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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:gutjnl-2024-332177. [PMID: 38782565 DOI: 10.1136/gutjnl-2024-332177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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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d'Humières C, Salmona M, Dellière S, Leo S, Rodriguez C, Angebault C, Alanio A, Fourati S, Lazarevic V, Woerther PL, Schrenzel J, Ruppé E. The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives. Drugs 2021; 81:1453-1466. [PMID: 34328626 PMCID: PMC8323086 DOI: 10.1007/s40265-021-01572-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2021] [Indexed: 12/24/2022]
Abstract
Clinical metagenomics (CMg) is the process of sequencing nucleic acid of clinical samples to obtain clinically relevant information such as the identification of microorganisms and their susceptibility to antimicrobials. Over the last decades, sequencing and bioinformatic solutions supporting CMg have much evolved and an increasing number of case reports and series covering various infectious diseases have been published. Metagenomics is a new approach to infectious disease diagnosis that is currently being developed and is certainly one of the most promising for the coming years. However, most CMg studies are retrospective, and few address the potential impact CMg could have on patient management, including initiation, adaptation, or cessation of antimicrobials. In this narrative review, we have discussed the potential role of CMg in bacteriology, virology, mycology, and parasitology. Several reports and case-series confirm that CMg is an innovative tool with which one can (i) identify more microorganisms than with conventional methods in a single test, (ii) obtain results within hours, and (iii) tailor the antimicrobial regimen of patients. However, the cost-efficiency of CMg and its real impact on patient management are still to be determined.
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Affiliation(s)
- Camille d'Humières
- Université de Paris, IAME, INSERM, 75018, Paris, France.,AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, 75018, Paris, France
| | - Maud Salmona
- Unité de Paris, INSERM U976, Insight Team, 75010, Paris, France.,AP-HP, Hôpital Saint-Louis, Laboratoire de Virologie, 75010, Paris, France
| | - Sarah Dellière
- AP-HP, Hôpital Saint-Louis, Laboratoire de Parasitologie-Mycologie, 75010, Paris, France.,Molecular Mycology Unit, Institut Pasteur, CNRS UMR2000, 75015, Paris, France
| | - Stefano Leo
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Christophe Rodriguez
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,INSERM U955, Université Paris-Est, 94000, Créteil, France
| | - Cécile Angebault
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,Université Paris Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, EA7380 Dynamic, 94000, Créteil, France
| | - Alexandre Alanio
- AP-HP, Hôpital Saint-Louis, Laboratoire de Parasitologie-Mycologie, 75010, Paris, France.,Molecular Mycology Unit, Institut Pasteur, CNRS UMR2000, 75015, Paris, France
| | - Slim Fourati
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,INSERM U955, Université Paris-Est, 94000, Créteil, France
| | - Vladimir Lazarevic
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Paul-Louis Woerther
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,Université Paris Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, EA7380 Dynamic, 94000, Créteil, France
| | - Jacques Schrenzel
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Etienne Ruppé
- Université de Paris, IAME, INSERM, 75018, Paris, France. .,AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, 75018, Paris, France.
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Gallardo-Flores CE, Colpitts CC. Cyclophilins and Their Roles in Hepatitis C Virus and Flavivirus Infections: Perspectives for Novel Antiviral Approaches. Pathogens 2021; 10:pathogens10070902. [PMID: 34358052 PMCID: PMC8308494 DOI: 10.3390/pathogens10070902] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/07/2021] [Accepted: 07/15/2021] [Indexed: 12/19/2022] Open
Abstract
Cyclophilins are cellular peptidyl-prolyl isomerases that play an important role in viral infections, with demonstrated roles in the replication of hepatitis C virus (HCV) and other viruses in the Flaviviridae family, such as dengue virus (DENV) and yellow fever virus (YFV). Here, we discuss the roles of cyclophilins in HCV infection and provide a comprehensive overview of the mechanisms underlying the requirement for cyclophilins during HCV replication. Notably, cyclophilin inhibitor therapy has been demonstrated to be effective in reducing HCV replication in chronically infected patients. While the roles of cyclophilins are relatively well-understood for HCV infection, cyclophilins are more recently emerging as host factors for flavivirus infection as well, providing potential new therapeutic avenues for these viral infections which currently lack antiviral therapies. However, further studies are required to elucidate the roles of cyclophilins in flavivirus replication. Here, we review the current knowledge of the role of cyclophilins in HCV infection to provide a conceptual framework to understand how cyclophilins may contribute to other viral infections, such as DENV and YFV. Improved understanding of the roles of cyclophilins in viral infection may open perspectives for the development of cyclophilin inhibitors as effective antiviral therapeutics for HCV and related viruses.
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