Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes

Kasper T Christensen¹, Florian Pierard¹, David Bonsall^{2

3}, Rory Bowden³, Eleanor Barnes^{4

5

6}, Eric Florence^{7

8}, M Azim Ansari⁹, Dung Nguyen³, Mariateresa de Cesare³, Frederik Nevens¹⁰, Geert Robaeys^{10

11

12}, Yoeri Schrooten^{1

13}, Dana Busschots^{11

12}, Peter Simmonds¹⁴, Anne-Mieke Vandamme^{1

15}, Eric Van Wijngaerden¹⁶, Tim Dierckx¹, Lize Cuypers^{1

13

17}, Kristel Van Laethem^{1

13}

Affiliations

¹ Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium.
² Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK.
³ The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
⁴ Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK.
⁵ Translational Gastroenterology Unit, University of Oxford, Oxford OX3 9DU, UK.
⁶ Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK.
⁷ Department of General Internal Medicine, Infectious Diseases and Tropical Medicine, Antwerp University Hospital, 2650 Edegem, Belgium.
⁸ Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium.
⁹ Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.
¹⁰ Department of Gastroenterology and Hepatology, University Hospitals Leuven, 3000 Leuven, Belgium.
¹¹ Faculty of Medicine and Life Sciences-LCRC, UHasselt, Agoralaan, 3590 Diepenbeek, Belgium.
¹² Department of Gastroenterology and Hepatology, Ziekenhuis Oost-Limburg, 3600 Genk, Belgium.
¹³ Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium.
¹⁴ Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK.
¹⁵ Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008 Lisbon, Portugal.
¹⁶ Department of General Internal Medicine, University Hospitals Leuven, 3000 Leuven, Belgium.
¹⁷ Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium.

PMID: 38140632
PMCID: PMC10747466
DOI: 10.3390/v15122391

Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes

Kasper T Christensen et al. Viruses. 2023.

. 2023 Dec 8;15(12):2391.

doi: 10.3390/v15122391.

Authors

Affiliations

¹ Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium.
² Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK.
³ The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
⁴ Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK.
⁵ Translational Gastroenterology Unit, University of Oxford, Oxford OX3 9DU, UK.
⁶ Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK.
⁷ Department of General Internal Medicine, Infectious Diseases and Tropical Medicine, Antwerp University Hospital, 2650 Edegem, Belgium.
⁸ Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium.
⁹ Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.
¹⁰ Department of Gastroenterology and Hepatology, University Hospitals Leuven, 3000 Leuven, Belgium.
¹¹ Faculty of Medicine and Life Sciences-LCRC, UHasselt, Agoralaan, 3590 Diepenbeek, Belgium.
¹² Department of Gastroenterology and Hepatology, Ziekenhuis Oost-Limburg, 3600 Genk, Belgium.
¹³ Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium.
¹⁴ Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK.
¹⁵ Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008 Lisbon, Portugal.
¹⁶ Department of General Internal Medicine, University Hospitals Leuven, 3000 Leuven, Belgium.
¹⁷ Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium.

PMID: 38140632
PMCID: PMC10747466
DOI: 10.3390/v15122391

Abstract

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.

Keywords: full-genome sequencing; hepatitis c; human immunodeficiency virus; men who have sex with men; next-generation sequencing; people who inject drugs; phylogenetic analysis.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

**Figure 1**
A maximum-likelihood tree was constructed based on HCV1a ORFs using MAFFT and IQ-Tree 2 with automatic substitution model detection (TVM + F + R10) and 1000 ultra-fast bootstrap replicates and was rooted using an HCV1b outgroup. Blue, red, and green branches correspond to samples originating from Leuven, Antwerp, and Genk, respectively. Clusters based on bootstrap and genetic distance thresholds of 90% and 4 and are highlighted in grey. Pictograms indicate the characteristics of each cluster.

**Figure 2**
A maximum-likelihood tree was constructed based on HCV4d ORFs using MAFFT and IQ-Tree 2 with automatic substitution model detection (TVM + F + R10) and 1000 ultra-fast bootstrap replicates and was rooted using a HCV1b outgroup. Blue, red, and green branches correspond to samples originating from Leuven, Antwerp, and Genk, respectively. Clusters based on bootstrap and genetic distance thresholds of 90% and 4 and are highlighted in grey. Pictograms indicate the characteristics of each cluster.

See this image and copyright information in PMC

References

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Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes

Affiliations

Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Medical