Few reports are available on HCV molecular epidemiology among IDUs in Eastern Europe, and none in Montenegro. The aim of this study was to investigate the HCV genotype distribution in Montenegro among IDUs and to perform Bayesian and evolutionary analysis of the most prevalent HCV genotype circulating in this population. Sixty-four HCV-positive IDUs in Montenegro were enrolled between 2013 and 2014, and the NS5B gene was sequenced. The Bayesian analysis showed that the most prevalent subtype was HCV-3a. Phylogenetic data showed that HCV-3a reached Montenegro in the late 1990s, causing an epidemic that exponentially grew between the 1995 and 2005. In the dated tree, four different entries, from 1990 (clade D), 1994 (clade A) to 1999 (clade B) and 2001 (clade C), were identified. In the NS5B protein model, the amino acids variations were located mainly in the palm domain, which contains most of the conserved structural elements of the active site. This study provides an analysis of the virus transmission pathway and the evolution of HCV genotype 3a among IDUs in Montenegro. These data could represent the basis for further strategies aimed to improve disease management and surveillance program development in high-risk populations.
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