Genomic surveillance uncovers regional variation in HCV transmission networks in rural United States

Hepatitis C virus (HCV) remains a public health concern in the United States, particularly in rural communities where the opioid epidemic accelerates transmission among people who use drugs (PWUD). Despite this growing burden, the genetic features and transmission dynamics of HCV in these settings are poorly understood. We analyze 692 HCV antibody-positive specimens collected from rural communities in ten U.S. states using amplicon-based deep sequencing and the Global Hepatitis Outbreak and Surveillance Technology (GHOST) platform to reconstruct transmission networks. Among sequenced individuals, 29.5% are linked within clusters. Cluster structure varies by region from sparse networks in Ohio to dense clusters in New England and phylogenetic analyses show that some networks persist for over a decade, indicating sustained transmission. Nearly half of all clusters involve individuals connected through social recruitment, suggesting peer-referral strategies effectively identify transmission chains. Penalized regression retains only a few individual factors including younger age, peer or partner recruitment, illegal income, methamphetamine use, each with modest effects. These findings suggest that clustering is shaped primarily by social and structural contexts rather than individual characteristics and underscore the importance of integrating genomic surveillance with social-network insights to detect emerging HCV clusters and guide targeted interventions in underserved rural communities.