of Transmission Networks
for Hepatitis C Elimination
Hepatitis C Virus (HCV) continues to be transmitted sexually among men who have sex with men (MSM), despite the availability of a highly effective cure. To eliminate HCV from the MSM population, more information is needed on transmission dynamics to identify the sources and timing of new HCV infections. In addition, mutations resulting in drug resistance can emerge and may be transmitted, and need to be monitored
HCV Surveillance tool
MS-TRACE is a surveillance tool that monitors HCV transmission clusters and drug resistance in the MSM population. Genomic data is curated and stored in a Castor EDC database. Metadata of the sequences is stored alongside the genomic data. This data is retrieved from the database and split into several subsets based on genotype and genomic region. For the cluster analyses a 525 base-pair fragment from the E1-E2 genomic region is used, which is diverse enough to infer transmission clusters. Resistance associated substitutions in the NS5A region of the genome is also monitored. To define clusters, a background dataset with sequences of subtypes of interest is obtained from HCV-GLUE, , and added to the sequences in the MS-TRACE database. For cluster assignment Phydelity is used which infers transmission clusters under a statistically principled and phylogeny-informed framework. The sequences in the database are then analysed and visualised using a custom version of the Nextstrain pipeline. The database will be updated in the nearby future with international and full-length genomic sequences.