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Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data

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  • Gonché Danesh
  • Victor Virlogeux
  • Christophe Ramière
  • Caroline Charre
  • Laurent Cotte
  • Samuel Alizon

Abstract

Opioid substitution and syringes exchange programs have drastically reduced hepatitis C virus (HCV) spread in France but HCV sexual transmission in men having sex with men (MSM) has recently arisen as a significant public health concern. The fact that the virus is transmitting in a heterogeneous population, with different transmission routes, makes prevalence and incidence rates poorly informative. However, additional insights can be gained by analyzing virus phylogenies inferred from dated genetic sequence data. By combining a phylodynamics approach based on Approximate Bayesian Computation (ABC) and an original transmission model, we estimate key epidemiological parameters of an ongoing HCV epidemic among MSMs in Lyon (France). We show that this new epidemic is largely independent of the previously observed non-MSM HCV epidemics and that its doubling time is ten times lower (0.44 years versus 4.37 years). These results have practical implications for HCV control and illustrate the additional information provided by virus genomics in public health.Author summary: Lyon (France) is witnessing a new epidemic of hepatitis C virus infection, which appears to be fuelled by sexual transmission. Upon detection, patients are found to belong to two main risk groups. The first group is referred to as non-MSM and typically corresponds to HIV-negative patients infected through nosocomial transmission or with a history of opioid intravenous drug use or blood transfusion or patients with haemophilia. The second group is more recent and mainly corresponds to Men Having Sex with Men (MSM) who are HIV-infected or HIV-negative MSMs. They tend to be detected during or shortly after the acute HCV infection phase and to use recreational drugs such as cocaine or cathinones. By taking advantage of recent developments in the emerging field of phylodynamics, we combine this patient information with virus sequence data to estimate key properties of the epidemics. We show that the current HCV spread via sexual transmission and MSM hosts is comparable to that before the advent of third-generation detection tests. We also find that the duration of the effective infectious period in MSM hosts is comparable to that of the acute phase. These results have timely public health implications, one of which is that treatment upon detection is necessary to slow down the ongoing HCV epidemics in Lyon.

Suggested Citation

  • Gonché Danesh & Victor Virlogeux & Christophe Ramière & Caroline Charre & Laurent Cotte & Samuel Alizon, 2021. "Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data," PLOS Pathogens, Public Library of Science, vol. 17(9), pages 1-19, September.
    • Handle: RePEc:plo:ppat00:1009916
    DOI: 10.1371/journal.ppat.1009916
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    References listed on IDEAS

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    1. Emma Saulnier & Olivier Gascuel & Samuel Alizon, 2017. "Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study," PLOS Computational Biology, Public Library of Science, vol. 13(3), pages 1-31, March.
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    3. Hui Zou & Trevor Hastie, 2005. "Regularization and variable selection via the elastic net," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 67(2), pages 301-320, April.
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