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Vo-Quang E, Pawlotsky JM. 'Unusual' HCV genotype subtypes: origin, distribution, sensitivity to direct-acting antiviral drugs and behaviour on antiviral treatment and retreatment. Gut 2024; 73:1570-1582. [PMID: 38782565 PMCID: PMC11347264 DOI: 10.1136/gutjnl-2024-332177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
The high genetic diversity of hepatitis C virus (HCV) has led to the emergence of eight genotypes and a large number of subtypes in limited geographical areas. Currently approved pangenotypic DAA regimens have been designed and developed to be effective against the most common subtypes (1a, 1b, 2a, 2b, 2c, 3a, 4a, 5a and 6a). However, large populations living in Africa and Asia, or who have migrated from these regions to industrialised countries, are infected with 'unusual', non-epidemic HCV subtypes, including some that are inherently resistant to currently available direct-acting antiviral (DAA) drugs due to the presence of natural polymorphisms at resistance-associated substitution positions. In this review article, we describe the origin and subsequent global spread of HCV genotypes and subtypes, the current global distribution of common and unusual HCV subtypes, the polymorphisms naturally present in the genome sequences of unusual HCV subtypes that may confer inherently reduced susceptibility to DAA drugs and the available data on the response of unusual HCV subtypes to first-line HCV therapy and retreatment. We conclude that the problem of unusual HCV subtypes that are inherently resistant to DAAs and its threat to the global efforts to eliminate viral hepatitis are largely underestimated and warrant vigorous action.
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Affiliation(s)
- Erwan Vo-Quang
- National Reference Centre for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
- Institut Mondor de Recherche Biomédicale (INSERM U955), Créteil, France
- Department of Hepatology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
| | - Jean-Michel Pawlotsky
- National Reference Centre for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
- Institut Mondor de Recherche Biomédicale (INSERM U955), Créteil, France
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2
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Ahovègbé L, Shah R, Kpossou AR, Davis C, Niebel M, Filipe A, Goldstein E, Alassan KS, Keke R, Sehonou J, Kodjoh N, Gbedo SE, Ray S, Wilkie C, Vattipally S, Tong L, Kamba PF, Gbenoudon SJ, Gunson R, Ogwang P, Thomson EC. Hepatitis C virus diversity and treatment outcomes in Benin: a prospective cohort study. THE LANCET. MICROBE 2024; 5:697-706. [PMID: 38889738 DOI: 10.1016/s2666-5247(24)00041-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/22/2023] [Accepted: 02/01/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND 10 million people are chronically infected with the hepatitis C virus (HCV) in sub-Saharan Africa. The assessment of viral genotypes and treatment response in this region is necessary to achieve the WHO target of worldwide elimination of viral hepatitis by 2030. We aimed to investigate the prevalence of HCV genotypes and outcomes of treatment with direct-acting antiviral agents in Benin, a country with a national HCV seroprevalence of 4%. METHODS This prospective cohort study was conducted at two referral hospitals in Benin. Individuals were eligible for inclusion if they were seropositive for HCV and willing to consent to participation in the study; exclusion criteria were an inability to give consent or incarceration. Viraemia was confirmed by PCR. The primary outcomes were to identify HCV genotypes and measure sustained virological response rates 12 weeks after completion of treatment (SVR12) with a 12-week course of sofosbuvir-velpatasvir or sofosbuvir-ledipasvir, with or without ribavirin. We conducted phylogenetic and resistance analyses after the next-generation sequencing of samples with a cycle threshold (Ct) value of 30 or fewer cycles. The in-vitro efficacy of NS5A inhibitors was tested using a subgenomic replicon assay. FINDINGS Between June 2, 2019, and Dec 30, 2020, 148 individuals were screened for eligibility, of whom 100 were recruited prospectively to the study. Plasma samples from 79 (79%) of the 100 participants were positive for HCV by PCR. At the time of the study, 52 (66%) of 79 patients had completed treatment, with an SVR12 rate of 94% (49 of 52). 57 (72%) of 79 samples had a Ct value of 30 or fewer cycles and were suitable for whole-genome sequencing, from which we characterised 29 (51%) samples as genotype 1 and 28 (49%) as genotype 2. Three new genotype 1 subtypes (1q, 1r, and 1s) and one new genotype 2 subtype (2xa) were identified. The most commonly detected subtype was 2d (12 [21%] of 57 samples), followed by 1s (eight [14%]), 1r (five [9%]), 1b (four [7%]), 1q (three [5%]), 2xa (three [5%]), and 2b (two [3%]). 20 samples (11 genotype 2 and nine genotype 1) were unassigned new singleton lineages. 53 (93%) of 57 sequenced samples had at least two resistance-associated substitutions within the NS5A gene. Subtype 2d was associated with a lower-than-expected SVR12 rate (eight [80%] of ten patients). For one patient, with subtype 2b, treatment was not successful. INTERPRETATION This study revealed a high SVR rate in Benin among individuals treated for HCV with sofosbuvir-velpatasvir, including those with highly diverse viral genotypes. Further studies of treatment effectiveness in genotypes 2d and 2b are indicated. FUNDING Medical Research Council, Wellcome, Global Challenges Research Fund, Academy of Medical Sciences, and PHARMBIOTRAC.
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Affiliation(s)
- Lucrèce Ahovègbé
- Mbarara University of Science and Technology, Mbarara, Uganda; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
| | - Rajiv Shah
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Aboudou Raïmi Kpossou
- Clinique Universitaire d'Hépato-gastroentérologie, Centre National Hospitalier et Universitaire Hubert Koutoukou Maga, Cotonou, Benin
| | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Marc Niebel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Ana Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Emily Goldstein
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, UK
| | | | - René Keke
- Programme National de Lutte contre le SIDA, Cotonou, Benin
| | - Jean Sehonou
- Clinique Universitaire d'Hépato-gastroentérologie, Centre National Hospitalier et Universitaire Hubert Koutoukou Maga, Cotonou, Benin
| | - Nicolas Kodjoh
- Programme National de Lutte contre les Hépatites, Cotonou, Benin
| | | | - Surajit Ray
- School of Mathematics and Statistics, University of Glasgow, Glasgow, UK
| | - Craig Wilkie
- School of Mathematics and Statistics, University of Glasgow, Glasgow, UK
| | | | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Pakoyo F Kamba
- Department of Pharmacy, School of Health Sciences, Makerere University, Kampala, Uganda
| | - S Judith Gbenoudon
- Laboratory of Immunology, Infectious and Allergic Diseases, Institute of Applied Biomedical Sciences, Faculty of Sciences and Technology, University of Abomey-Calavi, Cotonou, Benin
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Patrick Ogwang
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; London School of Hygiene & Tropical Medicine, London, UK.
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Loarec A, Gutierrez AG, Muvale G, Couto A, Nguyen A, Yerly S, Pinto Y, Madeira N, Gonzales A, Molfino L, Ciglenecki I, Antabak NT. Hepatitis C treatment program in Maputo, Mozambique, the challenge of genotypes and key populations: A 5-year retrospective analysis of routine programmatic data. Health Sci Rep 2023; 6:e1165. [PMID: 37008813 PMCID: PMC10061494 DOI: 10.1002/hsr2.1165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 04/04/2023] Open
Abstract
Background and Aims Hepatitis C (HCV) programs face challenges, especially linked to key populations to achieve World Health Organization (WHO) goals of eliminating hepatitis. Médecins Sans Frontières and Mozambique's Ministry of Health first implemented HCV treatment in Maputo, in 2016 and harm reduction activities in 2017. Methods We retrospectively analyzed routine data of patients enrolled between December 2016 and July 2021. Genotyping was systematically requested up to 2018 and subsequently in cases of treatment failure. Sustainable virological response was assessed 12 weeks after the end of treatment by sofosbuvir-daclatasvir or sofosbuvir-velpatasvir. Results Two hundred and two patients were enrolled, with 159 (78.71%) males (median age: 41 years [interquartile range (IQR): 37.10, 47.00]). Risk factors included drug use (142/202; 70.29%). One hundred and eleven genotyping results indicated genotype 1 predominant (87/111; 78.37%). Sixteen patients presented genotype 4, with various subtypes. The people who used drugs and HIV coinfected patients were found more likely to present a genotype 1. Intention-to-treat analysis showed 68.99% (89/129) cure rate among the patients initiated and per-protocol analysis, 88.12% (89/101) cure rate. Nineteen patients received treatment integrated with opioid substitution therapy, with a 100% cure rate versus 59.37% (38/64) for initiated ones without substitution therapy (p < 0.001). Among the resistance testing performed, NS5A resistance-associated substitutions were found in seven patients among the nine tested patients and NS5B ones in one patient. Conclusion We found varied genotypes, including some identified as difficult-to-treat subtypes. People who used drugs were more likely to present genotype 1. In addition, opioid substitution therapy was key for these patients to achieve cure. Access to second-generation direct-acting antivirals (DAAs) and integration of HCV care with harm reduction are crucial to program effectiveness.
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Affiliation(s)
- Anne Loarec
- Médecins Sans Frontières (MSF)MaputoMozambique
| | | | | | | | - Aude Nguyen
- Service des Maladies InfectieusesHôpitaux Universitaires de GenèveGenèveSwitzerland
| | - Sabine Yerly
- Laboratory of VirologyHôpitaux Universitaires de GenèveGenevaSwitzerland
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Diakite M, Shaw-Saliba K, Lau CY. Malignancy and viral infections in Sub-Saharan Africa: A review. FRONTIERS IN VIROLOGY (LAUSANNE, SWITZERLAND) 2023; 3:1103737. [PMID: 37476029 PMCID: PMC10358275 DOI: 10.3389/fviro.2023.1103737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
The burden of malignancy related to viral infection is increasing in Sub-Saharan Africa (SSA). In 2018, approximately 2 million new cancer cases worldwide were attributable to infection. Prevention or treatment of these infections could reduce cancer cases by 23% in less developed regions and about 7% in developed regions. Contemporaneous increases in longevity and changes in lifestyle have contributed to the cancer burden in SSA. African hospitals are reporting more cases of cancer related to infection (e.g., cervical cancer in women and stomach and liver cancer in men). SSA populations also have elevated underlying prevalence of viral infections compared to other regions. Of 10 infectious agents identified as carcinogenic by the International Agency for Research on Cancer, six are viruses: hepatitis B and C viruses (HBV and HCV, respectively), Epstein-Barr virus (EBV), high-risk types of human papillomavirus (HPV), Human T-cell lymphotropic virus type 1 (HTLV-1), and Kaposi's sarcoma herpesvirus (KSHV, also known as human herpesvirus type 8, HHV-8). Human immunodeficiency virus type 1 (HIV) also facilitates oncogenesis. EBV is associated with lymphomas and nasopharyngeal carcinoma; HBV and HCV are associated with hepatocellular carcinoma; KSHV causes Kaposi's sarcoma; HTLV-1 causes T-cell leukemia and lymphoma; HPV causes carcinoma of the oropharynx and anogenital squamous cell cancer. HIV-1, for which SSA has the greatest global burden, has been linked to increasing risk of malignancy through immunologic dysregulation and clonal hematopoiesis. Public health approaches to prevent infection, such as vaccination, safer injection techniques, screening of blood products, antimicrobial treatments and safer sexual practices could reduce the burden of cancer in Africa. In SSA, inequalities in access to cancer screening and treatment are exacerbated by the perception of cancer as taboo. National level cancer registries, new screening strategies for detection of viral infection and public health messaging should be prioritized in SSA's battle against malignancy. In this review, we discuss the impact of carcinogenic viruses in SSA with a focus on regional epidemiology.
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Affiliation(s)
- Mahamadou Diakite
- University Clinical Research Center, University of Sciences, Techniques, and Technologies, Bamako, Mali
| | - Kathryn Shaw-Saliba
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Chuen-Yen Lau
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
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5
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Brzdęk M, Dobrowolska K, Flisiak R, Zarębska-Michaluk D. Genotype 4 hepatitis C virus-a review of a diverse genotype. Adv Med Sci 2023; 68:54-59. [PMID: 36640687 DOI: 10.1016/j.advms.2022.12.003] [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: 06/16/2022] [Revised: 12/02/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023]
Abstract
PURPOSE Hepatitis C virus (HCV) infection remains a major health problem and one of the leading causes of chronic liver disease worldwide. The purpose of this paper was to summarize knowledge about the epidemiology of HCV genotype (GT) 4 infection, similarities and differences with other genotypes, specific problems associated with this genotype, and treatment regimens used to treat GT4-infected patients. METHODS We performed an accurate search for literature using the PubMed database to select high-quality reviews and original articles concerning this topic. RESULTS GT4 with a global prevalence of 8% takes third place, closing the global HCV podium in terms of frequency. However, there are regions where GT4 infections are dominant, such as sub-Saharan and North Africa, and the Middle East. The disease course and complications are generally similar to those of chronic hepatitis C caused by other genotypes, although the faster progression of fibrosis was demonstrated in patients with coexisting schistosomiasis. In the era of interferon-based therapy, GT4-infected patients were described as difficult to treat due to suboptimal response. A breakthrough in the treatment of HCV-infected patients, including those with GT4 infection, was the introduction of direct-acting antiviral drugs. CONCLUSIONS The availability of safe and effective therapy has created a real opportunity for HCV eradication in line with the goal set by the World Health Organization. An example of a country where this is happening is Egypt, where GT4 accounts for more than 90% of HCV infections. There, broad access to therapy has been effectively supported by population-based screening.
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Affiliation(s)
- Michał Brzdęk
- Collegium Medicum, Jan Kochanowski University, Kielce, Poland.
| | | | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Bialystok, Bialystok, Poland
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6
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Adeboyejo K, King BJ, Tsoleridis T, Tarr AW, McLauchlan J, Irving WL, Ball JK, McClure CP. Hepatitis C subtyping assay failure in UK patients born in sub-Saharan Africa: Implications for global treatment and elimination. J Med Virol 2023; 95:e28178. [PMID: 36168235 PMCID: PMC10092547 DOI: 10.1002/jmv.28178] [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: 08/01/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND AND AIMS: The newly developed direct-acting antivirals have revolutionized the treatment of chronic hepatitis C virus (HCV), with cure rates as high as 98% in some cohorts. Although genome sequencing has demonstrated that some subtypes of HCV naturally harbor drug resistance associated substitutions (RAS), these are often overlooked as "rarities." Furthermore, commercial subtyping assays and associated epidemiological findings are skewed towards Western cohorts and whole-genome sequencing can be problematic to deploy without significant infrastructure and training support. We thus aimed to develop a simple, robust and accurate HCV subtyping pipeline, to optimize and streamline molecular detection and sequence-based typing of diverse RAS-containing subtypes. METHODS HCV serum derived from 146 individuals, whose likely source of infection was from sub-Saharan Africa (SSA) was investigated with a novel panel of single round polymerase chain reaction (PCR) assays targeting NS5B and NS5A genomic regions. Virus subtype assignments were determined by pairwise-distance analysis and compared to both diagnostic laboratory assignments and free-to-use online typing tools. RESULTS Partial NS5A and NS5B sequences were respectively obtained from 131 to 135 HCV-positive patients born in 19 different countries from SSA but attending clinics in the UK. We determined that routine clinical diagnostic methods incorrectly subtyped 59.0% of samples, with a further 6.8% incorrectly genotyped. Of five commonly used online tools, Geno2Pheno performed most effectively in determining a subtype in agreement with pairwise distance analysis. CONCLUSION This study provides a simple low-cost pathway to accurately subtype in SSA, guide regional therapeutic choice and assist global surveillance and elimination initiatives.
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Affiliation(s)
- Kazeem Adeboyejo
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
| | - Barnabas J King
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
| | - Theocharis Tsoleridis
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
| | - Alexander W Tarr
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - William L Irving
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK.,Clinical Microbiology, Nottingham University Hospitals, Nottingham, UK.,Nottingham University Hospitals, Nottingham, UK
| | - Jonathan K Ball
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
| | - C Patrick McClure
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
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7
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Isfordink C, Boyd A, Mocroft A, Kusejko K, Smit C, de Wit S, Mahungu T, Falconer K, Wandeler G, Cavassini M, Stöckle M, Schinkel J, Rauch A, Peters L, van der Valk M. Low Risk of Failing Direct-Acting Antivirals in People With Human Immunodeficiency Virus/Hepatitis C Virus From Sub-Saharan Africa or Southeastern Asia: A European Cross-Sectional Study. Open Forum Infect Dis 2022; 9:ofac508. [PMID: 36320198 PMCID: PMC9605702 DOI: 10.1093/ofid/ofac508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/28/2022] [Indexed: 11/21/2022] Open
Abstract
Background Several studies have reported suboptimal efficacy of direct-acting antivirals (DAAs) to treat hepatitis C virus (HCV) subtypes endemic to sub-Saharan Africa (SSA) and Southeastern Asia (SEA). The extent of this issue in individuals with human immunodeficiency virus (HIV)/HCV from SSA or SEA residing in Europe is unknown. Methods We retrospectively analyzed data from several prospective European cohorts of people living with HIV. We included individuals with HIV/HCV who originated from SSA or SEA, were treated with interferon-free DAAs, and had an available HCV RNA result ≥12 weeks after the end of treatment. The primary outcome was sustained virological response at least 12 weeks after the end of treatment (SVR12). Results Of the 3293 individuals with HIV/HCV treated with DAA and with available SVR12 data, 142 were from SSA (n = 64) and SEA (n = 78). SVR12 was achieved by 60 (94% [95% confidence interval {CI}, 86%-98%]) individuals from SSA and 76 (97% [95% CI, 92%-99%]) from SEA. The genotypes of the 6 individuals failing DAA treatment were 2, 3a, 3h, 4a, 4c, and 6j. For 2 of the 4 unsuccessfully treated individuals with available sequence data at treatment failure, NS5A resistance-associated substitutions were present (30R/93S in an individual with genotype 4c and 31M in an individual with genotype 6j). Conclusions SVR12 rates were high in individuals with HIV/HCV residing in Europe and originating from regions where intrinsically NS5A-resistant HCV strains are endemic. HCV elimination for this population in Europe is unlikely to be hampered by suboptimal DAA efficacy.
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Affiliation(s)
- Cas Isfordink
- Division of Infectious Diseases, Department of Internal Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Anders Boyd
- Stichting HIV Monitoring, Amsterdam, The Netherlands
- Department of Infectious Diseases, Research and Prevention, Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Amanda Mocroft
- Centre for Clinical Research, Epidemiology, Modelling and Evaluation, Institute for Global Health, University College London, London, United Kingdom
- Centre of Excellence for Health, Immunity and Infections, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Colette Smit
- Stichting HIV Monitoring, Amsterdam, The Netherlands
| | - Stephane de Wit
- Division of Infectious Diseases, St Pierre Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Tabitha Mahungu
- Department of Infectious Diseases, Royal Free Hospital London NHS Foundation Trust, London, United Kingdom
| | - Karolin Falconer
- Department of Infectious Diseases/Venhälsan, Södersjukhuset, Stockholm, Sweden
| | - Gilles Wandeler
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Janke Schinkel
- Section of Clinical Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Andri Rauch
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Lars Peters
- Centre of Excellence for Health, Immunity and Infections, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Marc van der Valk
- Division of Infectious Diseases, Department of Internal Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Stichting HIV Monitoring, Amsterdam, The Netherlands
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Aranday-Cortes E, McClure CP, Davis C, Irving WL, Adeboyejo K, Tong L, da Silva Filipe A, Sreenu V, Agarwal K, Mutimer D, Stone B, Cramp ME, Thomson EC, Ball JK, McLauchlan J. Real-World Outcomes of Direct-Acting Antiviral Treatment and Retreatment in United Kingdom-Based Patients Infected With Hepatitis C Virus Genotypes/Subtypes Endemic in Africa. J Infect Dis 2022; 226:995-1004. [PMID: 33668068 PMCID: PMC9492310 DOI: 10.1093/infdis/jiab110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/23/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Chronic hepatitis C virus (HCV) infection affects 71 million individuals, mostly residing in low- and middle-income countries (LMICs). Direct-acting antivirals (DAAs) give high rates of sustained virological response (SVR) in high-income countries where a restricted range of HCV genotypes/subtypes circulate. METHODS We studied United Kingdom-resident patients born in Africa to examine DAA effectiveness in LMICs where there is far greater breadth of HCV genotypes/subtypes. Viral genome sequences were determined from 233 patients. RESULTS Full-length viral genomic sequences for 26 known subtypes and 5 previously unidentified isolates covering 5 HCV genotypes were determined. From 149 patients who received DAA treatment/retreatment, the overall SVR was 93%. Treatment failure was associated primarily with 2 subtypes, gt1l and gt4r, using sofosbuvir/ledipasvir. These subtypes contain natural resistance-associated variants that likely contribute to poor efficacy with this drug combination. Treatment failure was also significantly associated with hepatocellular carcinoma. CONCLUSIONS DAA combinations give high SVR rates despite the high HCV diversity across the African continent except for subtypes gt1l and gt4r, which respond poorly to sofosbuvir/ledipasvir. These subtypes are widely distributed across Western, Central, and Eastern Africa. Thus, in circumstances where accurate genotyping is absent, ledipasvir and its generic compounds should not be considered as a recommended treatment option.
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Affiliation(s)
| | - C Patrick McClure
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust and University of Nottingham, Nottingham, United Kingdom
- Wolfson Centre for Emerging Virus Research, University of Nottingham, Nottingham, United Kingdom
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Christopher Davis
- MRC–University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - William L Irving
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust and University of Nottingham, Nottingham, United Kingdom
- Wolfson Centre for Emerging Virus Research, University of Nottingham, Nottingham, United Kingdom
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Kazeem Adeboyejo
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust and University of Nottingham, Nottingham, United Kingdom
- Wolfson Centre for Emerging Virus Research, University of Nottingham, Nottingham, United Kingdom
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, United Kingdom
- Olabisi Onabanjo University, Ago Iwoje, Nigeria
| | - Lily Tong
- MRC–University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC–University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Vattipally Sreenu
- MRC–University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Kosh Agarwal
- Institute of Liver Studies, Kings College Hospital National Health Service Foundation Trust, London, United Kingdom
| | - David Mutimer
- Queen Elizabeth Hospital and University of Birmingham, Birmingham, United Kingdom
| | - Benjamin Stone
- Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals National Health Service Foundation Trust, Sheffield, United Kingdom
| | - Matthew E Cramp
- South West Liver Unit, Derriford Hospital and Peninsula Schools of Medicine and Dentistry, Plymouth, United Kingdom
| | - Emma C Thomson
- MRC–University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Jonathan K Ball
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust and University of Nottingham, Nottingham, United Kingdom
- Wolfson Centre for Emerging Virus Research, University of Nottingham, Nottingham, United Kingdom
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, United Kingdom
| | - John McLauchlan
- MRC–University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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9
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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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10
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Kateera F, Shumbusho F, Manirambona L, Kabihizi J, Murangwa A, Serumondo J, Makuza JD, Nsanzimana S, Muvunyi CM, Kabakambira JD, Sylvain H, Camus G, Grant PM, Gupta N. Safety and efficacy of sofosbuvir-velpatasvir to treat chronic hepatitis C virus infection in treatment-naive patients in Rwanda (SHARED-3): a single-arm trial. Lancet Gastroenterol Hepatol 2022; 7:533-541. [DOI: 10.1016/s2468-1253(21)00398-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023]
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11
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Stockdale AJ, Kreuels B, Shawa IT, Meiring JE, Thindwa D, Silungwe NM, Chetcuti K, Joekes E, Mbewe M, Mbale B, Patel P, Kachala R, Patel PD, Malewa J, Finch P, Davis C, Shah R, Tong L, da Silva Filipe A, Thomson EC, Geretti AM, Gordon MA. A clinical and molecular epidemiological survey of hepatitis C in Blantyre, Malawi, suggests a historic mechanism of transmission. J Viral Hepat 2022; 29:252-262. [PMID: 35075742 PMCID: PMC9305194 DOI: 10.1111/jvh.13646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/06/2022] [Indexed: 12/09/2022]
Abstract
Hepatitis C virus (HCV) is a leading cause of liver disease worldwide. There are no previous representative community HCV prevalence studies from Southern Africa, and limited genotypic data. Epidemiological data are required to inform an effective public health response. We conducted a household census-based random sampling serological survey, and a prospective hospital-based study of patients with cirrhosis and hepatocellular carcinoma (HCC) in Blantyre, Malawi. We tested participants with an HCV antigen/antibody ELISA (Monolisa, Bio-Rad), confirmed with PCR (GeneXpert, Cepheid) and used line immunoassay (Inno-LIA, Fujiribio) for RNA-negative participants. We did target-enrichment whole-genome HCV sequencing (NextSeq, Illumina). Among 96,386 censused individuals, we randomly selected 1661 people aged ≥16 years. Population-standardized HCV RNA prevalence was 0.2% (95% CI 0.1-0.5). Among 236 patients with cirrhosis and HCC, HCV RNA prevalence was 1.9% and 5.0%, respectively. Mapping showed that HCV RNA+ patients were from peri-urban areas surrounding Blantyre. Community and hospital HCV RNA+ participants were older than comparator HCV RNA-negative populations (median 53 vs 30 years for community, p = 0.01 and 68 vs 40 years for cirrhosis/HCC, p < 0.001). Endemic HCV genotypes (n = 10) were 4v (50%), 4r (30%) and 4w (10%). In this first census-based community serological study in Southern Africa, HCV was uncommon in the general population, was centred on peri-urban regions and was attributable for <5% of liver disease. HCV infection was observed only among older people, suggesting a historic mechanism of transmission. Genotype 4r, which has been associated with treatment failure with ledipasvir and daclatasvir, is endemic.
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Affiliation(s)
- Alexander J Stockdale
- Malawi-Liverpool-Wellcome Trust Programme, Blantyre, Malawi.,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Benno Kreuels
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine and 1st Department of Medicine, University Medical Centre, Hamburg-Eppendorf, Hamburg, Germany.,Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Isaac T Shawa
- Malawi-Liverpool-Wellcome Trust Programme, Blantyre, Malawi.,Kamuzu University of Health Sciences, Blantyre, Malawi
| | - James E Meiring
- Malawi-Liverpool-Wellcome Trust Programme, Blantyre, Malawi.,Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Deus Thindwa
- Malawi-Liverpool-Wellcome Trust Programme, Blantyre, Malawi.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Karen Chetcuti
- Malawi-Liverpool-Wellcome Trust Programme, Blantyre, Malawi.,Kamuzu University of Health Sciences, Blantyre, Malawi
| | | | - Maurice Mbewe
- Malawi-Liverpool-Wellcome Trust Programme, Blantyre, Malawi
| | | | | | - Rabson Kachala
- Malawi Ministry of Health, Capitol Hill, Lilongwe, Malawi
| | | | - Jane Malewa
- Kamuzu University of Health Sciences, Blantyre, Malawi.,Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Peter Finch
- Kamuzu University of Health Sciences, Blantyre, Malawi.,Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Chris Davis
- MRC - University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Rajiv Shah
- MRC - University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Lily Tong
- MRC - University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Ana da Silva Filipe
- MRC - University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Emma C Thomson
- MRC - University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Anna Maria Geretti
- Department of Infectious Diseases, Fondazione PTV, Faculty of Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Melita A Gordon
- Malawi-Liverpool-Wellcome Trust Programme, Blantyre, Malawi.,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,Kamuzu University of Health Sciences, Blantyre, Malawi
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12
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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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13
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Paper microfluidic implementation of loop mediated isothermal amplification for early diagnosis of hepatitis C virus. Nat Commun 2021; 12:6994. [PMID: 34848705 PMCID: PMC8632961 DOI: 10.1038/s41467-021-27076-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/27/2021] [Indexed: 12/26/2022] Open
Abstract
The early diagnosis of active hepatitis C virus (HCV) infection remains a significant barrier to the treatment of the disease and to preventing the associated significant morbidity and mortality seen, worldwide. Current testing is delayed due to the high cost, long turnaround times and high expertise needed in centralised diagnostic laboratories. Here we demonstrate a user-friendly, low-cost pan-genotypic assay, based upon reverse transcriptase loop mediated isothermal amplification (RT-LAMP). We developed a prototype device for point-of-care use, comprising a LAMP amplification chamber and lateral flow nucleic acid detection strips, giving a visually-read, user-friendly result in <40 min. The developed assay fulfils the current guidelines recommended by World Health Organisation and is manufactured at minimal cost using simple, portable equipment. Further development of the diagnostic test will facilitate linkage between disease diagnosis and treatment, greatly improving patient care pathways and reducing loss to follow-up, so assisting in the global elimination strategy. Current HCV nucleic acid-based diagnosis is largely performed in centralised laboratories. Here, the authors present a pan-genotypic RNA assay, based on reverse transcriptase loop mediated isothermal amplification and develop a low-cost prototype paper-based lateral flow device for point-of-care use, providing a visually read result within 40 min.
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14
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Mokaya J, Vasylyeva TI, Barnes E, Ansari MA, Pybus OG, Matthews PC. Global prevalence and phylogeny of hepatitis B virus (HBV) drug and vaccine resistance mutations. J Viral Hepat 2021; 28:1110-1120. [PMID: 33893696 PMCID: PMC8581767 DOI: 10.1111/jvh.13525] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/08/2021] [Indexed: 12/29/2022]
Abstract
Vaccination and anti-viral therapy with nucleos(t)ide analogues (NAs) are key approaches to reducing the morbidity, mortality and transmission of hepatitis B virus (HBV) infection. However, the efficacy of these interventions may be reduced by the emergence of drug resistance-associated mutations (RAMs) and/or vaccine escape mutations (VEMs). We have assimilated data on the global prevalence and distribution of HBV RAMs/VEMs from publicly available data and explored the evolution of these mutations. We analysed sequences downloaded from the HBV Database and calculated prevalence of 41 RAMs and 38 VEMs catalogued from published studies. We generated maximum likelihood phylogenetic trees and used treeBreaker to investigate the distribution and estimated the age of selected mutations across tree branches. RAM M204I/V had the highest prevalence, occurring in 3.8% (109/2838) of all HBV sequences in our data set, and a significantly higher rate in genotype C at 5.4% (60/1102, p = 0.0007). VEMs had an overall prevalence of 1.3% (37/2837) and had the highest prevalence in genotype C and in Asia at 2.2% (24/1102; p = 0.002) and 1.6% (34/2109; p = 0.009), respectively. Phylogenetic analysis suggested that RAM/VEMs can arise independently of treatment/vaccine exposure. In conclusion, HBV RAMs/VEMs have been found globally and across genotypes, with the highest prevalence observed in genotype C. Screening for genotype and for resistance-associated mutations may help to improve stratified patient treatment. As NAs and HBV vaccines are increasingly being deployed for HBV prevention and treatment, monitoring for resistance and advocating for better treatment regimens for HBV remains essential.
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Affiliation(s)
| | - Tetyana I. Vasylyeva
- Division of Infectious Diseases & Global Public HealthDepartment of MedicineUniversity of CaliforniaSan DiegoCAUSA
| | - Eleanor Barnes
- Nuffield Department of MedicineOxfordUK
- Department of HepatologyOxford University Hospitals NHS Foundation TrustJohn Radcliffe HospitalOxfordUK
- National Institutes of Health Research Health Informatics CollaborativeNIHR Oxford Biomedical Research CentreJohn Radcliffe HospitalOxfordUK
| | - M. Azim Ansari
- Nuffield Department of MedicineOxfordUK
- Wellcome Centre for Human GeneticsOxfordUK
| | | | - Philippa C. Matthews
- Nuffield Department of MedicineOxfordUK
- National Institutes of Health Research Health Informatics CollaborativeNIHR Oxford Biomedical Research CentreJohn Radcliffe HospitalOxfordUK
- Department of Infectious Diseases and MicrobiologyOxford University Hospitals NHS Foundation TrustJohn Radcliffe HospitalOxfordUK
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15
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Shah R, Ahovegbe L, Niebel M, Shepherd J, Thomson EC. Non-epidemic HCV genotypes in low- and middle-income countries and the risk of resistance to current direct-acting antiviral regimens. J Hepatol 2021; 75:462-473. [PMID: 33974951 PMCID: PMC8310923 DOI: 10.1016/j.jhep.2021.04.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/12/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023]
Abstract
The hepatitis C virus (HCV) is an extremely diverse virus, subtypes of which are distributed variably around the world. Viral genotypes may be divided into epidemic subtypes; those that have become prevalent globally, and endemic subtypes that have a more limited distribution, mainly in Africa and Asia. The high variability of endemic strains reflects evolutionary origins in the locations where they are found. This increased genetic diversity raises the possibility of resistance to pan-genotypic direct-acting antiviral regimens. While many endemic subtypes respond well to direct-acting antiviral therapies, others, for example genotypes 1l, 3b and 4r, do not respond as well as predicted. Many genotypes that are rare in high-income countries but common in other parts of the world have not yet been fully assessed in clinical trials. Further sequencing and clinical studies in sub-Saharan Africa and Asia are indicated to monitor response to treatment and to facilitate the World Health Organization's 2030 elimination strategy.
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Affiliation(s)
- Rajiv Shah
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Lucrece Ahovegbe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Mbarara University of Science and Technology, Mbarara, Uganda
| | - Marc Niebel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - James Shepherd
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; London School of Hygiene and Tropical Medicine, London, UK.
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16
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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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17
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Nankya-Mutyoba J, Apica BS, Otekat G, Kyeyune DB, Nakyagaba L, Nabunje J, Nakafeero M, Seremba E, Ocama P. Hepatitis C in Uganda: Identification of infected blood donors for micro-elimination. J Virus Erad 2021; 7:100041. [PMID: 34188952 PMCID: PMC8219885 DOI: 10.1016/j.jve.2021.100041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/12/2022] Open
Abstract
Background The drive to eliminate viral hepatitis by 2030 is underway. However, locally generated data on active infection is required to focus such efforts. We performed a regionally-inclusive survey to determine prevalence of active HCV, genotypes and related factors among Ugandan blood donors. Methods Participants from regional blood banks and blood collection centers were surveyed for information on demographic, clinical and lifestyle factors. Blood was assayed for HCV infection, HCV genotypes and subtypes. Logistic regression was performed to determine factors associated with active HCV infection. Results Of 1243 participants, 1041 (83.7%) were male, average age (SD), 27.7 (9.8). Prevalence of active HCV infection was 7.8% and we identified 3 genotypes. Median age (adj. OR (95% CI) = 1.03 (1.01-1.06), p-value = 0.040)), Northern region of birth versus Central or Eastern (adj. OR (95% CI) = 10.25 (2.65-39.68), p-value = 0.001)), Northern residence, versus Central or Eastern (adj. OR (95% CI) = 0.23 (0.08-0.65), p-value = 0.006)), and being married (versus single/divorced) adj. OR 2.49(1.3-4.79), p-value = 0.006 were associated with active HCV infection. Conclusion Targeted interventions in at-risk populations coupled with linkage to care and treatment will help achieve the WHO elimination goals in this setting.
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Affiliation(s)
- Joan Nankya-Mutyoba
- Makerere University College of Health Sciences, School of Public Health, Kampala, Uganda
| | - Betty S Apica
- Makerere University College of Health Sciences, School of Public Health, Kampala, Uganda.,Mulago National Referral Hospital, Kampala, Uganda
| | - Grace Otekat
- Makerere University College of Health Sciences, School of Public Health, Kampala, Uganda.,Mulago National Referral Hospital, Kampala, Uganda.,Uganda Uganda Blood Transfusion Service, Uganda
| | | | - Lourita Nakyagaba
- Makerere University College of Health Sciences, School of Public Health, Kampala, Uganda
| | - Joletta Nabunje
- Makerere University College of Health Sciences, School of Public Health, Kampala, Uganda
| | - Mary Nakafeero
- Makerere University College of Health Sciences, School of Public Health, Kampala, Uganda
| | - Emmanuel Seremba
- Makerere University College of Health Sciences, School of Public Health, Kampala, Uganda
| | - Ponsiano Ocama
- Makerere University College of Health Sciences, School of Public Health, Kampala, Uganda.,Makerere Unversity College of Health Sciences, School of Medicine
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18
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Carrasco T, Barquín D, Ndarabu A, Fernández-Alonso M, Rubio-Garrido M, Carlos S, Makonda B, Holguín Á, Reina G. HCV Diagnosis and Sequencing Using Dried Blood Spots from Patients in Kinshasa (DRC): A Tool to Achieve WHO 2030 Targets. Diagnostics (Basel) 2021; 11:522. [PMID: 33804260 PMCID: PMC8002119 DOI: 10.3390/diagnostics11030522] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/11/2022] Open
Abstract
The World Health Organization has established an elimination plan for hepatitis C virus (HCV) by 2030. In Sub-Saharan Africa (SSA) access to diagnostic tools is limited, and a number of genotype 4 subtypes have been shown to be resistant to some direct-acting antivirals (DAAs). This study aims to analyze diagnostic assays for HCV based on dried blood spots (DBS) specimens collected in Kinshasa and to characterize genetic diversity of the virus within a group of mainly HIV positive patients. HCV antibody detection was performed on 107 DBS samples with Vidas® anti-HCV and Elecsys anti-HCV II, and on 31 samples with INNO-LIA HCV. Twenty-six samples were subjected to molecular detection. NS3, NS5A, and NS5B regions from 11 HCV viremic patients were sequenced. HCV seroprevalence was 12.2% (72% with detectable HCV RNA). Both Elecsys Anti-HCV and INNO-LIA HCV were highly sensitive and specific, whereas Vidas® anti-HCV lacked full sensitivity and specificity when DBS sample was used. NS5B/NS5A/NS3 sequencing revealed exclusively GT4 isolates (50% subtype 4r, 30% 4c and 20% 4k). All 4r strains harbored NS5A resistance-associated substitutions (RAS) at positions 28, 30, and 31, but no NS3 RAS was detected. Elecsys Anti-HCV and INNO-LIA HCV are reliable methods to detect HCV antibodies using DBS. HCV subtype 4r was the most prevalent among our patients. RASs found in subtype 4r in NS5A region confer unknown susceptibility to DAA.
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Affiliation(s)
- Teresa Carrasco
- Microbiology Department, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (T.C.); (D.B.); (M.F.-A.)
| | - David Barquín
- Microbiology Department, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (T.C.); (D.B.); (M.F.-A.)
| | - Adolphe Ndarabu
- Department of Internal Medicine, Centre Hospitalier Monkole, 4484 Kinshasa, Democratic Republic of the Congo; (A.N.); (B.M.)
| | - Mirian Fernández-Alonso
- Microbiology Department, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (T.C.); (D.B.); (M.F.-A.)
- ISTUN, Institute of Tropical Health, Universidad de Navarra, 31008 Pamplona, Spain;
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Marina Rubio-Garrido
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department and Instituto Ramón y Cajal para la Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), 28034 Madrid, Spain; (M.R.-G.); (Á.H.)
| | - Silvia Carlos
- ISTUN, Institute of Tropical Health, Universidad de Navarra, 31008 Pamplona, Spain;
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- Department Preventive Medicine and Public Health, Universidad de Navarra, 31008 Pamplona, Spain
| | - Benit Makonda
- Department of Internal Medicine, Centre Hospitalier Monkole, 4484 Kinshasa, Democratic Republic of the Congo; (A.N.); (B.M.)
| | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department and Instituto Ramón y Cajal para la Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), 28034 Madrid, Spain; (M.R.-G.); (Á.H.)
| | - Gabriel Reina
- Microbiology Department, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (T.C.); (D.B.); (M.F.-A.)
- ISTUN, Institute of Tropical Health, Universidad de Navarra, 31008 Pamplona, Spain;
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
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19
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Terrault NA, Levy MT, Cheung KW, Jourdain G. Viral hepatitis and pregnancy. Nat Rev Gastroenterol Hepatol 2021; 18:117-130. [PMID: 33046891 DOI: 10.1038/s41575-020-00361-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/21/2020] [Indexed: 02/06/2023]
Abstract
The management of viral hepatitis in the setting of pregnancy requires special consideration. There are five liver-specific viruses (hepatitis A, B, C, D, E), each with unique epidemiology, tendency to chronicity, risk of liver complications and response to antiviral therapies. In the setting of pregnancy, the liver health of the mother, the influence of pregnancy on the clinical course of the viral infection and the effect of the virus or liver disease on the developing infant must be considered. Although all hepatitis viruses can harm the mother and the child, the greatest risk to maternal health and subsequently the fetus is seen with acute hepatitis A virus or hepatitis E virus infection during pregnancy. By contrast, the primary risks for hepatitis B virus (HBV), hepatitis C virus (HCV) and hepatitis D virus are related to the severity of the underlying liver disease in the mother and the risk of mother-to-child transmission (MTCT) for HBV and HCV. The prevention of MTCT is key to reducing the global burden of chronic viral hepatitis, and prevention strategies must take into consideration local health-care and socioeconomic challenges. This Review presents the epidemiology of acute and chronic viral hepatitis infection in pregnancy, the effect of pregnancy on the course of viral infection and, conversely, the influence of the viral infection on maternal and infant outcomes, including MTCT.
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Affiliation(s)
- Norah A Terrault
- Keck School of Medicine, University of Southern California, Los Angeles, USA.
| | - Miriam T Levy
- Department of Gastroenterology and Liver, Liverpool Hospital, University of New South Wales, Sydney, New South Wales, Australia
| | - Ka Wang Cheung
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, University of Hong Kong, Hong Kong, Hong Kong
| | - Gonzague Jourdain
- French National Research Institute for Sustainable Development (IRD), Marseille, France.,Chiang Mai University, Chiang Mai, Thailand
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20
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Isfordink CJ, van de Laar TJW, Rebers SPH, Wessels E, Molenkamp R, Knoester M, Baak BC, van Nieuwkoop C, van Hoek B, Brakenhoff SM, Blokzijl H, Arends JE, van der Valk M, Schinkel J. Direct-Acting Antiviral Treatment for Hepatitis C Genotypes Uncommon in High-Income Countries: A Dutch Nationwide Cohort Study. Open Forum Infect Dis 2021; 8:ofab006. [PMID: 33614815 PMCID: PMC7881754 DOI: 10.1093/ofid/ofab006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The majority of hepatitis C virus (HCV) infections are found in low- and middle-income countries, which harbor many region-specific HCV subtypes. Nevertheless, direct-acting antiviral (DAA) trials have almost exclusively been conducted in high-income countries, where mainly epidemically spread HCV subtypes are present. Recently, several studies have demonstrated suboptimal DAA efficacy for certain nonepidemic subtypes, which could hamper global HCV elimination. Therefore, we aimed to evaluate DAA efficacy in patients treated for a nonepidemic HCV genotype infection in the Netherlands. METHODS We performed a nationwide retrospective study including patients treated with interferon-free DAAs for an HCV genotype other than 1a/1b/2a/2b/3a/4a/4d. The genotype was determined by NS5B region phylogenetic analysis. The primary end point was SVR-12. If stored samples were available, NS5A and NS5B sequences were obtained for resistance-associated substitutions (RAS) evaluation. RESULTS We included 160 patients, mainly infected with nonepidemic genotype 2 (41%) and 4 (31%) subtypes. Most patients were from Africa (45%) or South America (24%); 51 (32%) were cirrhotic. SVR-12 was achieved in 92% (140/152) of patients with available SVR-12 data. Only 73% (8/11) genotype 3-infected patients achieved SVR-12, the majority being genotype 3b patients with 63% (5/8) SVR. Regardless of SVR, all genotype 3b patients had 30K and 31M RAS. CONCLUSIONS The DAA efficacy we observed in most nonepidemic genotypes in the Netherlands seems reassuring. However, the low SVR-12 rate in subtype 3b infections is alarming, especially as it is common in several HCV-endemic countries. Alongside earlier results, our results indicate that a remaining challenge for global HCV elimination is confirming and monitoring DAA efficacy in nonepidemic genotypes.
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Affiliation(s)
- Cas J Isfordink
- Department of Infectious Diseases, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, UMC Utrecht, Utrecht, the Netherlands
| | - Thijs J W van de Laar
- Department of Donor Medicine Research, Laboratory of Blood-borne infections, Sanquin Research, Sanquin Diagnostic Services, Amsterdam, the Netherlands
- Laboratory of Medical Microbiology, Onze Lieve Vrouwe Gasthuis, Amsterdam, the Netherlands
| | - Sjoerd P H Rebers
- Department of Medical Microbiology, Section of Clinical Virology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Els Wessels
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Marjolein Knoester
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bert C Baak
- Department of Gastroenterology and Hepatology, Onze Lieve Vrouwe Gasthuis locatie Oost, Amsterdam, the Netherlands
| | - Cees van Nieuwkoop
- Department of Internal Medicine, Haga Teaching Hospital, The Hague, the Netherlands
| | - Bart van Hoek
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sylvia M Brakenhoff
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Hans Blokzijl
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Joop E Arends
- Department of Internal Medicine and Infectious Diseases, UMC Utrecht, Utrecht, the Netherlands
| | - Marc van der Valk
- Department of Infectious Diseases, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Janke Schinkel
- Department of Medical Microbiology, Section of Clinical Virology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
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21
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Lassa Virus Circulation in Small Mammal Populations in Bo District, Sierra Leone. BIOLOGY 2021; 10:biology10010028. [PMID: 33466234 PMCID: PMC7824740 DOI: 10.3390/biology10010028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 11/26/2022]
Abstract
Simple Summary Lassa fever is a viral hemorrhagic fever caused by the Lassa virus (LASV). It is a deadly rodent-borne zoonosis with outbreaks occurring mostly in Sierra Leone, Guinea, Liberia, and Nigeria, in West Africa. In Sierra Leone, surveillance activities of LASV focus mainly on the Kenema area in the eastern region, known to be the epicentre. Little is known about the presence of the virus in the Bo area, where Mastomys natalensis and Rattus rattus share habitats with humans. Our study investigated the circulation and phylogeny of new LASV strains and virus seroprevalence in rodent populations of villages in Bo district. Information provided here will be of great importance in prioritizing areas for Lassa fever surveillance and preventive measures to mitigate future outbreaks. Our rodent longitudinal survey carried out over two years (2014–2016) identified Mastomys natalensis as the most prevalent species. While seropositive small mammals were found in every village, the four Mastomys natalensis rodents that tested PCR-positive for Lassa virus were found in only two villages. Phylogenetic analysis showed that these sequences belong to the Sierra Leonean clade, within lineage IV. In conclusion, LASV is present, with low circulation, in small mammals in rural settings around Bo. Abstract Lassa fever is a viral hemorrhagic fever caused by the Lassa virus LASV, which was first isolated in the rodent Mastomys natalensis in 1974 in Kenema, Sierra Leone. As little is known about the abundance and the presence of LASV in rodents living in the Bo area, we carried out a small mammal longitudinal population survey. A standardized trapping session was performed in various habitats and seasons in six villages over two years (2014–2016) and samples collected were tested for arenavirus IgG and LASV. A Bayesian phylogenetic analysis was performed on sequences identified by PCR. A total of 1490 small mammals were collected, and 16 rodent species were identified, with M. natalensis (355, 24%) found to be the most prevalent species. Forty-one (2.8%) samples were IgG positive, and 31 of these were trapped in homes and 10 in surrounding vegetation. Twenty-nine of 41 seropositive rodents were M. natalensis. We detected four LASV by PCR in two villages, all found in M. natalensis. Phylogenetic analysis showed that the sequences were distributed within the Sierra Leonean clade within lineage IV, distinguishing a Bo sub-clade older than a Kenema sub-clade. Compared to other settings, we found a low abundance of M. natalensis and a low circulation of LASV in rodents in villages around Bo district.
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22
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Dietz J, Kalinina OV, Vermehren J, Peiffer KH, Matschenz K, Buggisch P, Niederau C, Schattenberg JM, Müllhaupt B, Yerly S, Ringelhan M, Schmid RM, Antoni C, Müller T, Schulze Zur Wiesch J, Piecha F, Moradpour D, Deterding K, Wedemeyer H, Moreno C, Berg T, Berg CP, Zeuzem S, Welsch C, Sarrazin C. Resistance-associated substitutions in patients with chronic hepatitis C virus genotype 4 infection. J Viral Hepat 2020; 27:974-986. [PMID: 32396998 DOI: 10.1111/jvh.13322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 03/20/2020] [Accepted: 04/07/2020] [Indexed: 12/13/2022]
Abstract
Data on the prevalence of resistance-associated substitutions (RASs) and their implications for treatment with direct-acting antivirals (DAAs) are sparse in European patients with HCV genotype 4. This study investigated RASs before and after DAA failure in different genotype 4 subtypes and evaluated retreatment efficacies. Samples of 195 genotype 4-infected patients were collected in the European Resistance Database and investigated for NS3, NS5A and NS5B RASs. Retreatment efficacies in DAA failure patients were analysed retrospectively. After NS5A inhibitor (NS5Ai) failure, subtype 4r was frequent (30%) compared to DAA-naïve patients (5%) and the number of NS5A RASs was significantly higher in subtype 4r compared to 4a or 4d (median three RASs vs no or one RAS, respectively, P < .0001). RASsL28V, L30R and M31L pre-existed in subtype 4r and were maintained after NS5Ai failure. Typical subtype 4r RASs were located in subdomain 1a of NS5A, close to membrane interaction and protein-protein interaction sites that are responsible for multimerization and hence viral replication. Retreatment of 37 DAA failure patients was highly effective with 100% SVR in prior SOF/RBV, PI/SOF and PI/NS5Ai failures. Secondary virologic failures were rare (n = 2; subtype 4d and 4r) and only observed in prior NS5Ai/SOF failures (SVR 90%). In conclusion, subtype 4r harboured considerably more RASs compared to other subtypes. A resistance-tailored retreatment using first- and second-generation DAAs was highly effective with SVR rates ≥90% across all subtypes and first-line treatment regimens.
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Affiliation(s)
- Julia Dietz
- Department of Internal 1, University Hospital, Goethe University, Frankfurt, Germany.,German Center for Infection Research (DZIF), External Partner Site, Frankfurt, Germany
| | - Olga V Kalinina
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany.,Medical Faculty, Saarland University, Homburg, Germany
| | - Johannes Vermehren
- Department of Internal 1, University Hospital, Goethe University, Frankfurt, Germany.,German Center for Infection Research (DZIF), External Partner Site, Frankfurt, Germany
| | - Kai-Henrik Peiffer
- Department of Internal 1, University Hospital, Goethe University, Frankfurt, Germany.,German Center for Infection Research (DZIF), External Partner Site, Frankfurt, Germany
| | | | - Peter Buggisch
- Institute for Interdisciplinary Medicine IFI, Hamburg, Germany
| | - Claus Niederau
- St. Josef-Hospital, Katholisches Klinikum Oberhausen, Oberhausen, Germany
| | - Jörn M Schattenberg
- Department of Internal Medicine I, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Beat Müllhaupt
- Swiss Hepato-Pancreato-Biliary Center and Department of Gastroenterology and Hepatology, University Hospital Zürich, Zürich, Switzerland
| | - Sabine Yerly
- Laboratory of Virology, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Marc Ringelhan
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Roland M Schmid
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Christoph Antoni
- Department of Medicine II, Heidelberg University Hospital at Mannheim, Mannheim, Germany
| | - Tobias Müller
- Department of Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Julian Schulze Zur Wiesch
- Department of Internal Medicine I, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner Site, Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Felix Piecha
- Department of Internal Medicine I, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Darius Moradpour
- Division of Gastroenterology and Hepatology, University Hospital Lausanne, Lausanne, Switzerland
| | - Katja Deterding
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany.,Department of Gastroenterology, Hepatology and Endocrinology, Medizinische Hochschule Hannover, Hannover, Germany.,German Center for Infection Research (DZIF), Partner Site, Hannover-Braunschweig, Hannover, Germany
| | - Heiner Wedemeyer
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany.,Department of Gastroenterology, Hepatology and Endocrinology, Medizinische Hochschule Hannover, Hannover, Germany.,German Center for Infection Research (DZIF), Partner Site, Hannover-Braunschweig, Hannover, Germany
| | - Christophe Moreno
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology, CUB Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Thomas Berg
- Department of Gastroenterology and Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Christoph P Berg
- Department of Internal Medicine I, University of Tübingen, Tübingen, Germany
| | - Stefan Zeuzem
- Department of Internal 1, University Hospital, Goethe University, Frankfurt, Germany.,German Center for Infection Research (DZIF), External Partner Site, Frankfurt, Germany
| | - Christoph Welsch
- Department of Internal 1, University Hospital, Goethe University, Frankfurt, Germany.,German Center for Infection Research (DZIF), External Partner Site, Frankfurt, Germany
| | - Christoph Sarrazin
- Department of Internal 1, University Hospital, Goethe University, Frankfurt, Germany.,German Center for Infection Research (DZIF), External Partner Site, Frankfurt, Germany.,St. Josefs-Hospital, Medizinische Klinik II, Wiesbaden, Germany
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23
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Mokaya J, Maponga TG, McNaughton AL, Van Schalkwyk M, Hugo S, Singer JB, Sreenu VB, Bonsall D, de Cesare M, Andersson M, Gabriel S, Taljaard J, Barnes E, Preiser W, Van Rensburg C, Matthews PC. Evidence of tenofovir resistance in chronic hepatitis B virus (HBV) infection: An observational case series of South African adults. J Clin Virol 2020; 129:104548. [PMID: 32663786 PMCID: PMC7408481 DOI: 10.1016/j.jcv.2020.104548] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/07/2020] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Tenofovir disoproxil fumarate (TDF) is widely recommended for treatment of chronic hepatitis B virus (HBV) infection because it is safe, affordable and has a high genetic barrier to resistance. TDF resistance associated mutations (RAMs) have been reported, but data are limited, particularly for Africa. We set out to identify potential RAMs in individuals with detectable HBV viraemia on TDF treatment. METHODS We recruited adults with chronic HBV infection from Cape Town, South Africa, identifying individuals with a TDF resistance phenotype, defined as persistent HBV vireamia despite >12 months of TDF treatment. We sequenced HBV DNA using MiSeq Illumina with whole genome target enrichment, and sought potential TDF RAMs, based on a pre-defined list of polymorphisms. RESULTS Among 66 individuals with chronic HBV (genotypes A and D), three met our clinical definition for TDF resistance, of whom two were coinfected with HIV. In one participant, the consensus HBV sequence contained nine polymorphisms that have been described in association with TDF resistance. Significant treatment non-adherence in this individual was unlikely, as HIV RNA was suppressed. TDF RAMs were also present in HBV sequences from the other two participants, but other factors including treatment non-adherence may also have had a role in failure of HBV DNA suppression in these cases. DISCUSSION Our findings add to the evidence that RAMs in HBV reverse transcriptase may underpin a TDF resistant phenotype. This is the first time these RAMs have been reported from Africa in association with clinical evidence of TDF resistance.
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Affiliation(s)
- Jolynne Mokaya
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Road, Oxford OX1 3SY, UK
| | - Tongai G Maponga
- Division of Medical Virology, Stellenbosch University / National Health Laboratory Service Tygerberg, Cape Town, South Africa
| | - Anna L McNaughton
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Road, Oxford OX1 3SY, UK
| | - Marije Van Schalkwyk
- Division of Infectious Diseases, Department of Medicine, Stellenbosch University / Tygerberg Academic Hospital, Cape Town, South Africa
| | - Susan Hugo
- Division of Infectious Diseases, Department of Medicine, Stellenbosch University / Tygerberg Academic Hospital, Cape Town, South Africa
| | - Joshua B Singer
- MRC-University of Glasgow Centre for Virus Research, Bearsden Road, Glasgow, G61 1QH, UK
| | - Vattipally B Sreenu
- MRC-University of Glasgow Centre for Virus Research, Bearsden Road, Glasgow, G61 1QH, UK
| | - David Bonsall
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Road, Oxford OX1 3SY, UK; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; Big Data Institute, Old Road, Oxford OX3 7FZ, UK
| | | | - Monique Andersson
- Division of Medical Virology, Stellenbosch University / National Health Laboratory Service Tygerberg, Cape Town, South Africa; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Shiraaz Gabriel
- Division of Gastroenterology, Department of Medicine, Stellenbosch University / Tygerberg Academic Hospital, Cape Town, South Africa
| | - Jantje Taljaard
- Division of Infectious Diseases, Department of Medicine, Stellenbosch University / Tygerberg Academic Hospital, Cape Town, South Africa
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Road, Oxford OX1 3SY, UK; Department of Hepatology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; National Institutes of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Wolfgang Preiser
- Division of Medical Virology, Stellenbosch University / National Health Laboratory Service Tygerberg, Cape Town, South Africa
| | - Christo Van Rensburg
- Division of Gastroenterology, Department of Medicine, Stellenbosch University / Tygerberg Academic Hospital, Cape Town, South Africa
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Road, Oxford OX1 3SY, UK; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; National Institutes of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK.
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24
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Sonderup MW, Smuts H, Spearman CW. A novel variant of genotype 7b hepatitis C virus emphasizing viral hepatitis elimination challenges for sub-Saharan Africa. Pan Afr Med J 2020; 36:232. [PMID: 33708323 PMCID: PMC7908326 DOI: 10.11604/pamj.2020.36.232.24726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/20/2020] [Indexed: 11/11/2022] Open
Abstract
Sub-Saharan Africa has approximately 10.15 million people viraemic with chronic hepatitis C virus infection, extensive genotype and sub-genotype diversity is present, in addition to novel hepatitis C genotypes. Many of the unusual genotypes have extensive baseline resistance associated substitutions with direct acting antiviral therapy treatment outcome data, limited. We report a patient found to have a novel genotype 7b variant with extensive baseline resistance associated substitutions. There is a clear need for a better understanding of the virological characteristics of hepatitis C populations in sub-Saharan Africa to guide best optimal treatment decisions in national hepatitis C elimination programmes.
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Affiliation(s)
- Mark Wayne Sonderup
- Division of Hepatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Heidi Smuts
- Division of Medical Virology, National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Catherine Wendy Spearman
- Division of Hepatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
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25
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Mokaya J, McNaughton AL, Bester PA, Goedhals D, Barnes E, Marsden BD, Matthews PC. Hepatitis B virus resistance to tenofovir: fact or fiction? A systematic literature review and structural analysis of drug resistance mechanisms. Wellcome Open Res 2020; 5:151. [PMID: 33869791 PMCID: PMC8033640 DOI: 10.12688/wellcomeopenres.15992.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2020] [Indexed: 12/17/2022] Open
Abstract
Background: Tenofovir (TFV) is a widely used treatment for chronic hepatitis B virus (HBV) infection. There is a high genetic barrier to the selection of TFV resistance-associated mutations (RAMs), but the distribution and clinical significance of TFV RAMs are not well understood. We here present assimilated evidence for putative TFV RAMs with the aims of cataloguing and characterising mutations that have been reported, and starting to develop insights into mechanisms of resistance. Methods: We carried out a systematic literature search in PubMed and Scopus to identify clinical, in vitro and in silico evidence of TFV resistance. We included peer-reviewed studies presenting original data regarding virological TFV breakthrough, using published methods to assess the quality of each study. We generated a list of RAMs that have been reported in association with TFV resistance, developing a 'long-list' (all reported RAMs) and a 'short-list' (a refined list supported by the most robust evidence). We assessed the potential functional and structural consequences by mapping onto the crystal structure for HIV reverse transcriptase (RT), as the structure of HBV RT has not been solved. Results: We identified a 'long-list' of 37 putative TFV RAMs in HBV RT, occurring within and outside sites of enzyme activity, some of which can be mapped onto a homologous HIV RT structure. A 'short-list' of nine sites are supported by the most robust evidence. If clinically significant resistance arises, it is most likely to be in the context of suites of multiple RAMs. Other factors including adherence, viral load, HBeAg status, HIV coinfection and NA dosage may also influence viraemic suppression. Conclusion: There is emerging evidence for polymorphisms that may reduce susceptibility to TVF. However, good correlation between viral sequence and treatment outcomes is currently lacking; further studies are essential to optimise individual treatment and public health approaches.
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Affiliation(s)
- Jolynne Mokaya
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Anna L. McNaughton
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Phillip A Bester
- Division of Virology, National Health Laboratory Service/University of the Free State, Bloemfontein, South Africa
| | - Dominique Goedhals
- Division of Virology, National Health Laboratory Service/University of the Free State, Bloemfontein, South Africa
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
- Department of Hepatology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
- National Institutes of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, Garsington Road, Oxford, OX4 2PG, UK
| | - Brian D Marsden
- Structural Genomics Consortium, University of Oxford, Oxford, UK
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Headington, Oxford, UK
| | - Philippa C. Matthews
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
- National Institutes of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, Garsington Road, Oxford, OX4 2PG, UK
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
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26
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Ruiz I, Nevers Q, Hernández E, Ahnou N, Brillet R, Softic L, Donati F, Berry F, Hamadat S, Fourati S, Pawlotsky JM, Ahmed-Belkacem A. MK-571, a Cysteinyl Leukotriene Receptor 1 Antagonist, Inhibits Hepatitis C Virus Replication. Antimicrob Agents Chemother 2020; 64:e02078-19. [PMID: 32179525 PMCID: PMC7269486 DOI: 10.1128/aac.02078-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 02/20/2020] [Indexed: 12/13/2022] Open
Abstract
The quinoline MK-571 is the most commonly used inhibitor of multidrug resistance protein-1 (MRP-1) but was originally developed as a cysteinyl leukotriene receptor 1 (CysLTR1) antagonist. While studying the modulatory effect of MRP-1 on anti-hepatitis C virus (HCV) direct-acting antiviral (DAA) efficiency, we observed an unexpected anti-HCV effect of compound MK-571 alone. This anti-HCV activity was characterized in Huh7.5 cells stably harboring a subgenomic genotype 1b replicon. A dose-dependent decrease of HCV RNA levels was observed upon MK-571 administration, with a 50% effective concentration (EC50 ± standard deviation) of 9 ± 0.3 μM and a maximum HCV RNA level reduction of approximatively 1 log10 MK-571 also reduced the replication of the HCV full-length J6/JFH1 model in a dose-dependent manner. However, probenecid and apigenin homodimer (APN), two specific inhibitors of MRP-1, had no effect on HCV replication. In contrast, the CysLTR1 antagonist SR2640 increased HCV-subgenomic replicon (SGR) RNA levels in a dose-dependent manner, with a maximum increase of 10-fold. In addition, a combination of natural CysLTR1 agonist (LTD4) or antagonists (zafirlukast, cinalukast, and SR2640) with MK-571 completely reversed its antiviral effect, suggesting its anti-HCV activity is related to CysLTR1 rather to MRP-1 inhibition. In conclusion, we showed that MK-571 inhibits HCV replication in hepatoma cell cultures by acting as a CysLTR1 receptor antagonist, thus unraveling a new host-virus interaction in the HCV life cycle.
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Affiliation(s)
- Isaac Ruiz
- Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Team "Viruses, Hepatology, Cancers", Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- Department of Hepatology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Quentin Nevers
- Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Team "Viruses, Hepatology, Cancers", Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Eva Hernández
- Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Team "Viruses, Hepatology, Cancers", Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Nazim Ahnou
- Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Team "Viruses, Hepatology, Cancers", Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Rozenn Brillet
- Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Team "Viruses, Hepatology, Cancers", Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Laurent Softic
- Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Team "Viruses, Hepatology, Cancers", Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Flora Donati
- Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Team "Viruses, Hepatology, Cancers", Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Francois Berry
- Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Team "Viruses, Hepatology, Cancers", Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Sabah Hamadat
- Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Team "Viruses, Hepatology, Cancers", Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Slim Fourati
- Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Team "Viruses, Hepatology, Cancers", Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Jean-Michel Pawlotsky
- Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Team "Viruses, Hepatology, Cancers", Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Abdelhakim Ahmed-Belkacem
- Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Team "Viruses, Hepatology, Cancers", Hôpital Henri Mondor, Université Paris-Est, Créteil, France
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McNaughton AL, Revill PA, Littlejohn M, Matthews PC, Ansari MA. Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences. J Gen Virol 2020; 101:271-283. [PMID: 32134374 PMCID: PMC7416611 DOI: 10.1099/jgv.0.001387] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) is a diverse, partially double-stranded DNA virus, with 9 genotypes (A-I), and a putative 10th genotype (J), characterized thus far. Given the broadening interest in HBV sequencing, there is an increasing requirement for a consistent, unified approach to HBV genotype and subgenotype classification. We set out to generate an updated resource of reference sequences using the diversity of all genomic-length HBV sequences available in public databases. We collated and aligned genomic-length HBV sequences from public databases and used maximum-likelihood phylogenetic analysis to identify genotype clusters. Within each genotype, we examined the phylogenetic support for currently defined subgenotypes, as well as identifying well-supported clades and deriving reference sequences for them. Based on the phylogenies generated, we present a comprehensive set of HBV reference sequences at the genotype and subgenotype level. All of the generated data, including the alignments, phylogenies and chosen reference sequences, are available online (https://doi.org/10.6084/m9.figshare.8851946) as a simple open-access resource.
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Affiliation(s)
- Anna L. McNaughton
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
| | - Peter A. Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Philippa C. Matthews
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - M. Azim Ansari
- Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
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28
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Gupta N, Kateera F, Desalegn H, Ocama P, Njouom R, Lacombe K. Is resistance to direct-acting antivirals in sub-Saharan Africa a threat to HCV elimination? Recommendations for action. J Hepatol 2020; 72:583-584. [PMID: 31836263 DOI: 10.1016/j.jhep.2019.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 10/25/2019] [Indexed: 01/26/2023]
Affiliation(s)
- Neil Gupta
- Partners In Health, Boston, USA; Division of Global Health Equity, Brigham & Women's Hospital, Boston, USA.
| | - Fredrick Kateera
- Research Department, Partners in Health/ Inshuti Mu Buzima, Kigali, Rwanda
| | - Hailemichael Desalegn
- Medical Department, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Ponsiano Ocama
- Makerere University College of Health Sciences, Kampala, Uganda
| | - Richard Njouom
- Virology Department, Centre Pasteur of Cameroon, Yaounde, Cameroon
| | - Karine Lacombe
- Department of Infectious and Tropical Diseases, Saint-Antoine Hospital, Paris, France; Institut Pierre Louis d'Épidémiologie et de Santé Publique, INSERM, Sorbonne Université, Paris, France
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29
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Childs K, Davis C, Cannon M, Montague S, Filipe A, Tong L, Simmonds P, Smith D, Thomson EC, Dusheiko G, Agarwal K. Suboptimal SVR rates in African patients with atypical genotype 1 subtypes: Implications for global elimination of hepatitis C. J Hepatol 2019; 71:1099-1105. [PMID: 31400349 PMCID: PMC7057256 DOI: 10.1016/j.jhep.2019.07.025] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/09/2019] [Accepted: 07/26/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS HCV subtypes which are unusual in Europe are more prevalent in the African region, but little is known of their response to direct-acting antivirals (DAAs). These include non-1a/1b/ non-subtypeable genotype 1 (G1) or non-4a/4d (G4). In this report we aimed to describe the genotype distribution and treatment outcome in a south London cohort of African patients. METHODS We identified all patients born in Africa who attended our clinic from 2010-2018. Information on HCV genotype, treatment regimen and outcome were obtained. Non-subtypeable samples were analysed using Glasgow NimbleGen next-generation sequencing (NGS). Phylogenetic analysis was carried out by generating an uncorrected nucleotide p-distance tree from the complete coding regions of our sequences. RESULTS Of 91 African patients, 47 (52%) were infected with an unusual subtype. Fourteen novel, as yet undesignated subtypes (G1*), were identified by NGS. Three individuals were infected with the same subtype, now designated as subtype 1p. Baseline sequences were available for 22 patients; 18/22 (82%) had baseline NS5A resistance-associated substitutions (RASs). Sustained virological response (SVR) was achieved in 56/63 (89%) overall, yet only in 21/28 (75%) of those with unusual G1 subtypes, with failure in 3/16 G1*, 1/2 G1p and 3/3 in G1l. Six treatment failures occurred with sofosbuvir/ledipasvir compared to 1 failure on a PI-based regimen. The SVR rate for all other genotypes and subtypes was 35/35 (100%). CONCLUSIONS Most individuals in an unselected cohort of African patients were infected with an unusual genotype, including novel subtype 1p. The SVR rate of those with unusual G1 subtypes was 75%, raising concern about expansion of DAAs across Africa. Depending on the regimen used, higher failure rates in African cohorts could jeopardise HCV elimination. LAY SUMMARY Direct-acting antiviral medications are able to cure hepatitis C in the majority of patients. The most common genotype of hepatitis C in Europe and the United States is genotype 1a or 1b and most clinical trials focused on these genotypes. We report that in a group of African patients, most of them had unusual (non-1a/1b) genotype 1 subtypes, and that the cure rate in these unusual genotypes was lower than in genotypes 1a and 1b.
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Affiliation(s)
- Kate Childs
- Institute of Liver Studies, King's College Hospital Trust, United Kingdom.
| | - Christopher Davis
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Mary Cannon
- Institute of Liver Studies, King's College Hospital Trust, United Kingdom
| | - Sarah Montague
- Institute of Liver Studies, King's College Hospital Trust, United Kingdom
| | - Ana Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Donald Smith
- Nuffield Department of Medicine, University of Oxford, United Kingdom; ICTV Online (10th) Report, University of Edinburgh, United Kingdom
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Geoff Dusheiko
- Institute of Liver Studies, King's College Hospital Trust, United Kingdom
| | - Kosh Agarwal
- Institute of Liver Studies, King's College Hospital Trust, United Kingdom
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30
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Bradshaw D, Mbisa JL, Geretti AM, Healy BJ, Cooke GS, Foster GR, Thomson EC, McLauchlan J, Agarwal K, Sabin C, Mutimer D, Moss P, Irving WL, Barnes E. Consensus recommendations for resistance testing in the management of chronic hepatitis C virus infection: Public Health England HCV Resistance Group. J Infect 2019; 79:503-512. [PMID: 31629015 DOI: 10.1016/j.jinf.2019.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/10/2019] [Accepted: 10/13/2019] [Indexed: 12/12/2022]
Abstract
The treatment of hepatitis C virus (HCV) infection has been revolutionised by the advent of oral, well-tolerated, direct acting antiviral therapies (DAA), with high cure rates. However, in some scenarios, HCV resistance to antiviral therapies may have an impact on treatment success. Public Health England's HCV Resistance Group was established to support clinicians treating people with HCV, where the issue of resistance may be a factor in clinical decision-making, and this review includes the Group's current recommendations on the use of HCV resistance testing. The authors describe the principles behind and approach to HCV resistance testing and consider evidence from in vitro studies, clinical trials and real world cohorts on the impact of HCV resistance on treatment outcomes for particular DAA regimens. Five scenarios are identified in the UK and similar settings, where, in the Group's opinion, resistance testing should be performed.
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Affiliation(s)
- Daniel Bradshaw
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK.
| | - Jean L Mbisa
- National Infection Service, Public Health England, London, UK
| | | | | | | | | | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Kosh Agarwal
- Institute of Liver Studies, King's College Hospital, London, UK
| | | | | | - Peter Moss
- Hull University Teaching Hospitals NHS Trust, UK
| | - William L Irving
- Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham, UK
| | - Ellie Barnes
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
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31
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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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