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De Francesco MA, Gargiulo F, Zaltron S, Spinetti A, Castelli F, Caruso A. DAA Treatment Failure in a HIV/HBV/HCV Co-Infected Patient Carrying a Chimeric HCV Genotype 4/1b. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:11655. [PMID: 36141921 PMCID: PMC9517502 DOI: 10.3390/ijerph191811655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Approved direct antiviral agent (DAA) combinations are associated with high rates of sustained virological response (SVR) and the absence of a detectable hepatitis C viral load 12-24 weeks after treatment discontinuation. However, a low percentage of individuals fail DAA therapy. Here, we report the case of a HIV/HBV/HCV co-infected patient who failed to respond to DAA pangenotypic combination therapy. The sequencing of NS5a, NS5b, NS3 and core regions evidenced a recombinant intergenotypic strain 4/1b with a recombination crossover point located inside the NS3 region. The identification of this natural recombinant virus underlines the concept that HCV recombination, even if it occurs rarely, may play a key role in the virus fitness and evolution.
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Affiliation(s)
- Maria Antonia De Francesco
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia ASST Spedali Civili, 25123 Brescia, Italy
| | - Franco Gargiulo
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia ASST Spedali Civili, 25123 Brescia, Italy
| | - Serena Zaltron
- Division of Infectious and Tropical Diseases, Department of Clinical and Experimental Sciences, University of Brescia and ASST Spedali Civili, 25123 Brescia, Italy
| | - Angiola Spinetti
- Division of Infectious and Tropical Diseases, Department of Clinical and Experimental Sciences, University of Brescia and ASST Spedali Civili, 25123 Brescia, Italy
| | - Francesco Castelli
- Division of Infectious and Tropical Diseases, Department of Clinical and Experimental Sciences, University of Brescia and ASST Spedali Civili, 25123 Brescia, Italy
| | - Arnaldo Caruso
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia ASST Spedali Civili, 25123 Brescia, Italy
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Lopez Luis BA, Rodríguez-Díaz R, Angulo-Medina L, Soto-Ramírez LE. The Emergence of Hepatitis C Virus Genotype 4d Among Human Immunodeficiency Virus-Infected Patients in Mexico City: A Molecular Epidemiological Study. Sex Transm Dis 2022; 49:e90-e94. [PMID: 35001015 DOI: 10.1097/olq.0000000000001596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
ABSTRACT The recent detection of hepatitis C virus genotype 4 infection in human immunodeficiency virus-infected patients prompted performing molecular characterization of these isolates. All the Mexican isolates belonged to a subcluster within the 4d group and shared a common ancestor with a French isolate. The estimated timing of introduction in Mexico City was as recent as December 2015.
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Affiliation(s)
- Bruno Ali Lopez Luis
- From the Laboratory of Molecular Virology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Avenida Vasco de Quiroga No. 15, Colonia Belisario Domínguez Sección XVI, Delegación Tlalpan, Mexico City, Mexico
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3
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Pham LV, Pedersen MS, Fahnøe U, Fernandez-Antunez C, Humes D, Schønning K, Ramirez S, Bukh J. HCV genome-wide analysis for development of efficient culture systems and unravelling of antiviral resistance in genotype 4. Gut 2022; 71:627-642. [PMID: 33833066 PMCID: PMC8862099 DOI: 10.1136/gutjnl-2020-323585] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/17/2021] [Accepted: 02/03/2021] [Indexed: 01/14/2023]
Abstract
OBJECTIVE HCV-genotype 4 infections are a major cause of liver diseases in the Middle East/Africa with certain subtypes associated with increased risk of direct-acting antiviral (DAA) treatment failures. We aimed at developing infectious genotype 4 cell culture systems to understand the evolutionary genetic landscapes of antiviral resistance, which can help preserve the future efficacy of DAA-based therapy. DESIGN HCV recombinants were tested in liver-derived cells. Long-term coculture with DAAs served to induce antiviral-resistance phenotypes. Next-generation sequencing (NGS) of the entire HCV-coding sequence identified mutation networks. Resistance-associated substitutions (RAS) were studied using reverse-genetics. RESULT The in-vivo infectious ED43(4a) clone was adapted in Huh7.5 cells, using substitutions identified in ED43(Core-NS5A)/JFH1-chimeric viruses combined with selected NS5B-changes. NGS, and linkage analysis, permitted identification of multiple genetic branches emerging during culture adaptation, one of which had 31 substitutions leading to robust replication/propagation. Treatment of culture-adapted ED43 with nine clinically relevant protease-DAA, NS5A-DAA and NS5B-DAA led to complex dynamics of drug-target-specific RAS with coselection of genome-wide substitutions. Approved DAA combinations were efficient against the original virus, but not against variants with RAS in corresponding drug targets. However, retreatment with glecaprevir/pibrentasvir remained efficient against NS5A inhibitor and sofosbuvir resistant variants. Recombinants with specific RAS at NS3-156, NS5A-28, 30, 31 and 93 and NS5B-282 were viable, but NS3-A156M and NS5A-L30Δ (deletion) led to attenuated phenotypes. CONCLUSION Rapidly emerging complex evolutionary landscapes of mutations define the persistence of HCV-RASs conferring resistance levels leading to treatment failure in genotype 4. The high barrier to resistance of glecaprevir/pibrentasvir could prevent persistence and propagation of antiviral resistance.
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Affiliation(s)
- Long V. Pham
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Schou Pedersen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark,Department of Clinical Microbiology, Hvidovre Hospital, Hvidovre, Denmark
| | - Ulrik Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Carlota Fernandez-Antunez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Daryl Humes
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Schønning
- Department of Clinical Microbiology, Hvidovre Hospital, Hvidovre, Denmark,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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4
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Leumi S, El Kassas M, Zhong J. Hepatitis C virus genotype 4: A poorly characterized endemic genotype. J Med Virol 2021; 93:6079-6088. [PMID: 34185316 DOI: 10.1002/jmv.27165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/26/2021] [Indexed: 12/16/2022]
Abstract
Globally, 13% of all hepatitis C virus (HCV) infections are caused by genotype 4 (GT4), which consists of 17 subtypes with various levels of susceptibility to anti-HCV therapy. This genotype is endemic in the Middle East and Africa and has considerably spread to Europe lately. The molecular features of HCV-GT4 infection, as well as its appropriate therapeutics, are poorly characterized as it has not been the subject of widespread basic research. As such, in this review, we aim to gather the current state of knowledge of this genotype with a particular emphasis on its heterogeneity, sequence signatures, resistance-associated substitutions, and available in vivo and in vitro models used for its study. We urge developing more cell-culture models based on different GT4 subtypes to better understand the virology and therapeutic response of this particular genotype. This review may raise more awareness about this genotype and trigger more basic research work to develop its research tools. This will be critical to design better therapeutics and help to provide adequate guidelines for physicians working with HCV-GT4 patients.
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Affiliation(s)
- Steve Leumi
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mohamed El Kassas
- Department of Endemic Medicine, Faculty of Medicine, Helwan University, Cairo, Egypt
| | - Jin Zhong
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
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Nguyen T, Valantin MA, Delaugerre C, Amiel C, Netzer E, L'Yavanc T, Ohayon M, Valin N, Day N, Kreplak G, Pialoux G, Calvez V, Molina JM, Marcelin AG, Todesco E. Low level of baseline resistance in recently HCV-infected men who have sex with men with high-risk behaviours. J Glob Antimicrob Resist 2021; 24:311-315. [PMID: 33540082 DOI: 10.1016/j.jgar.2021.01.012] [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: 04/30/2020] [Revised: 12/11/2020] [Accepted: 01/23/2021] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES Presence of baseline hepatitis C virus (HCV) resistance-associated substitutions (RASs) can impair treatment outcome of direct-acting antivirals. We investigated the prevalence of pre-treatment HCV resistance among recently HCV-infected men who have sex with men (MSM) with high risk behaviours, either human immunodeficiency virus (HIV) co-infected or at high risk of HIV acquisition and under pre-exposure prophylaxis (PrEP). METHODS NS5A and NS3 fragments were deep sequenced on pre-treatment samples of 72 subjects using Illumina MiSeq paired-end sequencing technology. Ultra-deep sequencing data were analysed by SmartGene® platform. RASs mentioned in the literature were analysed and interpreted depending on genotype (GT) at 10% cut-off. RESULTS HCV genotyping showed 36 (50.0%) GT1a, 31 (43.1%) GT4d and 5 (6.9%) GT3a infections. Fifty-five patients (76.4%) were co-infected with HIV and 15 (20.8%) received PrEP. In GT1a viruses, NS3 RASs were found in 4/30 viruses (13.3%; S122 G/N, R155 K and I170 V) and Q80 K polymorphism was present in 14/30 viruses (46.7%). No NS3 RASs were detected in GT4d and GT3a viruses. NS5A RASs were detected in 3/36 GT1a viruses (8.3%; Q30E/R, L31 M and H58 L). NS5A subtype-specific polymorphisms L30R and T58 P were found at high frequencies in 31/31 (100%) and 16/31 (51.6%) GT4d viruses, respectively. One RAS M31 L was also observed along with the polymorphisms L30R and T58 P. No NS5A RASs were detected in GT3a viruses. CONCLUSION A low level of RASs to NS3 and NS5A inhibitors in pre-treatment samples was detected in the study population. Our findings reassure the clinical management of HCV infection in this high-risk population.
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Affiliation(s)
- Thuy Nguyen
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - Marc-Antoine Valantin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Services de maladies infectieuses et tropicales, F-75013 Paris, France
| | - Constance Delaugerre
- AP-HP, Hôpital Saint-Louis, Laboratoire de virologie, Paris, France; INSERM UMR 941, Université de Paris Diderot, Paris, France
| | - Corinne Amiel
- Sorbonne Université, Centre d'Immunologie et de Maladies Infectieuses (CIMI) UMRS CR7, Persistent Viral Infection (PVI) Team, Inserm U1135, AP-HP, Groupe Hospitalier Paris Est, Hôpital Tenon, Laboratoire de virologie, F-75020 Paris, France
| | | | - Thomas L'Yavanc
- Centre de santé sexuelle Le 190, Paris, France; Sorbonne Université, AP-HP, Hôpital Tenon, Department of Infectious Diseases, Paris, France
| | - Michel Ohayon
- Centre de santé sexuelle Le 190, Paris, France; Sorbonne Université, AP-HP, Hôpital Tenon, Department of Infectious Diseases, Paris, France
| | - Nadia Valin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Saint Antoine, Department of Infectious Diseases, F-75012 Paris, France
| | | | | | - Gilles Pialoux
- Sorbonne Université, AP-HP, Hôpital Tenon, Department of Infectious Diseases, Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - Jean-Michel Molina
- INSERM UMR 941, Université de Paris Diderot, Paris, France; AP-HP, Hôpital Saint-Louis, Department of Infectious Diseases, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - Eve Todesco
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France.
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Caputo V, Diotti RA, Boeri E, Hasson H, Sampaolo M, Criscuolo E, Bagaglio S, Messina E, Uberti-Foppa C, Castelli M, Burioni R, Mancini N, Clementi M, Clementi N. Detection of low-level HCV variants in DAA treated patients: comparison amongst three different NGS data analysis protocols. Virol J 2020; 17:103. [PMID: 32660499 PMCID: PMC7359454 DOI: 10.1186/s12985-020-01381-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/03/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Notwithstanding the efforts of direct-acting antivirals (DAAs) for the treatment of chronically infected hepatitis C virus (HCV) patients, concerns exist regarding the emergence of resistance-associated substitutions (RAS) related to therapy failure. Sanger sequencing is still the reference technique used for the detection of RAS and it detects viral variants present up to 15%, meaning that minority variants are undetectable, using this technique. To date, many studies are focused on the analysis of the impact of HCV low variants using next-generation sequencing (NGS) techniques, but the importance of these minority variants is still debated, and importantly, a common data analysis method is still not defined. METHODS Serum samples from four patients failing DAAs therapy were collected at baseline and failure, and amplification of NS3, NS5A and NS5B genes was performed on each sample. The genes amplified were sequenced using Sanger and NGS Illumina sequencing and the data generated were analyzed with different approaches. Three different NGS data analysis methods, two homemade in silico pipeline and one commercially available certified user-friendly software, were used to detect low-level variants. RESULTS The NGS approach allowed to infer also very-low level virus variants. Moreover, data processing allowed to generate high accuracy data which results in reduction in the error rates for each single sequence polymorphism. The results improved the detection of low-level viral variants in the HCV quasispecies of the analyzed patients, and in one patient a low-level RAS related to treatment failure was identified. Importantly, the results obtained from only two out of the three data analysis strategies were in complete agreement in terms of both detection and frequency of RAS. CONCLUSIONS These results highlight the need to find a robust NGS data analysis method to standardize NGS results for a better comprehension of the clinical role of low-level HCV variants. Based on the extreme importance of data analysis approaches for wet-data interpretation, a detailed description of the used pipelines and further standardization of the in silico analysis could allow increasing diagnostic laboratory networking to unleash true potentials of NGS.
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Affiliation(s)
- Valeria Caputo
- Laboratory of Medical Microbiology and Virology at "Vita-Salute" San Raffaele University, 20132, Milan, Italy
| | - Roberta Antonia Diotti
- Laboratory of Medical Microbiology and Virology at "Vita-Salute" San Raffaele University, 20132, Milan, Italy
| | - Enzo Boeri
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Hospital, 20132, Milan, Italy
| | - Hamid Hasson
- Department of Infectious Diseases, San Raffaele Hospital, 20132, Milan, Italy
| | - Michela Sampaolo
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Hospital, 20132, Milan, Italy
| | - Elena Criscuolo
- Laboratory of Medical Microbiology and Virology at "Vita-Salute" San Raffaele University, 20132, Milan, Italy
| | - Sabrina Bagaglio
- Department of Infectious Diseases, San Raffaele Hospital, 20132, Milan, Italy
| | - Emanuela Messina
- Department of Infectious Diseases, San Raffaele Hospital, 20132, Milan, Italy
| | | | - Matteo Castelli
- Laboratory of Medical Microbiology and Virology at "Vita-Salute" San Raffaele University, 20132, Milan, Italy
| | - Roberto Burioni
- Laboratory of Medical Microbiology and Virology at "Vita-Salute" San Raffaele University, 20132, Milan, Italy
| | - Nicasio Mancini
- Laboratory of Medical Microbiology and Virology at "Vita-Salute" San Raffaele University, 20132, Milan, Italy.,Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Hospital, 20132, Milan, Italy
| | - Massimo Clementi
- Laboratory of Medical Microbiology and Virology at "Vita-Salute" San Raffaele University, 20132, Milan, Italy.,Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Hospital, 20132, Milan, Italy
| | - Nicola Clementi
- Laboratory of Medical Microbiology and Virology at "Vita-Salute" San Raffaele University, 20132, Milan, Italy. .,Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Hospital, 20132, Milan, Italy.
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Merli M, Rossotti R, Travi G, Ferla F, Lauterio A, Angelini Zucchetti T, Alcantarini C, Bargiacchi O, De Carlis L, Puoti M. Sustained virological response with 16-week glecaprevir/pibrentasvir after failure to sofosbuvir/velpatasvir in post-transplant severe HCV recurrence in HIV. Transpl Infect Dis 2019; 21:e13165. [PMID: 31487082 DOI: 10.1111/tid.13165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 07/20/2019] [Accepted: 08/25/2019] [Indexed: 12/01/2022]
Abstract
Direct-acting antivirals (DAAs) demonstrated high efficacy and safety even in the post-liver transplant (LT) setting and in HIV-infected patients, but data are very limited in the early post-LT period with the most recently available DAA. Two HIV/HCV-coinfected LT recipients (both grafts from HIV/HCV-negative donors) experienced early HCV recurrence with severe hepatitis and were treated with sofosbuvir/velpatasvir for 12 weeks. Unfortunately, both patients failed: one (genotype 4d) showed virological breakthrough at week 3 with resistance-associated substitutions (RASs) for both NS5A and NS5B, while the other (genotype 1a) experienced virological relapse without RAS. Both progressed to fibrosing cholestatic hepatitis and were successfully retreated with glecaprevir/pibrentasvir for 16 weeks achieving sustained virological response. The higher prevalence of RAS in experienced genotype 4 patients and the long time to viral suppression observed in subjects with fibrosing cholestatic hepatitis should be taken into account, considering longer treatment duration to increase the chances of achieving sustained virological response.
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Affiliation(s)
- Marco Merli
- Division of Infectious Diseases, ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
| | - Roberto Rossotti
- Division of Infectious Diseases, ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
| | - Giovanna Travi
- Division of Infectious Diseases, ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
| | - Fabio Ferla
- Division of General Surgery & Abdominal Transplantation, ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
| | - Andrea Lauterio
- Division of General Surgery & Abdominal Transplantation, ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
| | | | - Chiara Alcantarini
- Department of Medical Sciences, Unit of Infectious Diseases, Amedeo di Savoia Hospital, University of Torino, Torino, Italy
| | - Olivia Bargiacchi
- Infectious Diseases Section, "Maggiore della Carità" Hospital, Novara, Italy
| | - Luciano De Carlis
- Division of General Surgery & Abdominal Transplantation, ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy.,School of Medicine, University of Milano-Bicocca, Milano, Italy
| | - Massimo Puoti
- Division of Infectious Diseases, ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
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Cuypers L, Thijssen M, Shakibzadeh A, Sabahi F, Ravanshad M, Pourkarim MR. Next-generation sequencing for the clinical management of hepatitis C virus infections: does one test fits all purposes? Crit Rev Clin Lab Sci 2019; 56:420-434. [PMID: 31317801 DOI: 10.1080/10408363.2019.1637394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
While the prospect of viral cure is higher than ever for individuals infected with the hepatitis C virus (HCV) due to ground-breaking progress in antiviral treatment, success rates are still negatively influenced by HCV's high genetic variability. This genetic diversity is represented in the circulation of various genotypes and subtypes, mixed infections, recombinant forms and the presence of numerous drug resistant variants among infected individuals. Common misclassifications by commercial genotyping assays in combination with the limitations of currently used targeted population sequencing approaches have encouraged researchers to exploit alternative methods for the clinical management of HCV infections. Next-generation sequencing (NGS), a revolutionary and powerful tool with a variety of applications in clinical virology, can characterize viral diversity and depict viral dynamics in an ultra-wide and ultra-deep manner. The level of detail it provides makes it the method of choice for the diagnosis and clinical assessment of HCV infections. The sequence library provided by NGS is of a higher magnitude and sensitivity than data generated by conventional methods. Therefore, these technologies are helpful to guide clinical practice and at the same time highly valuable for epidemiological studies. The decreasing costs of NGS to determine genotypes, mixed infections, recombinant strains and drug resistant variants will soon make it feasible to employ NGS in clinical laboratories, to assist in the daily care of patients with HCV.
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Affiliation(s)
- Lize Cuypers
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven , Leuven , Belgium
| | - Marijn Thijssen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven , Leuven , Belgium
| | - Arash Shakibzadeh
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University , Tehran , Iran
| | - Farzaneh Sabahi
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University , Tehran , Iran
| | - Mehrdad Ravanshad
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University , Tehran , Iran
| | - Mahmoud Reza Pourkarim
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven , Leuven , Belgium.,Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences , Shiraz , Iran.,Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine , Tehran , Iran
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