LAUSR

China is one of the countries with the heaviest burden of hepatitis C virus (HCV) worldwide, especially subtype 1b. To better control hepatitis C, insights into the characteristics of dynamic spread and genomic mutations are urgently needed. We retrieved sequences of HCV‐1b NS5B among intravenous drug users (IDUs) and general people (Non‐IDUs) in China from 2000 to 2011 in NCBI. Bayesian phylogenetic and phylogeographic analyses were used to evaluate the transmission dynamics of HCV‐1b. Non‐synonymous substitutions were detected to illustrate immune adaptation. Evolutionary history demonstrated that HCV‐1b effective population size experienced a sharp increase in 1990. HCV‐1b sequences among IDUs had a higher estimated evolutionary rate (5.7185 × 10−3 substitutions/site/year) than overall (7.7332 × 10−4). 105/136 (77.2%) of HCV‐1b sequences clustered into 38 networks. The average non‐synonymous HCV‐1b immune epitopes among IDUs were 0.211, higher than non‐IDUs, especially in the HLA‐A*02 molecular recognition region. All of these posed significant challenges for the prevention and treatment of HCV. Heterogeneity and genetic linkages of HCV‐1b suggest that evolutionary surveillance of HCV in cities in east‐central China and among IDUs could not be neglected.