Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes
The hepatitis C virus (HCV) epidemic in Western countries is primarily perpetuated by the sub-populations of men who have sex with men (MSM) and people who inject drugs (PWID). Understanding the dynamics of transmission in these communities is crucial for removing the remaining hurdles towards HCV e...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-12-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/15/12/2391 |
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| author | Kasper T. Christensen Florian Pierard David Bonsall Rory Bowden Eleanor Barnes Eric Florence M. Azim Ansari Dung Nguyen Mariateresa de Cesare Frederik Nevens Geert Robaeys Yoeri Schrooten Dana Busschots Peter Simmonds Anne-Mieke Vandamme Eric Van Wijngaerden Tim Dierckx Lize Cuypers Kristel Van Laethem |
| author_facet | Kasper T. Christensen Florian Pierard David Bonsall Rory Bowden Eleanor Barnes Eric Florence M. Azim Ansari Dung Nguyen Mariateresa de Cesare Frederik Nevens Geert Robaeys Yoeri Schrooten Dana Busschots Peter Simmonds Anne-Mieke Vandamme Eric Van Wijngaerden Tim Dierckx Lize Cuypers Kristel Van Laethem |
| author_sort | Kasper T. Christensen |
| collection | DOAJ |
| description | The hepatitis C virus (HCV) epidemic in Western countries is primarily perpetuated by the sub-populations of men who have sex with men (MSM) and people who inject drugs (PWID). Understanding the dynamics of transmission in these communities is crucial for removing the remaining hurdles towards HCV elimination. We sequenced 269 annotated HCV plasma samples using probe enrichment and next-generation sequencing, obtaining 224 open reading frames of HCV (OR497849-OR498072). Maximum likelihood phylogenies were generated on the four most prevalent subtypes in this study (HCV1a, 1b, 3a, 4d) with a subsequent transmission cluster analysis. The highest rate of clustering was observed for HCV4d samples (13/17 (76.47%)). The second highest rate of clustering was observed in HCV1a samples (42/78 (53.85%)) with significant association with HIV-positive MSM. HCV1b and HCV3a had very low rates of clustering (2/83 (2.41%) and (0/29)). The spread of the prevalent subtype HCV1b appears to have been largely curtailed, and we demonstrate the onwards transmission of HCV1a and HCV4d in the HIV-positive MSM population across municipal borders. More systematic data collection and sequencing is needed to allow a better understanding of the HCV transmission among the community of PWID and overcome the remaining barriers for HCV elimination in Belgium. |
| first_indexed | 2024-03-08T20:17:05Z |
| format | Article |
| id | doaj.art-68065b242c224395bd35e6aa2784fa34 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-08T20:17:05Z |
| publishDate | 2023-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-68065b242c224395bd35e6aa2784fa342023-12-22T14:49:18ZengMDPI AGViruses1999-49152023-12-011512239110.3390/v15122391Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length GenomesKasper T. Christensen0Florian Pierard1David Bonsall2Rory Bowden3Eleanor Barnes4Eric Florence5M. Azim Ansari6Dung Nguyen7Mariateresa de Cesare8Frederik Nevens9Geert Robaeys10Yoeri Schrooten11Dana Busschots12Peter Simmonds13Anne-Mieke Vandamme14Eric Van Wijngaerden15Tim Dierckx16Lize Cuypers17Kristel Van Laethem18Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, BelgiumLaboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, BelgiumBig Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UKThe Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UKPeter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UKDepartment of General Internal Medicine, Infectious Diseases and Tropical Medicine, Antwerp University Hospital, 2650 Edegem, BelgiumNuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UKThe Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UKThe Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UKDepartment of Gastroenterology and Hepatology, University Hospitals Leuven, 3000 Leuven, BelgiumDepartment of Gastroenterology and Hepatology, University Hospitals Leuven, 3000 Leuven, BelgiumLaboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, BelgiumFaculty of Medicine and Life Sciences—LCRC, UHasselt, Agoralaan, 3590 Diepenbeek, BelgiumHenry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UKLaboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, BelgiumDepartment of General Internal Medicine, University Hospitals Leuven, 3000 Leuven, BelgiumLaboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, BelgiumLaboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, BelgiumLaboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, BelgiumThe hepatitis C virus (HCV) epidemic in Western countries is primarily perpetuated by the sub-populations of men who have sex with men (MSM) and people who inject drugs (PWID). Understanding the dynamics of transmission in these communities is crucial for removing the remaining hurdles towards HCV elimination. We sequenced 269 annotated HCV plasma samples using probe enrichment and next-generation sequencing, obtaining 224 open reading frames of HCV (OR497849-OR498072). Maximum likelihood phylogenies were generated on the four most prevalent subtypes in this study (HCV1a, 1b, 3a, 4d) with a subsequent transmission cluster analysis. The highest rate of clustering was observed for HCV4d samples (13/17 (76.47%)). The second highest rate of clustering was observed in HCV1a samples (42/78 (53.85%)) with significant association with HIV-positive MSM. HCV1b and HCV3a had very low rates of clustering (2/83 (2.41%) and (0/29)). The spread of the prevalent subtype HCV1b appears to have been largely curtailed, and we demonstrate the onwards transmission of HCV1a and HCV4d in the HIV-positive MSM population across municipal borders. More systematic data collection and sequencing is needed to allow a better understanding of the HCV transmission among the community of PWID and overcome the remaining barriers for HCV elimination in Belgium.https://www.mdpi.com/1999-4915/15/12/2391hepatitis chuman immunodeficiency virusphylogenetic analysisfull-genome sequencingmen who have sex with menpeople who inject drugs |
| spellingShingle | Kasper T. Christensen Florian Pierard David Bonsall Rory Bowden Eleanor Barnes Eric Florence M. Azim Ansari Dung Nguyen Mariateresa de Cesare Frederik Nevens Geert Robaeys Yoeri Schrooten Dana Busschots Peter Simmonds Anne-Mieke Vandamme Eric Van Wijngaerden Tim Dierckx Lize Cuypers Kristel Van Laethem Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes Viruses hepatitis c human immunodeficiency virus phylogenetic analysis full-genome sequencing men who have sex with men people who inject drugs |
| title | Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes |
| title_full | Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes |
| title_fullStr | Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes |
| title_full_unstemmed | Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes |
| title_short | Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes |
| title_sort | phylogenetic analysis of hepatitis c virus infections in a large belgian cohort using next generation sequencing of full length genomes |
| topic | hepatitis c human immunodeficiency virus phylogenetic analysis full-genome sequencing men who have sex with men people who inject drugs |
| url | https://www.mdpi.com/1999-4915/15/12/2391 |
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