles M Rice
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller UniversityNew York, NY, USA
| | - Jack T Stapleton
- Medical Service, Iowa City Veterans Affairs Medical Center, Departments of Internal Medicine and Microbiology, University of IowaIowa City, IA, USA
| | - Peter Simmonds
- Centre for Immunity, Infection and Evolution, University of EdinburghScotland, UK
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Bunchorntavakul C, Chavalitdhamrong D, Tanwandee T. Hepatitis C genotype 6: A concise review and response-guided therapy proposal. World J Hepatol 2013; 5:496-504. [PMID: 24073301 PMCID: PMC3782687 DOI: 10.4254/wjh.v5.i9.496] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 08/05/2013] [Accepted: 08/13/2013] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C genotype 6 is endemic in Southeast Asia [prevalence varies between 10%-60% among all hepatitis C virus (HCV) infection], as well as also sporadically reported outside the area among immigrations. The diagnosis of HCV genotype can be inaccurate with earlier methods of genotyping due to identical 5’-UTR between genotype 6 and 1b, hence the newer genotyping methods with core sequencing are preferred. Risk factors and clinical course of HCV genotype 6 do not differ considerably from other genotypes. Treatment outcome of HCV genotype 6 with a combination of pegylated interferon and ribavirin is superior to genotype 1, and nearly comparable to genotype 3, with expected sustained virological response (SVR) rates of 60%-90%. Emerging data suggests that a shorter course 24-wk treatment is equally effective as a standard 48-wk treatment, particularly for those patients who attained undetectable HCV RNA at week 4 (RVR). In addition, baseline and on-treatment predictors of response used for other HCV genotypes appear effective with genotype 6. Although some pan-genotypic direct-acting antivirals have completed phase II/III studies (sofosbuvir and simeprevir) with clinical benefit demonstrated in small number of patients with genotype 6, broad availability of these agents in Southeast Asia may not be expected in the near future. While awaiting the newer therapy, response-guided therapy seems appropriate for patients with HCV genotype 6. Patients with RVR (representing > 70% of patients) are suitable for 24-wk treatment with expected SVR rates > 80%. Patients without RVR and/or those with poor response predictors may benefit from 48 wk of therapy, and a detectable HCV RNA at week 12 (with no early virological response) serves as a stopping rule. This treatment scheme is likely to have a major economic impact on HCV therapy, particularly in Southeast Asia, wherein treatment can be truncated securely in the majority of patients with HCV genotype 6.
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Khaliq S, Latief N, Jahan S. Role of different regions of the hepatitis C virus genome in the therapeutic response to interferon-based treatment. Arch Virol 2013; 159:1-15. [PMID: 23851652 DOI: 10.1007/s00705-013-1780-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 05/28/2013] [Indexed: 12/21/2022]
Abstract
Hepatitis C virus (HCV) is considered a significant risk factor in HCV-induced liver diseases and development of hepatocellular carcinoma (HCC). Nucleotide substitutions in the viral genome result in its diversification into quasispecies, subtypes and distinct genotypes. Different genotypes vary in their infectivity and immune response due to these nucleotide/amino acid variations. The current combination treatment for HCV infection is pegylated interferon α (PEG-IFN-α) with ribavirin, with a highly variable response rate mainly depending upon the HCV genotype. Genotypes 2 and 3 are found to respond better than genotypes 1 and 4, which are more resistant to IFN-based therapies. Different studies have been conducted worldwide to explore the basis of this difference in therapy response, which identified some putative regions in the HCV genome, especially in Core and NS5a, and to some extent in the E2 region, containing specific sequences in different genotypes that act differently with respect to the IFN response. In the review, we try to summarize the role of HCV proteins and their nucleotide sequences in association with treatment outcome in IFN-based therapy.
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Affiliation(s)
- Saba Khaliq
- Department of Immunology, University of Health Sciences, Lahore, Pakistan,
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Zhou XM, Chan PKS, Tam JS. Mutations around interferon sensitivity-determining region: A pilot resistance report of hepatitis C virus 1b in a Hong Kong population. World J Gastroenterol 2011; 17:5317-23. [PMID: 22219602 PMCID: PMC3247697 DOI: 10.3748/wjg.v17.i48.5317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 10/28/2011] [Accepted: 11/05/2011] [Indexed: 02/06/2023] Open
Abstract
AIM: To explore mutations around the interferon sensitivity-determining region (ISDR) which are associated with the resistance of hepatitis C virus 1b (HCV-1b) to interferon-α treatment.
METHODS: Thirty-seven HCV-1b samples were obtained from Hong Kong patients who had completed the combined interferon-α/ribavirin treatment for more than one year with available response data. Nineteen of them were sustained virological responders, while 18 were non-responders. The amino acid sequences of the extended ISDR (eISDR) covering 64 amino acids upstream and 67 amino acids downstream from the previously reported ISDR were analyzed.
RESULTS: One amino acid variation (I2268V, P = 0.023) was significantly correlated with treatment outcome in this pilot study with a limited number of patients, while two amino acid variations (R2260H, P = 0.05 and S2278T, P = 0.05) were weakly associated with treatment outcome. The extent of amino acid variations within the ISDR or eISDR was not correlated with treatment outcome as previously reported.
CONCLUSION: Three amino acid mutations near but outside of ISDR may associate with interferon treatment resistance of HCV-1b patients in Hong Kong.
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