Evolutionary characteristics and positive selection site of hepatitis C virus isolated in intravenous drug users in Pudong new district, Shanghai

Abstract

Objective: To understand the genotypes of hepatitis C virus (HCV) circulating in intravenous drug users (IDUs) in Pudong new district, Shanghai, and explore the population growth and selection pressure of the HCV strains isolated. Methods: A total of 200 serum specimens sampled from IDUs in local methadone maintenance treatment clinic in Pudong were used for amplification of a HCV NS5B 377-nt partial sequence. Mean evolutionary rate and effective number of infections were estimated based on the 377-nt partial sequences of the HCV strains isolated from IDUs and isolated contemporarily from local voluntary blood donors, men who have sex with men and reported hepatitis C cases by using BEAST software. Selection pressure sites were identified with online Datamonkey software for subsequent comparison with direct-acting antiviral (DAA) drug binding sites. Results: A total of 39 (19.5%) serum specimens were positive for HCV RNA. The genotypes were determined based on the HCV NS5B 377-nt partial sequences as follows: subtype 3a (n=14), 3b (n=13), 1b (n=7), 6a (n=4) and 6n (n=1). The partial sequences of the HCV strains isolated in IDUs shared high homology with the sequences of the HCV strains isolated in other populations. The Bayesian Skyline Plot indicated that the estimated infections with HCV subtype 1b increased exponentially during the 1990s, whereas that of subtypes 3a and 3b increased slowly since the mid-1990s. In the NS5B 377-nt partial sequences of the HCV strains isolated in IDUs, there were two positive selection sites and seventy-eight negative selection sites recognized. The mutation rate was as low as 2.2% in the 377-nt partial sequences corresponding to the known seven DAA drug binding sites. Conclusions: HCV subtype 3a and 3b were the predominant genotypes in the IDUs in Pudong. Subtype 1b was prevalent in different populations and evolved very rapidly, and more infections might be caused, suggesting further attention to its prevention, control and treatment. Although DAA treatment based on HCV NS5B binding sites targeting local IDUs might be effective, it is still necessary to strengthen the surveillance.