A molecular phylogenetics-based approach for identifying recent hepatitis C virus transmission events

Infect Genet Evol. 2015 Jul;33:101-9. doi: 10.1016/j.meegid.2015.04.017. Epub 2015 Apr 24.


Improved surveillance methods are needed to better understand the current hepatitis C virus (HCV) disease burden and to monitor the impact of prevention and treatment interventions on HCV transmission dynamics. Sanger sequencing (HCV NS5B, HVR1 and Core-E1-HVR1) and phylogenetics were applied to samples from individuals diagnosed with HCV in British Columbia, Canada in 2011. This included individuals with two or three sequential samples collected <1 year apart. Patristic distances between sequential samples were used to set cutoffs to identify recent transmission clusters. Factors associated with transmission clustering were analyzed using logistic regression. From 618 individuals, 646 sequences were obtained. Depending on the cutoff used, 63 (10%) to 92 (15%) unique individuals were identified within transmission clusters of predicted recent origin. Clustered individuals were more likely to be <40 years old (Adjusted Odds Ratio (AOR) 2.12, 95% CI 1.21-3.73), infected with genotype 1a (AOR 6.60, 95% CI 1.98-41.0), and to be seroconverters with estimated infection duration of <1 year (AOR 3.13, 95% CI 1.29-7.36) or >1 year (AOR 2.19, 95% CI 1.22-3.97).

Conclusion: Systematic application of molecular phylogenetics may be used to enhance traditional surveillance methods through identification of recent transmission clusters.

Keywords: British Columbia; Epidemiology; Hepatitis C virus; Phylogenetics; Recent transmission clusters; Sequencing; Seroconversion; Surveillance.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • British Columbia / epidemiology
  • Cluster Analysis
  • Female
  • Genotype
  • Hepacivirus / classification*
  • Hepacivirus / genetics*
  • Hepatitis C / epidemiology
  • Hepatitis C / transmission*
  • Hepatitis C / virology*
  • Humans
  • Male
  • Middle Aged
  • Phylogeny*
  • RNA, Viral / genetics
  • Risk Factors
  • Sequence Analysis, DNA
  • Young Adult


  • RNA, Viral