Country-Wide Hepatitis C Virus Transmission Networks Among People Who Inject Drugs in Kenya

Abstract

BackgroundHepatitis C virus (HCV) infection is a global health problem especially among people who inject drugs (PWID). Low-and-middle income countries (LMIC) carry a high burden of HCV, but little is known about the HCV transmission dynamics in these settings.MethodsWe recruited PWID in Nairobi and coastal cities of Mombasa, Kilifi and Malindi in Kenya at needle and syringe programs using respondent-driven sampling. Next-generation sequencing (NGS) data from HCV hypervariable region 1 were analyzed using Global Hepatitis Outbreak and Surveillance Technology (GHOST) to identify transmission clusters.ResultsHCV strains belonged to genotype 1a (HCV/1a, n=64, 46.0%), 4a (HCV/4a, n=72, 51.8%), and n=3 (2.2%) were mixed HCV/1a/4a. HCV/1a was dominant (61.2%) in Nairobi and HCV/4a in Malindi (85.7%) and Kilifi (60.9%), both genotypes were evenly sampled in Mombasa (45.3%, for HCV/1a and 50.9% for HCV/4a). GHOST identified 11 transmission clusters involving 90 cases. HCV strains in the two large clusters (n=38 predominantly HCV/4a, and n=32 HCV/1a) were sampled from all four cities. The remaining 9 clusters ranged in size from 2-4 cases.ConclusionTransmission clusters involving 64.7% of cases indicate an effective sampling of major HCV strains circulating among PWID. Large clusters involving 77.8% of all clustered HCV strains from Nairobi and Coast suggest a successful introduction of two ancestral HCV/1a and HCV/4a strains to PWID, progeny of which widely spread across the country. The findings indicate the existence of a country-wide transmission network, disruption of which is essential for a national HCV elimination strategy, prioritizing such sites as Mombasa for reducing transmission.

Keywords: Hepatitis C, people who inject drugs (PWID), next-generation sequencing (NGS), GHOST, transmission network, Kenya