Molecular Surveillance
of Transmission Networks
for Hepatitis C Elimination
among MSM


Hepatitis C Virus (HCV) continues to be transmitted among men who have sex with men (MSM), despite the availability of a highly effective cure. Transmission dynamics need to be understood to identify the sources and timing of new HCV infections. This data can provide insights for prevention and control efforts required for HCV elimination. In addition, mutations in the HCV genome resulting in variants resistant to currently available drugs can emerge and could be transmitted. MS-TRACE is an HCV genomic surveillance framework to monitor transmission networks and resistance emergence among MSM.

HCV Surveillance tool

MS-TRACE is a surveillance tool that monitors HCV transmission clusters and drug resistance in the MSM population. MS-TRACE consists of a database of HCV whole genome sequences and associated metadata, a sequence analysis pipeline, and a set of visualisation tools. Genomic data and metadata is curated and securely stored in a Castor EDC database.  Sequences are analysed for each genotype seperately. Clusters are assigned using Phydelity which infers transmission clusters under a statistically principled and phylogeny-informed framework. The sequences are then analysed and visualised using a custom version of the Nextstrain pipeline.