Temporal trends of hepatitis C virus transmission in internally displaced people who inject drugs in Odessa, Ukraine

Background Due to practical challenges associated with genetic sequencing in low resource environments, the burden of hepatitis C virus (HCV) in forcibly displaced people is understudied. We examined the use of field-applicable HCV sequencing methods and phylogenetic analysis to determine HCV transmission dynamics in internally displaced people who inject drugs (IDPWID) due to war in eastern Ukraine. Methods In this cross-sectional study, we used modified respondent-driven sampling to recruit IDPWID who have settled in Odessa, Ukraine. We generated partial and near full length genome (NFLG) HCV sequences using Oxford Nanopore MinION in a simulated field environment. Maximum likelihood and Bayesian methods were used to establish phylodynamic relationships. Findings Between June and September 2020, we collected epidemiological data and whole blood samples from 164 IDPWID. Rapid testing identified an HIV, anti-HCV, and HIV/HCV co-infection prevalence of 39%, 67.7%, and 31.1%, respectively. We generated 57 partial or NFLG HCV sequences and identified eight transmission clusters, of which at least two originated within a year and a half post-migration. Unstable housing post-migration was associated with more reports of injection drug use in the past 30 days (p=0.048). Interpretation Local generation of viral sequencing data and phylogenetic analysis in rapidly changing low-resource environments, such as those faced by forcibly displaced people, can inform timely adaptation of prevention and treatment. Funding Oxford University John Fell Fund, ISS Wellcome Trust, Branco Weiss Fellowship.