Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes
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
Affiliations
Kasper T. Christensen
Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
Florian Pierard
Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
David Bonsall
Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
Rory Bowden
The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
Eleanor Barnes
Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
Eric Florence
Department of General Internal Medicine, Infectious Diseases and Tropical Medicine, Antwerp University Hospital, 2650 Edegem, Belgium
M. Azim Ansari
Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
Dung Nguyen
The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
Mariateresa de Cesare
The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
Frederik Nevens
Department of Gastroenterology and Hepatology, University Hospitals Leuven, 3000 Leuven, Belgium
Geert Robaeys
Department of Gastroenterology and Hepatology, University Hospitals Leuven, 3000 Leuven, Belgium
Yoeri Schrooten
Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
Dana Busschots
Faculty of Medicine and Life Sciences—LCRC, UHasselt, Agoralaan, 3590 Diepenbeek, Belgium
Peter Simmonds
Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
Anne-Mieke Vandamme
Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
Eric Van Wijngaerden
Department of General Internal Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
Tim Dierckx
Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
Lize Cuypers
Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
Kristel Van Laethem
Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
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.
