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Chatterjee K, Kalita D, Omar BJ, Gupta R, Jha MK, Gupta P. Hepatitis C virus subtyping in Uttarakhand, India: a comparative study. Virusdisease 2021; 32:576-581. [PMID: 34631982 DOI: 10.1007/s13337-021-00729-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 07/15/2021] [Indexed: 11/24/2022] Open
Abstract
The objective of this study was to compare Reverse Hybridisation Assay with conventional sequencing for determination of Hepatitis C Virus Genotype and Subtypes. Anti-HCV antibody was determined followed by HCV RNA extraction which was used for (1) viral load determination (2) qualitative real-time PCR RHA for genotyping and (3) conventional sequencing. Compared to conventional sequencing, accuracy of RHA results was 96.55% for determination of genotype (κ = 0.93) and 89.66% for subtype (κ = 0.85). Sensitivity, specificity, negative predictive value (NPV) and positive predictive value (PPV) of the qualitative PCR were 82.29%, 100%, 44.44% and 100% respectively with an accuracy of 86.84%. RHA is a less time consuming and cheaper method for determination of HCV genotype and subtype yet results must be interpreted with caution and quality control monitoring should be strictly followed to ensure validity. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-021-00729-9.
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Affiliation(s)
- Kuhu Chatterjee
- Department of Microbiology, All India Institute of Medical Sciences, Veerbhadra Marg, Dehradun, Rishikesh, 249203 Uttarakhand India
| | - Deepjyoti Kalita
- Department of Microbiology, All India Institute of Medical Sciences, Veerbhadra Marg, Dehradun, Rishikesh, 249203 Uttarakhand India
| | - Balram Ji Omar
- Department of Microbiology, All India Institute of Medical Sciences, Veerbhadra Marg, Dehradun, Rishikesh, 249203 Uttarakhand India
| | - Rohit Gupta
- Department of Gastroenterology, All India Institute of Medical Sciences, Rishikesh, India
| | - Mithilesh Kumar Jha
- Department of Microbiology, All India Institute of Medical Sciences, Veerbhadra Marg, Dehradun, Rishikesh, 249203 Uttarakhand India.,Department of Microbiology, All India Institute of Medical Sciences, Patna, India
| | - Pratima Gupta
- Department of Microbiology, All India Institute of Medical Sciences, Veerbhadra Marg, Dehradun, Rishikesh, 249203 Uttarakhand India
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Di Maio VC, Barbaliscia S, Teti E, Fiorentino G, Milana M, Paolucci S, Pollicino T, Morsica G, Starace M, Bruzzone B, Gennari W, Micheli V, Yu La Rosa K, Foroghi L, Calvaruso V, Lenci I, Polilli E, Babudieri S, Aghemo A, Raimondo G, Sarmati L, Coppola N, Pasquazzi C, Baldanti F, Parruti G, Perno CF, Angelico M, Craxì A, Andreoni M, Ceccherini-Silberstein F. Resistance analysis and treatment outcomes in hepatitis C virus genotype 3-infected patients within the Italian network VIRONET-C. Liver Int 2021; 41:1802-1814. [PMID: 33497016 DOI: 10.1111/liv.14797] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/29/2020] [Accepted: 01/14/2021] [Indexed: 12/20/2022]
Abstract
AIM This study aimed to investigate the role of resistance-associated substitutions (RASs) to direct-acting-antivirals (DAAs) in HCV genotype 3 (GT3). METHODS Within the Italian VIRONET-C network, a total of 539 GT3-infected patients (417 DAA-naïve and 135 DAA-failures, of them, 13 at both baseline and failure) were analysed. Sanger sequencing of NS3/NS5A/NS5B was performed following home-made protocols. RESULTS The majority of patients were male (79.4%), 91.4% were injection drug users, 49.3% were cirrhotic and 13.9% were HIV co-infected. Phylogenetic analysis classified sequences as GT3a-b-g-h (98%-0.4%-0.2%-1.2%) respectively. Overall, 135 patients failed a DAA regimen: sofosbuvir (SOF)/daclatasvir (DCV) or velpatasvir (VEL)±ribavirin (RBV) (N = 91/15) and glecaprevir (G)/pibrentasvir (P) (N = 9). Moreover, 14.8% of patients were treated with suboptimal regimens for GT3: 3D ± RBV (Paritaprevir/r + Ombitasvir+Dasabuvir, N = 15), SOF + Simeprevir (SIM) (N = 1) or SOF/Ledipasvir (LDV) ± RBV (N = 4). RAS prevalence was 15.8% in DAA-naïve patients. At failure, 81.5% patients showed at least one RAS: 11/25 (44.0%) in NS3, 109/135 (80.7%) in NS5A, 7/111 (6.3%) in NS5B SOF-failures. In NS5A-failures, Y93H RAS was the most prevalent (68.5% vs 5.1% DAA-naïve, P < .001) followed by A30K (12.7% vs 2.8% in DAA-naïve, P < .001). Analysing baseline samples, a higher prevalence of NS5A-RASs was observed before treatment in DAA-failures (5/13, 38.5%) vs DAA-naïves (61/393, 15.5%, P = .04). Regarding 228 DAA-naïve patients with an available outcome, 93.9% achieved a SVR. Interestingly, patients with baseline Y93H and/or A30K had SVR rate of 72.2% vs 95.7% for patients without NS5A-RASs (P = .002). CONCLUSIONS In this real-life GT3 cohort, the majority of failures harboured resistant variants carrying NS5A-RASs, the most frequent being Y93H. The presence of natural NS5A-RASs before treatment was associated with failure. Further analyses are needed to confirm this observation, particularly for the new current regimens.
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Affiliation(s)
- Velia Chiara Di Maio
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Silvia Barbaliscia
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Elisabetta Teti
- Infectious Diseases, University Hospital of Rome Tor Vergata, Rome, Italy
| | | | - Martina Milana
- Hepatology Unit, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Stefania Paolucci
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinic Foundation San Matteo, Pavia, Italy
| | - Teresa Pollicino
- Department of Internal Medicine, University Hospital of Messina, Messina, Italy
| | - Giulia Morsica
- Division of Infectious Diseases, IRCCS, Ospedale San Raffaele, Milan, Italy
| | - Mario Starace
- Laboratory for the identification of prognostic factors of response to the treatment against infectious diseases, University of Campania "L. Vanvitelli", Napoli, Italy
| | | | - William Gennari
- Microbiology Unit, University Hospital of Modena, Modena, Italy
| | - Valeria Micheli
- Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco University Hospital, Milan, Italy
| | - Katia Yu La Rosa
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Luca Foroghi
- Infectious Diseases, University Hospital of Rome Tor Vergata, Rome, Italy
| | | | - Ilaria Lenci
- Hepatology Unit, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Ennio Polilli
- Infectious Disease Unit, Pescara General Hospital, Pescara, Italy
| | - Sergio Babudieri
- Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Alessio Aghemo
- Division of Internal Medicine and Hepatology, Humanitas Clinical and Research Center IRCCS, Rozzano, Italy
| | - Giovanni Raimondo
- Department of Internal Medicine, University Hospital of Messina, Messina, Italy
| | - Loredana Sarmati
- Infectious Diseases, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Nicola Coppola
- Laboratory for the identification of prognostic factors of response to the treatment against infectious diseases, University of Campania "L. Vanvitelli", Napoli, Italy.,Department of Mental Health and Public Medicine, Infectious Diseases Unit, University of Campania "L. Vanvitelli", Naples, Italy
| | | | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinic Foundation San Matteo, Pavia, Italy
| | - Giustino Parruti
- Infectious Disease Unit, Pescara General Hospital, Pescara, Italy
| | | | - Mario Angelico
- Hepatology Unit, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Antonio Craxì
- Gastroenterology, "P. Giaccone" University Hospital, Palermo, Italy
| | - Massimo Andreoni
- Infectious Diseases, University Hospital of Rome Tor Vergata, Rome, Italy
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NS5A resistance - associated substitutions in chronic hepatitis C patients with direct acting antiviral treatment failure in Turkey. Int J Infect Dis 2020; 95:84-89. [PMID: 32302766 DOI: 10.1016/j.ijid.2020.03.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 03/19/2020] [Accepted: 03/24/2020] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVES Chronic hepatitis C (CHC) is now a more curable disease with new direct acting antivirals (DAA). Although high sustained virologic response rates, failures still occur in DAA regimens. Our objective in this study was to characterize the real-life presence of clinically relevant resistance - associated substitutions (RASs) in the HCV NS5A gene in CHC patients whose DAA regimen has failed. METHODS The study enrolled 53 CHC patients who experienced failure with DAA regimen as the prospective longitudinal cohort between 2017-2019. Genotypic resistance testing was performed via the viral population sequencing method and The Geno2pheno HCV tool was used for RAS analysis. RESULTS The most frequent failure category was relapse (88%) followed by non-responder (12%). For a total of 36% of patients, RASs was detected in NS5A, Y93H was the most detected RAS in GT1b infected patients (89%). CONCLUSIONS This study establishes an HCV failure registry for Turkey in which samples were combined with clinical, virologic and molecular data of adult patients whose DAA therapy failed. RASs can occur in CHC patients with DAA treatment failures. Evaluation of RAS after DAA failure is very important before re-treatment is initiated to prevent virologic failure.
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4
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Kao JH, Lin CY, Chuang WL, Cheng YY, Hu JY, Liang WK, Friebe P, Palmer S, Huang CS. Clinical evaluation of IntelliPlex TM HCV genotyping kit for hepatitis C virus genotyping. Diagn Microbiol Infect Dis 2019; 94:344-348. [PMID: 30975461 DOI: 10.1016/j.diagmicrobio.2019.02.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 02/12/2019] [Accepted: 02/27/2019] [Indexed: 12/24/2022]
Abstract
Genotyping of the hepatitis C virus (HCV) is crucial for determining the most efficient anti-viral therapy. The clinical sensitivity and specificity of the IntelliPlexTM HCV Genotyping Kit was determined by comparing the assay results of 307 specimens with the results obtained by Sanger sequencing. Out of 202 HCV-positive specimens tested, 8 samples yielded discrepant results between the IntelliPlex HCV Genotyping Kit and Sanger sequencing. For 5 of these discrepant samples, the IntelliPlex HCV Genotyping Kit classified the correct genotype but failed to show the same single or dual infected status as determined by Sanger sequencing. A total of 105 samples which tested negative for HCV by In-Vitro-Diagnostics (IVD)-approved viral load assay tested negative for HCV by the IntelliPlex HCV Genotyping Kit. The IntelliPlex HCV Genotyping Kit has a clinical specificity of 100% and a clinical sensitivity of 96.9% and is suited to be used in clinical laboratories to genotype HCV.
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Affiliation(s)
- Jia-Horng Kao
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Division of Gastroenterology and Hepatology, the National Taiwan University Hospital, Taipei, Taiwan
| | - Chun-Yen Lin
- School of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Wan-Long Chuang
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University, Kaohsiung. Taiwan; Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | | | - Jui-Yu Hu
- PlexBio Co., Ltd., Neihu District, Taipei, Taiwan
| | | | - Peter Friebe
- PlexBio Co., Ltd., Neihu District, Taipei, Taiwan.
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Saludes V, Antuori A, Reinhardt B, Viciana I, Clavijo E, Schreiber L, Tenenbaum M, Rodriguez-Frias F, Quer J, Matas L, Martró E. Reliable resolution of ambiguous hepatitis C virus genotype 1 results with the Abbott HCV Genotype Plus RUO assay. Sci Rep 2019; 9:3678. [PMID: 30842623 PMCID: PMC6403303 DOI: 10.1038/s41598-019-40099-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/27/2018] [Indexed: 12/19/2022] Open
Abstract
Accurate subtyping of hepatitis C virus genotype 1 (HCV-1) remains clinically and epidemiologically relevant. The Abbott HCV Genotype Plus RUO (GT Plus) assay, targeting the core region, was evaluated as a reflex test to resolve ambiguous HCV-1 results in a challenging sample collection. 198 HCV-1 specimens were analysed with GT Plus (38 specimens with and 160 without subtype assigned by the Abbott RealTime Genotype II (GT II) assay targeting the 5'NC and NS5B regions). Sanger sequencing of the core and/or NS5B regions were performed in 127 specimens without subtype assignment by GT II, with "not detected" results by GT Plus, or with mixed genotypes/subtypes. The remaining GT Plus results were compared to LiPA 2.0 (n = 45) or just to GT II results if concordant (n = 26). GT Plus successfully assigned the subtype in 142/160 (88.8%) samples. "Not detected" results indicated other HCV-1 subtypes/genotypes or mismatches in the core region in subtype 1b. The subtyping concordance between GT Plus and either sequencing or LiPA was 98.6% (140/142). Therefore, combined use of GT II and GT Plus assays represents a reliable and simple approach which considerably reduced the number of ambiguous HCV-1 results and enabled a successful subtyping of 98.9% of all HCV-1 samples.
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Affiliation(s)
- V Saludes
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol; Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - A Antuori
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol; Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Badalona, Spain
| | | | - I Viciana
- Microbiology Service, Hospital Virgen de la Victoria, Málaga, Spain
| | - E Clavijo
- Microbiology Service, Hospital Virgen de la Victoria, Málaga, Spain
| | | | | | - F Rodriguez-Frias
- Liver Pathology Lab, Biochemistry and Microbiology Department, University Hospital Vall d'Hebron, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - J Quer
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Liver Unit, Liver Diseases-Viral Hepatitis, Vall d'Hebron Institute of Research (VHIR-HUVH), Barcelona, Spain
| | - L Matas
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol; Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Badalona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - E Martró
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol; Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Badalona, Spain.
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.
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6
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Bagaglio S, Messina E, Hasson H, Galli A, Uberti-Foppa C, Morsica G. Geographic Distribution of HCV-GT3 Subtypes and Naturally Occurring Resistance Associated Substitutions. Viruses 2019; 11:v11020148. [PMID: 30754682 PMCID: PMC6410151 DOI: 10.3390/v11020148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 01/07/2019] [Indexed: 02/07/2023] Open
Abstract
Background: Little is known about the frequency or geographic distributions of naturally occurring resistance-associated substitutions (RASs) in the nonstructural protein 5A (NS5A) domain of hepatitis-C virus (HCV) genotype-3 (GT-3) different subtypes. We investigated naturally occurring GT-3 RASs that confer resistance to NS5A inhibitors. Methods: From a publicly accessible database, we retrieved 58 complete GT-3 genomes and an additional 731 worldwide NS5A sequences from patients infected with GT-3 that were naive to direct-acting antiviral treatment. Results: We performed a phylogenetic analysis of NS5A domains in complete HCV genomes to determine more precisely HCV-GT-3 subtypes, based on commonly used target regions (e.g., 5′untranslated region and NS5B partial domain). Among 789 NS5A sequences, GT-3nonA subtypes were more prevalent in Asia than in other geographic regions (p < 0.0001). The A30K RAS was detected more frequently in HCV GT-3nonA (84.6%) than in GT-3A subtypes (0.8%), and the amino acid change was polymorphic in isolates from Asia. Conclusions: These results provided information on the accuracy of HCV-3 subtyping with a phylogenetic analysis of the NS5A domain with data from the Los Alamos HCV genome database. This information and the worldwide geographic distribution of RASs according to HCV GT-3 subtypes are crucial steps in meeting the challenges of treating HCV GT-3.
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Affiliation(s)
- Sabrina Bagaglio
- Division of Infectious Diseases, Ospedale San Raffaele, 20132 Milan, Italy.
| | - Emanuela Messina
- Division of Infectious Diseases, Ospedale San Raffaele, 20132 Milan, Italy.
| | - Hamid Hasson
- Division of Infectious Diseases, Ospedale San Raffaele, 20132 Milan, Italy.
| | - Andrea Galli
- Division of Infectious Diseases, Ospedale San Raffaele, 20132 Milan, Italy.
| | | | - Giulia Morsica
- Division of Infectious Diseases, Ospedale San Raffaele, 20132 Milan, Italy.
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Loggi E, Vukotic R, Andreone P. Managing HCV treatment failure and the potential of resistance testing in informing second-line therapy options. Expert Rev Anti Infect Ther 2018; 16:833-838. [PMID: 30336699 DOI: 10.1080/14787210.2018.1538783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
INTRODUCTION Direct acting antivirals have completely changed the landscape of the treatment of chronic hepatitis C. The management of the few patients who relapse to direct acting antivirals requires a careful analysis of the chances to achieve therapeutic success with a second antiviral course. In this context, the usefulness of viral resistances testing, able to detect resistance-associated substitutions in the viral sequence, is at present a matter of debate. Areas covered: The role of resistance associated substitutions is examined through the evaluation of the data from clinical trials that have assessed the impact of viral resistances on the treatment outcome. Special attention has been paid on the data from re-treatment studies. Expert commentary: The treatment failure in chronic hepatitis C is still a possible event. Therefore, additional real-world clinical data on relapse rates and on the relapse management are welcome to definitely address the clinical guidelines. At present, the testing of viral resistances is an exquisite tool for the choice of the re-treatment schedule. In the near future, widespread use of the most recently registered direct acting antivirals with high barrier to resistance will probably weaken the need of resistance testing as a support in clinical decisions.
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Affiliation(s)
- Elisabetta Loggi
- a Dipartimento di Scienze Mediche e Chirurgiche, Centro Studi e Ricerca sulle Epatiti , Università di Bologna , Bologna , Italy
| | - Ranka Vukotic
- a Dipartimento di Scienze Mediche e Chirurgiche, Centro Studi e Ricerca sulle Epatiti , Università di Bologna , Bologna , Italy
| | - Pietro Andreone
- a Dipartimento di Scienze Mediche e Chirurgiche, Centro Studi e Ricerca sulle Epatiti , Università di Bologna , Bologna , Italy
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8
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Loggi E, Vukotic R, Conti F, Gitto S, Andreone P. Gold standard assays for the monitoring of patients with chronic hepatitis C. Future Virol 2018. [DOI: 10.2217/fvl-2018-0032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Chronic HCV infection continues to be an important concern of public health, with still a high mortality from HCV-related disease. The landscape of chronic HCV infection has been dramatically changed by the introduction of the new antiviral agents, able to cure the infection in the large majority of patients. The laboratory management of HCV infection relies on serological and molecular tests, which have undergone significant technological advancements, able to ameliorate the performance both in diagnosis of infection and in the treatment monitoring. This article describes the main laboratory tools in the chronic HCV infection, with particular emphasis on the recent changes coming along with the new therapeutic approaches.
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Affiliation(s)
- Elisabetta Loggi
- Dipartimento di Scienze Mediche e Chirurgiche, Centro di Ricerca per lo Studio delle Epatiti, Università degli Studi di Bologna, Bologna, Italy
- Current address: UOC Patologia Clinica, ASUR Area Vasta 4, Fermo (FM), Italy
| | - Ranka Vukotic
- Dipartimento di Scienze Mediche e Chirurgiche, Centro di Ricerca per lo Studio delle Epatiti, Università degli Studi di Bologna, Bologna, Italy
| | - Fabio Conti
- Dipartimento di Scienze Mediche e Chirurgiche, Centro di Ricerca per lo Studio delle Epatiti, Università degli Studi di Bologna, Bologna, Italy
| | - Stefano Gitto
- Dipartimento di Scienze Mediche e Chirurgiche, Centro di Ricerca per lo Studio delle Epatiti, Università degli Studi di Bologna, Bologna, Italy
| | - Pietro Andreone
- Dipartimento di Scienze Mediche e Chirurgiche, Centro di Ricerca per lo Studio delle Epatiti, Università degli Studi di Bologna, Bologna, Italy
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Cuypers L, Pérez AB, Chueca N, Aldamiz-Echevarría T, Alados JC, Martínez-Sapiña AM, Merino D, Pineda JA, Téllez F, Espinosa N, Salméron J, Rivero-Juarez A, Vivancos MJ, Hontañón V, Vandamme AM, García F. Relapse or reinfection after failing hepatitis C direct acting antiviral treatment: Unravelled by phylogenetic analysis. PLoS One 2018; 13:e0201268. [PMID: 30044871 PMCID: PMC6059487 DOI: 10.1371/journal.pone.0201268] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/11/2018] [Indexed: 12/14/2022] Open
Abstract
Despite high response rates associated to hepatitis C virus (HCV) treatment, no protective immunity is acquired, allowing for reinfection and continued infectiousness. Distinguishing between relapse and reinfection is crucial for patient counselling and to choose the most appropriate retreatment. Here, refined phylogenetic analysis using multiple genes served to assess genotype and reinfection for 53 patients for whom the virus was sampled before start of therapy and at time of sustained virological response evaluation at week 12. At baseline, genotypes were determined as HCV1a (41.5%), HCV1b (24.5%), HCV4 (18.9%) and HCV3a (15.1%), while six cases revealed to be discordantly assigned by phylogeny and commercial assays. Overall, 60.4% was co-infected with HIV. The large majority was classified as people who inject drugs (78.6%), often co-infected with HIV. Transmission was sexual in seven cases, of which five in HIV-positive men-who-have-sex-with-men. Overall, relapse was defined for 44 patients, while no conclusion was drawn for four patients. Five patients were reinfected with a different HCV strain, of which three with a different genotype, showing that phylogeny is needed not only to determine the genotype, but also to distinguish between relapse and intra-subtype reinfection. Of note, phylogenies are more reliable when longer fragments of the viral genome are being sequenced.
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Affiliation(s)
- Lize Cuypers
- KU Leuven–University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ana Belén Pérez
- Clinical Microbiology Department, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. Granada, Spain
| | - Natalia Chueca
- Clinical Microbiology Department, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. Granada, Spain
| | | | | | | | - Dolores Merino
- Clinical Microbiology, Hospital Infanta Elena, Huelva, Spain
| | | | - Francisco Téllez
- UGC Enfermedades Infecciosas y Microbiología, Hospital La Línea, AGS Campo de Gibraltar, Cadiz, Spain
| | - Nuria Espinosa
- Clinical Microbiology, Hospital Virgen del Rocío, Sevilla, Spain
| | - Javier Salméron
- Hepatology Unit, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. CIBERehd, Granada, Spain
| | - Antonio Rivero-Juarez
- Infectious Diseases Unit. Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC). Hospital Universitario Reina Sofía de Córdoba. Universidad de Córdoba, Córdoba, Spain
| | | | - Víctor Hontañón
- Clinical Microbiology, University Hospital La Paz, Madrid, Spain
| | - Anne-Mieke Vandamme
- KU Leuven–University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Microbiology Unit, Institute for Hygiene and Tropical Medicine, University Nova de Lisboa, Lisbon, Portugal
| | - Féderico García
- Clinical Microbiology Department, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. Granada, Spain
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Bruzzone B, Canepa P, De Rosa G, Delucis S, D'Ambrosio B, Icardi G, Setti M. Correct Identification of Dual HCV Infections in HIV/HCV CoInfected Patients. AIDS Res Hum Retroviruses 2018; 34:325-326. [PMID: 29314861 DOI: 10.1089/aid.2017.0133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Paola Canepa
- Department of Health Sciences (DiSSal), University of Genoa, Genoa, Italy
| | | | - Sabrina Delucis
- Department of Health Sciences (DiSSal), University of Genoa, Genoa, Italy
| | | | - Giancarlo Icardi
- Hygiene Unit, San Martino Polyclinic Hospital, Genoa, Italy
- Department of Health Sciences (DiSSal), University of Genoa, Genoa, Italy
| | - Maurizio Setti
- Internal Medicine and Clinical Immunology Unit, San Martino Polyclinic Hospital, Genoa, Italy
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11
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Minichini C, Starace M, De Pascalis S, Macera M, Occhiello L, Caroprese M, Vitrone M, Iovinella V, Guerrera B, Masarone M, Coppola N. HCV genotype-3h, a difficult-to-diagnose sub-genotype in the DAA era. Antivir Ther 2018; 23:605-609. [PMID: 29504510 DOI: 10.3851/imp3228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2018] [Indexed: 10/17/2022]
Abstract
BACKGROUND No data are available on the clinical presentation and virological pattern in the case of failure of interferon (IFN)-free regimens in patients with genotype-3h. In this paper authors identified the virological and clinical characteristics of patients with genotype-3h treated with suboptimal or not indicated IFN-free regimens for the misclassification of HCV genotype. METHODS A total of 87 consecutive patients with failure to an IFN-free regimen were re-tested for HCV genotype by HCV NS5B sequencing; the 26 patients identified as harbouring HCV-3 were enrolled. RESULTS Of the 26 patients enrolled, 4 (15.4%) harboured sub-genotype-3h and 22 (84.6%) 3a. All patients were Italian. Patients with genotype-3a infection were younger (median age 56 years, range 47-78) compared to those with genotype-3h infection (median 74 years, range 65-79; P<0.006). With regard to the failed direct-acting antiviral (DAA)-regimens, three of the four patients with genotype-3h (75%) had been treated with an ineffective DAA regimen (paritaprevir, ombitasvir, dasabuvir ± ribavirin for 3 months) more frequently than those with genotype-3a (13.6%; P=0.02), because of previous erroneous identification of HCV-1 genotype. NS5A resistance-associated substitutions (RASs) were observed in 10 (45.4%) genotype-3a-infected patients and in 2 (50%) with genotype-3h. NS5B RASs were observed in only two genotype-3a-infected patients and in none of the 3h-infected patients. CONCLUSIONS This is the first time genotype-3h has been identified in Italian patients failing an IFN-free regimen, in the majority of cases because of a misclassification of the HCV genotype.
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Affiliation(s)
- Carmine Minichini
- Infectious Diseases Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania L. Vanvitelli, Naples, Italy
| | - Mario Starace
- Infectious Diseases Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania L. Vanvitelli, Naples, Italy
| | - Stefania De Pascalis
- Infectious Diseases Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania L. Vanvitelli, Naples, Italy
| | - Margherita Macera
- Infectious Diseases Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania L. Vanvitelli, Naples, Italy
| | - Laura Occhiello
- Infectious Diseases Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania L. Vanvitelli, Naples, Italy
| | - Mara Caroprese
- Infectious Diseases Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania L. Vanvitelli, Naples, Italy
| | - Martina Vitrone
- Internal Medicine, University of Campania & AORN Ospedali dei Colli-Monaldi Hospital, Naples, Italy
| | | | - Barbara Guerrera
- Internal Medicine, University of Campania L. Vanvitelli, Naples, Italy
| | - Mario Masarone
- Gastroenterology Unit, University of Salerno, Salerno, Italy
| | - Nicola Coppola
- Infectious Diseases Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania L. Vanvitelli, Naples, Italy
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12
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Iqbal MS, Ashfaq UA, Aslam S, Khaliq S, Ghani MU, Batool F. Analysis of polymorphism rs1990760 of IFIH1 gene and treatment outcomes in HCV infection. Future Virol 2018. [DOI: 10.2217/fvl-2017-0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hepatitis C virus (HCV) is endemic in Pakistan, infecting approximately 12 million people and expected to increase in the coming decades. IFIH1 is a viral RNA sensor gene essential for the activation of innate immunity against RNA viruses. Aim: The aim of the study was to analyze the association of the polymorphism (rs1990760) in IFIH1 gene among HCV infected Pakistani patients and healthy controls. Materials & methods: Blood samples from 400 chronic HCV patients (including 323 responders and 77 nonresponders) and 100 healthy individuals were collected. Results: Frequencies of heterozygous computed tomography genotype significantly associated with decreased HCV risk (χ2 = 0.072; 95% Cl: 1.06; 0.68−1.65; p ≤ 0.788). Conclusion: No significant differences were observed in alleles and genotype frequencies of IFIH1 (rs1990760) in Pakistani HCV infected patients.
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Affiliation(s)
- Muhammad Sarfaraz Iqbal
- Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Pakistan
| | - Sadia Aslam
- Allama Iqbal Medical College, Lahore, Pakistan
| | - Saba Khaliq
- Department of Physiology, University of Health Sciences, Lahore, Pakistan
| | - Muhammad Usman Ghani
- Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Pakistan
| | - Farzana Batool
- Department of Biochemistry, Government College University Faisalabad, Pakistan
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13
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Starace M, Minichini C, De Pascalis S, Macera M, Occhiello L, Messina V, Sangiovanni V, Adinolfi LE, Claar E, Precone D, Stornaiuolo G, Stanzione M, Ascione T, Caroprese M, Zampino R, Parrilli G, Gentile I, Brancaccio G, Iovinella V, Martini S, Masarone M, Fontanella L, Masiello A, Sagnelli E, Punzi R, Salomone Megna A, Santoro R, Gaeta GB, Coppola N. Virological patterns of HCV patients with failure to interferon-free regimens. J Med Virol 2018; 90:942-950. [PMID: 29315640 DOI: 10.1002/jmv.25022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 12/29/2017] [Indexed: 01/02/2023]
Abstract
The study characterized the virological patterns and the resistance-associated substitutions (RASs) in patients with failure to IFN-free regimens enrolled in the real-life setting. All 87 consecutive HCV patients with failed IFN-free regimens, observed at the laboratory of the University of Campania, were enrolled. All patients had been treated with DAA regimens according to the HCV genotype, international guidelines, and local availability. Sanger sequencing of NS3, NS5A, and NS5B regions was performed at failure by home-made protocols. Of the 87 patients enrolled, 13 (14.9%) showed a misclassified HCV genotype, probably causing DAA failure, 16 had been treated with a sub-optimal DAA regimen, 19 with a simeprevir-based regimen and 39 with an optimal DAA regimen. A major RAS was identified more frequently in the simeprevir regimen group (68.4%) and in the optimal regimen group (74.4%) than in the sub-optimal regimen group (56.3%). The prevalence of RASs in NS3 was similar in the three groups (30.8-57.9%), that in NS5A higher in the optimal regimen group (71.8%) than in the sub-optimal regimen group (12.5%, P < 0.0001) and in the simeprevir regimen group (31.6%, P < 0.0005), and that in NS5B low in all groups (0-25%). RASs in two or more HCV regions were more frequently identified in the optimal regimen group (46.6%) than in the simeprevir-based regimen group (31.6%) and sub-optimal regimen group (18.7%). In our real-life population the prevalence of RASs was high, especially in NS3 and NS5A and in those treated with suitable DAA regimens.
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Affiliation(s)
- Mario Starace
- Laboratory for the Identification of Prognostic Factors of Response to the Treatment Against Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Carmine Minichini
- Laboratory for the Identification of Prognostic Factors of Response to the Treatment Against Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Stefania De Pascalis
- Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Margherita Macera
- Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Laura Occhiello
- Laboratory for the Identification of Prognostic Factors of Response to the Treatment Against Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | | | | | - Ernesto Claar
- Internal Medicine Unit, Evangelical Hospital Villa Betania, Naples, Italy
| | | | - Gianfranca Stornaiuolo
- Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Maria Stanzione
- Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Tiziana Ascione
- IX Interventional Ultrasound Unit for Infectious Diseases, AORN dei Colli, Naples, Italy
| | - Mara Caroprese
- Laboratory for the Identification of Prognostic Factors of Response to the Treatment Against Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Rosa Zampino
- Department of Medical, Surgical, Neurological, Metabolic, and Geriatric Sciences, University of Campania L. Vanvitelli, and Infectious and Transplant Medicine, AORN Ospedali dei Colli-Monaldi Hospital, Naples, Italy
| | - Gianpaolo Parrilli
- Gastroenterology Unit, AOU San Giovanni di Dio Ruggi d'Aragona, Salerno, Italy
| | - Ivan Gentile
- Department of Clinical Medicine and Surgery, University Federico II, Naples, Italy
| | - Giuseppina Brancaccio
- Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | | | - Mario Masarone
- Internal Medicine and Hepatology Unit, University of Salerno, Naples, Italy
| | - Luca Fontanella
- Internal Medicine Unit, AO Madonna del Buon Consiglio FATEBENEFRATELLI, Naples, Italy
| | | | - Evangelista Sagnelli
- Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Rodolfo Punzi
- Infectious Diseases Unit, AORN dei Colli, Naples, Italy
| | | | - Renato Santoro
- Infectious Diseases Unit, AOU San Giovanni di Dio Ruggi d'Aragona, Salerno, Italy
| | - Giovanni B Gaeta
- Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Nicola Coppola
- Laboratory for the Identification of Prognostic Factors of Response to the Treatment Against Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy.,Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
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14
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Cabezas J, Llerena S, Puente Á, Fábrega E, Crespo J. Causes of treatment failure for hepatitis C in the era of direct-acting antiviral therapy. REVISTA ESPANOLA DE ENFERMEDADES DIGESTIVAS 2017; 108:421-30. [PMID: 26666379 DOI: 10.17235/reed.2015.3894/2015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Hepatitis C therapy in the era of the newer direct-acting antiviral agents has radically changed our treatment schemes by achieving very high rates of sustained virological response. However, treatment with direct antiviral agents fails in a subgroup of patients. This group of so-called difficult-to-treat individuals is the subject of this paper, which reviews the causes of virological failure, their clinical implications, and some final recommendations.
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Affiliation(s)
- Joaquín Cabezas
- Aparato Digestivo/Unidad de Hepatología, Hospital Universitario Marqués de Valdecilla, España
| | - Susana Llerena
- Aparato Digestivo/ Unidad de Hepatologia, Hospital Universitario Marqués de Valdecilla, España
| | - Ángela Puente
- Aparato Digestivo/Unidad de Hepatología, Hospital Universitario Marqués de Valdecilla, España
| | | | - Javier Crespo
- Servicio Aparato Digestivo, Hospital Universitario Marqués de Valdecilla, 39002
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15
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Treatment of Hepatitis C virus infection in Italy: A consensus report from an expert panel. Dig Liver Dis 2017; 49:731-741. [PMID: 28456519 DOI: 10.1016/j.dld.2017.03.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 03/31/2017] [Indexed: 12/11/2022]
Abstract
Hepatitis C virus (HCV) infection remains one of the main causes of chronic liver disease worldwide. The advent of direct-acting antivirals (DAAs) has significantly improved the course of patients with chronic HCV infection (CHC), due to the ability of these drugs to achieve high rates of sustained virological response (SVR). These exceedingly high rates of SVR and the excellent safety data have been confirmed in real life practice. Evolving guidelines have been issued by national and international scientific societies in accordance with the progression of clinical knowledge and the availability of new DAAs. These recommendations, however, may not be applied universally because of delays in drugs reimbursability in different countries and because some National Health Systems identify only patients with advanced disease as a treatment priority. Italy in this regard is a prototype about DAAs treatment of CHC patients. With the aim to assess the Italian treatment experience with DAAs and to respond to unmet needs in treatment optimization of antiviral therapy in specific settings of CHC patients, a group of Italian experts met in Stresa in February 2017. The summary of the considerations arising from this two-day meeting and some statements regarding a few open issues are reported in this position paper.
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16
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Fernández-Caballero JA, Alvarez M, Chueca N, Pérez AB, García F. The cobas® HCV GT is a new tool that accurately identifies Hepatitis C virus genotypes for clinical practice. PLoS One 2017; 12:e0175564. [PMID: 28410425 PMCID: PMC5391928 DOI: 10.1371/journal.pone.0175564] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 03/28/2017] [Indexed: 12/24/2022] Open
Abstract
Objective We aimed to evaluate the correct assignment of HCV genotype/subtypes 1a and 1b by cobas® HCV genotyping (GT) assay (Roche Molecular Diagnostics) compared with nonstructural protein 5B (NS5B) sequencing. Patients and methods Clinical samples from 153 patients submitted for HCV genotyping were studied. After genotyping with the cobas® HCV GT, sequencing of a 387 bp fragment in the NS5B gene and phylogenetic analysis was employed to compare genotyping results. Major discrepancies were defined as differences in the assigned genotype by cobas® HCV GT and NS5B sequencing (including genotype 1 subtypes 1a and 1b misclassification). Results Overall agreement between the cobas® HCV GT and NS5B sequencing was 98%; all the 1a, 1b, 2, 3 and 4 genotypes identified by cobas® HCV GT were concordant with NS5B sequencing. Three samples tested “indetermined” by cobas® HCV GT assay and were genotyped as 1a, 3a, and 4d by NS5B sequencing. Conclussion These results indicate that the cobas® HCV GT assay correctly identifies HCV genotypes, and points out the importance of additional methods based on DNA sequencing for resolving indeterminate results.
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Affiliation(s)
- J. A. Fernández-Caballero
- Servicio de Microbiología, Complejo Hospitalario Universitario Granada-Hospital PTS, Instituto de Investigación Biosanitaria IBS, Granada, Spain
| | - M. Alvarez
- Servicio de Microbiología, Complejo Hospitalario Universitario Granada-Hospital PTS, Instituto de Investigación Biosanitaria IBS, Granada, Spain
- * E-mail:
| | - N. Chueca
- Servicio de Microbiología, Complejo Hospitalario Universitario Granada-Hospital PTS, Instituto de Investigación Biosanitaria IBS, Granada, Spain
| | - A. B. Pérez
- Servicio de Microbiología, Complejo Hospitalario Universitario Granada-Hospital PTS, Instituto de Investigación Biosanitaria IBS, Granada, Spain
| | - F. García
- Servicio de Microbiología, Complejo Hospitalario Universitario Granada-Hospital PTS, Instituto de Investigación Biosanitaria IBS, Granada, Spain
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17
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Di Maio VC, Cento V, Lenci I, Aragri M, Rossi P, Barbaliscia S, Melis M, Verucchi G, Magni CF, Teti E, Bertoli A, Antonucci F, Bellocchi MC, Micheli V, Masetti C, Landonio S, Francioso S, Santopaolo F, Pellicelli AM, Calvaruso V, Gianserra L, Siciliano M, Romagnoli D, Cozzolongo R, Grieco A, Vecchiet J, Morisco F, Merli M, Brancaccio G, Di Biagio A, Loggi E, Mastroianni CM, Pace Palitti V, Tarquini P, Puoti M, Taliani G, Sarmati L, Picciotto A, Vullo V, Caporaso N, Paoloni M, Pasquazzi C, Rizzardini G, Parruti G, Craxì A, Babudieri S, Andreoni M, Angelico M, Perno CF, Ceccherini-Silberstein F. Multiclass HCV resistance to direct-acting antiviral failure in real-life patients advocates for tailored second-line therapies. Liver Int 2017; 37:514-528. [PMID: 28105744 DOI: 10.1111/liv.13327] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/12/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Despite the excellent efficacy of direct-acting antivirals (DAA) reported in clinical trials, virological failures can occur, often associated with the development of resistance-associated substitutions (RASs). This study aimed to characterize the presence of clinically relevant RASs to all classes in real-life DAA failures. METHODS Of the 200 virological failures that were analyzed in 197 DAA-treated patients, 89 with pegylated-interferon+ribavirin (PegIFN+RBV) and 111 without (HCV-1a/1b/1g/2/3/4=58/83/1/6/24/25; 56.8% treatment experienced; 65.5% cirrhotic) were observed. Sanger sequencing of NS3/NS5A/NS5B was performed by home-made protocols, at failure (N=200) and whenever possible at baseline (N=70). RESULTS The majority of the virological failures were relapsers (57.0%), 22.5% breakthroughs, 20.5% non-responders. RAS prevalence varied according to IFN/RBV use, DAA class, failure type and HCV genotype/subtype. It was 73.0% in IFN group vs 49.5% in IFN free, with the highest prevalence of NS5A-RASs (96.1%), compared to NS3-RASs (75.9% with IFN, 70.5% without) and NS5B-RASs (66.6% with IFN, 20.4% without, in sofosbuvir failures). In the IFN-free group, RASs were higher in breakthrough/non-responders than in relapsers (90.5% vs 40.0%, P<.001). Interestingly, 57.1% of DAA IFN-free non-responders had a misclassified genotype, and 3/4 sofosbuvir breakthroughs showed the major-RAS-S282T, while RAS-L159F was frequently found in sofosbuvir relapsers (18.2%). Notably, 9.0% of patients showed also extra target RASs, and 47.4% of patients treated with ≥2 DAA classes showed multiclass resistance, including 11/11 NS3+NS5A failures. Furthermore, 20.0% of patients had baseline-RASs, which were always confirmed at failure. CONCLUSIONS In our failure setting, RAS prevalence was remarkably high in all genes, with a partial exception for NS5B, whose limited resistance is still higher than previously reported. This multiclass resistance advocates for HCV resistance testing at failure, in all three genes for the best second-line therapeutic tailoring.
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Affiliation(s)
- Velia C Di Maio
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Valeria Cento
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Ilaria Lenci
- Hepatology Unit, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Marianna Aragri
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Piera Rossi
- Hepatology Unit, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Silvia Barbaliscia
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Michela Melis
- Infectious Diseases Unit, University of Sassari, Sassari, Italy
| | | | - Carlo F Magni
- Division of Infectious Disease, Hospital Sacco of Milan, Milan, Italy
| | - Elisabetta Teti
- Infectious Diseases, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Ada Bertoli
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | | | - Maria C Bellocchi
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | | | - Chiara Masetti
- Hepatology Unit, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Simona Landonio
- Division of Infectious Disease, Hospital Sacco of Milan, Milan, Italy
| | - Simona Francioso
- Hepatology Unit, University Hospital of Rome Tor Vergata, Rome, Italy
| | | | - Adriano M Pellicelli
- Liver Disease Unit, Department of Liver Transplantation, San Camillo Forlanini Hospital, Rome, Italy
| | | | - Laura Gianserra
- Infectious Diseases, Sant'Andrea Hospital - Sapienza University of Rome, Rome, Italy
| | | | - Dante Romagnoli
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Raffaele Cozzolongo
- Department of Gastroenterology, Scientific Institute for Digestive Disease "Saverio de Bellis" Hospital, Castellana Grotte, Bari, Italy
| | - Antonio Grieco
- Gastroenterology, Catholic University of Rome, Rome, Italy
| | - Jacopo Vecchiet
- Infectious Disease Clinic, Hospital of Chieti, Chieti, Italy
| | - Filomena Morisco
- Gastroenterology, Department of Clinical Medicine and Surgery, University of Naples "Federico II", Naples, Italy
| | - Manuela Merli
- Gastroenterology, Department of Clinical Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Antonio Di Biagio
- Infectious Diseases Unit, Department of Social Health (DISSAL) of the University of Genoa, IRCCS S. Martino-IST, Genoa, Italy
| | - Elisabetta Loggi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Claudio M Mastroianni
- Department of Public Health and Infectious Diseases, Sapienza University, Polo Pontino, Latina, Italy
| | | | | | - Massimo Puoti
- Department of Infectious Diseases, Hospital Niguarda Ca'Granda, Milan, Italy
| | - Gloria Taliani
- Infectious and Tropical Diseases Unit, Department of Clinical Medicine, Sapienza University of Rome, Rome, Italy
| | - Loredana Sarmati
- Infectious Diseases, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Antonino Picciotto
- Department of Internal Medicine, Gastroenterology Unit, University of Genova, Genoa, Italy
| | - Vincenzo Vullo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Nicola Caporaso
- Gastroenterology, Department of Clinical Medicine and Surgery, University of Naples "Federico II", Naples, Italy
| | - Maurizio Paoloni
- Infectious Disease Unit, Avezzano General Hospital, Avezzano, Italy
| | - Caterina Pasquazzi
- Infectious Diseases, Sant'Andrea Hospital - Sapienza University of Rome, Rome, Italy
| | - Giuliano Rizzardini
- Division of Infectious Disease, Hospital Sacco of Milan, Milan, Italy.,School of Clinical Medicine, Faculty of Health Science University of the Witwatersrand, Johannesburg, South Africa
| | - Giustino Parruti
- Infectious Disease Unit, Pescara General Hospital, Pescara, Italy
| | - Antonio Craxì
- Gastroenterology, "P. Giaccone" University Hospital, Palermo, Italy
| | | | - Massimo Andreoni
- Infectious Diseases, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Mario Angelico
- Hepatology Unit, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Carlo F Perno
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
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18
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Polilli E, Cento V, Restelli U, Ceccherini-Silberstein F, Aragri M, Di Maio VC, Sciacca A, Santoleri F, Fazii P, Costantini A, Perno CF, Parruti G. Consequences of inaccurate hepatitis C virus genotyping on the costs of prescription of direct antiviral agents in an Italian district. CLINICOECONOMICS AND OUTCOMES RESEARCH 2016; 8:467-473. [PMID: 27695353 PMCID: PMC5028103 DOI: 10.2147/ceor.s106238] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Available commercial assays may yield inaccurate hepatitis C virus (HCV) genotype assignment in up to 10% of cases. We investigated the cost-effectiveness of re-evaluating HCV genotype by population sequencing, prior to choosing a direct acting antiviral (DAA) regimen. Between March and September 2015, HCV sequence analysis was performed in order to confirm commercial LiPA-HCV genotype (Versant® HCV Genotype 2.0) in patients eligible for treatment with DAAs. Out of 134 consecutive patients enrolled, sequencing yielded 21 (15.7%) cases of discordant results. For three cases of wrong genotype assignment, the putative reduction in efficacy was gauged between 15% and 40%. Among the eight cases for whom G1b was assigned by commercial assays instead of G1a, potentially suboptimal treatments would have been prescribed. Finally, for five patients with G1 and indeterminate subtype, the choice of regimens would have targeted the worst option, with a remarkable increase in costs, as in the case of the four mixed HCV infections for whom pan-genotypic regimens would have been mandatory. Precise assignment of HCV genotype and subtype by sequencing may, therefore, be more beneficial than expected, until more potent pan-genotypic regimens are available for all patients.
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Affiliation(s)
- Ennio Polilli
- Infectious Diseases Unit, Pescara General Hospital, Pescara
| | - Valeria Cento
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome
| | - Umberto Restelli
- CREMS - Centre for Research on Health Economics, Social and Health Care Management, Carlo Cattaneo - LIUC University, Castellanza, Italy; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Marianna Aragri
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome
| | - Velia Chiara Di Maio
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome
| | | | | | - Paolo Fazii
- Microbiology and Virology Unit, Pescara General Hospital, Pescara, Italy
| | | | - Carlo Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome
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19
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Cuypers L, Ceccherini-Silberstein F, Van Laethem K, Li G, Vandamme AM, Rockstroh JK. Impact of HCV genotype on treatment regimens and drug resistance: a snapshot in time. Rev Med Virol 2016; 26:408-434. [PMID: 27401933 DOI: 10.1002/rmv.1895] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/11/2016] [Accepted: 06/15/2016] [Indexed: 12/11/2022]
Abstract
The introduction of highly potent direct-acting antivirals (DAAs) has revolutionized hepatitis C virus treatment. Nevertheless, viral eradication worldwide remains a challenge also in the era of DAA treatment, because of the high associated costs, high numbers of undiagnosed patients, high re-infection rates in some risk groups and suboptimal drug efficacies associated with host and viral factors as well as advanced stages of liver disease. A correct determination of the HCV genotype allows administration of the most appropriate antiviral regimen. Additionally, HCV genetic sequencing improves our understanding of resistance-associated variants, either naturally occurring before treatment, acquired by transmission at HCV infection, or emerging after virological failure. Because treatment response rates, and the prevalence and development of drug resistance variants differ for each DAA regimen and HCV genotype, this review summarizes treatment opportunities per HCV genotype, and focuses on viral genetic sequencing to guide clinical decision making. Although approval of the first pan-genotypic DAA-only regimen is expected soon, HCV genetic sequencing will remain important because when DAA therapies fail, genotyping and resistance testing to select a new active DAA combination will be essential. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Lize Cuypers
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
| | | | - Kristel Van Laethem
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
| | - Guangdi Li
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium.,Department of Metabolism and Endocrinology, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Anne-Mieke Vandamme
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium.,Center for Global Health and Tropical Medicine, Microbiology Unit, Institute for Hygiene and Tropical Medicine, University Nova de Lisboa, Lisbon, Portugal
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Using NS5B Sequencing for Hepatitis C Virus Genotyping Reveals Discordances with Commercial Platforms. PLoS One 2016; 11:e0153754. [PMID: 27097040 PMCID: PMC4838212 DOI: 10.1371/journal.pone.0153754] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/04/2016] [Indexed: 12/17/2022] Open
Abstract
We aimed to evaluate the correct assignment of HCV genotypes by three commercial methods-Trugene HCV genotyping kit (Siemens), VERSANT HCV Genotype 2.0 assay (Siemens), and Real-Time HCV genotype II (Abbott)-compared to NS5B sequencing. We studied 327 clinical samples that carried representative HCV genotypes of the most frequent geno/subtypes in Spain. After commercial genotyping, the sequencing of a 367 bp fragment in the NS5B gene was used to assign genotypes. Major discrepancies were defined, e.g. differences in the assigned genotype by one of the three methods and NS5B sequencing, including misclassification of subtypes 1a and 1b. Minor discrepancies were considered when differences at subtype levels, other than 1a and 1b, were observed. The overall discordance with the reference method was 34% for Trugene and 15% for VERSANT HCV2.0. The Abbott assay correctly identified all 1a and 1b subtypes, but did not subtype all the 2, 3, 4 and 5 (34%) genotypes. Major discordances were found in 16% of cases for Trugene HCV, and the majority were 1b- to 1a-related discordances; major discordances were found for VERSANT HCV 2.0 in 6% of cases, which were all but one 1b to 1a cases. These results indicated that the Trugene assay especially, and to a lesser extent, Versant HCV 2.0, can fail to differentiate HCV subtypes 1a and 1b, and lead to critical errors in clinical practice for correctly using directly acting antiviral agents.
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Di Maio VC, Cento V, Di Paolo D, Aragri M, De Leonardis F, Tontodonati M, Micheli V, Bellocchi MC, Antonucci FP, Bertoli A, Lenci I, Milana M, Gianserra L, Melis M, Di Biagio A, Sarrecchia C, Sarmati L, Landonio S, Francioso S, Lambiase L, Nicolini LA, Marenco S, Nosotti L, Giannelli V, Siciliano M, Romagnoli D, Pellicelli A, Vecchiet J, Magni CF, Babudieri S, Mura MS, Taliani G, Mastroianni C, Vespasiani-Gentilucci U, Romano M, Morisco F, Gasbarrini A, Vullo V, Bruno S, Baiguera C, Pasquazzi C, Tisone G, Picciotto A, Andreoni M, Parruti G, Rizzardini G, Angelico M, Perno CF, Ceccherini-Silberstein F. HCV NS3 sequencing as a reliable and clinically useful tool for the assessment of genotype and resistance mutations for clinical samples with different HCV-RNA levels. J Antimicrob Chemother 2015; 71:739-50. [DOI: 10.1093/jac/dkv403] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/29/2015] [Indexed: 12/22/2022] Open
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