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Garcia-Cehic D, Rando A, Rodriguez-Frias F, Gregori J, Costa JG, Carrión JA, Macenlle R, Pamplona J, Castro-Iglesias A, Cañizares A, Tabernero D, Campos C, Buti M, Esteban JI, Quer J. Resistance-associated substitutions after sofosbuvir/velpatasvir/voxilaprevir triple therapy failure. J Viral Hepat 2021; 28:1319-1324. [PMID: 33720484 DOI: 10.1111/jvh.13497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 02/05/2023]
Abstract
Direct-acting antivirals (DAAs) resolve chronic HCV infection in >95% of patients, but a small percentage do not respond to DAA-based therapy. These may be difficult to treat because of resistance-associated substitutions (RAS) emerging after treatment failure. Triple therapy with sofosbuvir (SOF)/velpatasvir (VEL)/voxilaprevir (VOX) is the recommended retreatment after DAA-based failure. However, in rare cases, failure to triple therapy occurs, and there is little information characterizing the viruses that relapse. To determine the RAS profile after failing SOF/VEL/VOX, and seek suitable alternatives for retreatment, samples from 5 patients were analysed using MiSeq Illumina deep sequencing before and after triple therapy. All patients were men, aged 59-78 years, 2 HCV genotype (G) 1b and 3 G3a. The most prevalent NS3 substitutions after SOF/VEL/VOX failure were Y56F and A166T. Four patients had the NS5A RAS, Y93H, after triple failure, and Y93H was observed in both G1b patients before retreatment and after SOF/ledipasvir failure. In 2 G3a patients, Y93H appeared at triple failure, and on the other G3a, A30K persisted in 100% of viral genomes. Finally, G1b patients showed C316N in NS5B, associated with SOF failure, but G3a patients had no known NS5B substitutions. HCV RAS analysis identified the following substitutions present at higher rates after triple failure: Y56F in NS3 (G1b), A166T in NS3 (G3a), A30K or Y93H in NS5A, and C316N in NS5B (G1b). A RAS-based salvage treatment (SOF + glecaprevir/pibrentasvir + RBV) was successfully used in one G3a patient.
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Affiliation(s)
- Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Ariadna Rando
- Biochemistry and Microbiology Departments, Vall d'Hebron Institut de Recerca (VHIR, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Microbiology Departments, Vall d'Hebron Institut de Recerca (VHIR, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics SL, Sant Cugat del Vallès, Barcelona, Spain
| | - Juan Garcia Costa
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | - José Antonio Carrión
- Liver Section, Gastroenterology Department, Hospital del Mar, Parc de Salur Mar, Barcelona, Spain
| | - Ramiro Macenlle
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | - Javier Pamplona
- Gastroenterology Department, Hospital de Santa Caterina, Salt. Girona, Spain
| | | | - Angelina Cañizares
- Microbiology Department, Institut de Investigación Biomédica de a Coruña (INIBIC) - Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Microbiology Departments, Vall d'Hebron Institut de Recerca (VHIR, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Maria Buti
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
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Boyd A, Miailhes P, Chas J, Valantin MA, Yazdanpanah Y, Rosenthal E, Chevaliez S, Piroth L, Rougier H, Peytavin G, Pialoux G, Girard PM, Lacombe K. Grazoprevir/elbasvir for the immediate treatment of recently acquired HCV genotype 1 or 4 infection in MSM. J Antimicrob Chemother 2021; 75:1961-1968. [PMID: 32306039 DOI: 10.1093/jac/dkaa091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 02/06/2020] [Accepted: 02/19/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND In Europe, increases in HCV infection have been observed over the last two decades in MSM, making them a key population for recently acquired HCV. Alternative combinations of direct-acting antiviral agents against early HCV infection need to be assessed. PATIENTS AND METHODS In this pilot trial, MSM with recently acquired genotype 1 or 4 HCV infection were prospectively included and received 8 weeks of oral grazoprevir 100 mg and elbasvir 50 mg in a fixed-dose combination administered once daily. The primary endpoint was sustained virological response evaluated 12 weeks after the end of treatment (EOT) (SVR12). Secondary endpoints were the virological characterization of failures, the quality of life before, during and after treatment and the rate of reinfection. RESULTS In a 15 month period, 30 patients were enrolled, all of whom were MSM. Of the 29 patients completing follow-up, 28 (96%, 95% CI = 82%-99%) achieved SVR12. One patient interrupted follow-up (suicide) but had undetectable plasma HCV RNA at EOT. One patient with suboptimal adherence confirmed by plasma drug monitoring relapsed and developed NS3, NS5A and NS5B resistance-associated substitutions (V36M, M28V and S556G). The most common adverse events related to study drug were diarrhoea (n = 4, 13%), insomnia (n = 2, 7%) and fatigue (n = 2, 7%), although no patient discontinued treatment. No HIV RNA breakthrough was reported in the 28 patients with HIV coinfection. At Week 48, reinfection was diagnosed in three patients. CONCLUSIONS Our data support the use of grazoprevir/elbasvir for immediate treatment against HCV in order to reduce HCV transmission in MSM.
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Affiliation(s)
- Anders Boyd
- INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75012 Paris, France
| | - Patrick Miailhes
- Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Service de Maladies Infectieuses et Tropicales, Lyon, France
| | - Julie Chas
- AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et tropicales, Paris, France
| | - Marc-Antoine Valantin
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Maladies Infectieuses et tropicales, Paris, France
| | - Yazdan Yazdanpanah
- AP-HP, Hôpital Bichat-Claude Bernard, Service de Maladies Infectieuses et tropicales, Paris, France
| | - Eric Rosenthal
- Hôpital de l'Archet, Service de médecine interne, Nice, France
| | - Stephane Chevaliez
- AP-HP, département de Virologie, Hôpital Henri Mondor, National Reference Center for Viral Hepatitis B, C and delta, INSERM U955, Créteil, France
| | - Lionel Piroth
- Département d'infectiologie, CHU de Dijon, 21079 Dijon, France; INSERM CIC 1432, Université de Bourgogne, 21079 Dijon, France
| | | | - Gilles Peytavin
- AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Pharmacologie-Toxicologie and IAME, UMR 1137, Université Paris Diderot, Sorbonne Paris Cité and INSERM, Paris, France
| | - Gilles Pialoux
- AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et tropicales, Paris, France.,Sorbonne Université, Paris, France
| | - Pierre-Marie Girard
- Service de maladies infectieuses et tropicales, Hôpital St Antoine, AP-HP, Paris, France.,Sorbonne Université, INSERM UMR-S1136, Institut Pierre Louis de Santé Publique, Paris, France
| | - Karine Lacombe
- Service de maladies infectieuses et tropicales, Hôpital St Antoine, AP-HP, Paris, France.,Sorbonne Université, INSERM UMR-S1136, Institut Pierre Louis de Santé Publique, Paris, France
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Pawlotsky JM, Negro F, Aghemo A, Berenguer M, Dalgard O, Dusheiko G, Marra F, Puoti M, Wedemeyer H. EASL recommendations on treatment of hepatitis C: Final update of the series ☆. J Hepatol 2020; 73:1170-1218. [PMID: 32956768 DOI: 10.1016/j.jhep.2020.08.018] [Citation(s) in RCA: 573] [Impact Index Per Article: 143.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 02/08/2023]
Abstract
Hepatitis C virus (HCV) infection is a major cause of chronic liver disease, with approximately 71 million chronically infected individuals worldwide. Clinical care for patients with HCV-related liver disease has advanced considerably thanks to an enhanced understanding of the pathophysiology of the disease, as well as developments in diagnostic procedures and improvements in therapy and prevention. These therapies make it possible to eliminate hepatitis C as a major public health threat, as per the World Health Organization target, although the timeline and feasibility vary from region to region. These European Association for the Study of the Liver recommendations on treatment of hepatitis C describe the optimal management of patients with recently acquired and chronic HCV infections in 2020 and onwards.
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Manso CF, Bibby DF, Lythgow K, Mohamed H, Myers R, Williams D, Piorkowska R, Chan YT, Bowden R, Ansari MA, Ip CLC, Barnes E, Bradshaw D, Mbisa JL. Technical Validation of a Hepatitis C Virus Whole Genome Sequencing Assay for Detection of Genotype and Antiviral Resistance in the Clinical Pathway. Front Microbiol 2020; 11:576572. [PMID: 33162957 PMCID: PMC7583327 DOI: 10.3389/fmicb.2020.576572] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/14/2020] [Indexed: 01/05/2023] Open
Abstract
Choice of direct acting antiviral (DAA) therapy for Hepatitis C Virus (HCV) in the United Kingdom and similar settings usually requires knowledge of the genotype and, in some cases, antiviral resistance (AVR) profile of the infecting virus. To determine these, most laboratories currently use Sanger technology, but next-generation sequencing (NGS) offers potential advantages in throughput and accuracy. However, NGS poses unique technical challenges, which require idiosyncratic development and technical validation approaches. This applies particularly to virology, where sequence diversity is high and the amount of starting genetic material is low, making it difficult to distinguish real data from artifacts. We describe the development and technical validation of a sequence capture-based HCV whole genome sequencing (WGS) assay to determine viral genotype and AVR profile. We use clinical samples of known subtypes and viral loads, and simulated FASTQ datasets to validate the analytical performances of both the wet laboratory and bioinformatic pipeline procedures. We show high concordance of the WGS assay compared to current "gold standard" Sanger assays. Specificity was 92.3 and 96.1% for AVR and genotyping, respectively. Discordances were due to the inability of Sanger assays to assign the correct subtype or accurately call mixed drug-resistant variants. We show high repeatability and reproducibility with >99.8% sequence similarity between sequence runs as well as high precision for variant frequency detection at >98.8% in the 95th percentile. Post-sequencing bioinformatics quality control workflows allow the accurate distinction between mixed infections, cross-contaminants and recombinant viruses at a threshold of >5% for the minority population. The sequence capture-based HCV WGS assay is more accurate than legacy AVR and genotyping assays. The assay has now been implemented in the clinical pathway of England's National Health Service HCV treatment programs, representing the first validated HCV WGS pipeline in clinical service. The data generated will additionally provide granular national-level genomic information for public health policy making and support the WHO HCV elimination strategy.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Rory Bowden
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - M. Azim Ansari
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Peter Medawar Building for Pathogen Research and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Camilla L. C. Ip
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | | | - Jean L. Mbisa
- Public Health England, London, United Kingdom
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
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Dailey PJ, Elbeik T, Holodniy M. Companion and complementary diagnostics for infectious diseases. Expert Rev Mol Diagn 2020; 20:619-636. [PMID: 32031431 DOI: 10.1080/14737159.2020.1724784] [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] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Companion diagnostics (CDx) are important in oncology therapeutic decision-making, but specific regulatory-approved CDx for infectious disease treatment are officially lacking. While not approved as CDx, several ID diagnostics are used as CDx. The diagnostics community, manufacturers, and regulatory agencies have made major efforts to ensure that diagnostics for new antimicrobials are available at or near release of new agents. AREAS COVERED This review highlights the status of Complementary and companion diagnostic (c/CDx) in the infectious disease literature, with a focus on genotypic antimicrobial resistance testing against pathogens as a class of diagnostic tests. EXPERT OPINION CRISPR, sepsis markers, and narrow spectrum antimicrobials, in addition to current and emerging technologies, present opportunities for infectious disease c/CDx. Challenges include slow guideline revision, high costs for regulatory approval, lengthy buy in by agencies, discordant pharmaceutical/diagnostic partnerships, and higher treatment costs. The number of patients and available medications used to treat different infectious diseases is well suited to support competing diagnostic tests. However, newer approaches to treatment (for example, narrow spectrum antibiotics), may be well suited for a small number of patients, i.e. a niche market in support of a CDx. The current emphasis is rapid and point-of-care (POC) diagnostic platforms as well as changes in treatment.
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Affiliation(s)
- Peter J Dailey
- School of Public Health, University of California, Berkeley , Berkeley, CA, USA.,The Foundation for Innovative New Diagnostics (FIND) , Geneva, Switzerland
| | - Tarek Elbeik
- VA Palo Alto Health Care System, Department of Veterans Affairs , Palo Alto, CA, USA
| | - Mark Holodniy
- VA Palo Alto Health Care System, Department of Veterans Affairs , Palo Alto, CA, USA.,Division of Infectious Diseases and Geographic Medicine, Stanford University , Stanford, CA, USA
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