ABSTRACT
【Objective】 To learn the situation of the evolution process of HCV virus population and the selection pressure of HCV NS5B in intravenous drug users (IDUs) in Guangdong. 【Methods】 141 blood samples from hepatitis C virus (HCV) RNA-positive blood donors and 58 from HCV patients in Guangdong were randomly collected for HCV NS5B sequence amplification, combined with HCV NS5B sequences from blood donors and IDUs obtained by sequencing previously(between 2009 and 2011). Homology analysis was performed by Molecular Evolutionary Genetics Analysis (MEGA) software, evolutionary analysis were performed by Bayesian Evolutionary Analysis Sampling Trees (BEAST) software package. Selection pressure analysis was performed on sequences isolated from IDUs by Datamonkey online software package with Mixed Effects Model Evolution (MEME) method, and the population expansion of species were analyzed using Tajima and Fu neutrality test by Arlequin software. 【Results】 The comparison results of internal homology among different subtypes of IDUs in this group were as follows : HCV-3b had the highest homology (97%), followed by HCV-3a (96%), HCV-6a (95%) and HCV-1b (94%); HCV evolution rate analysis showed that HCV-1b had the fastest evolution rate [2.17E-03 substitutions/site/year (y/y/y)], followed by HCV-3b (2.12E-0 y/y/y), HCV-3a (1.58E-03 y/y/y) and HCV-6a (1.28E-03 y/y/y). The analysis on effective population of HCV: 1980~1990 was rapid growth period for HCV-6a, 1990~1995 period for HCV-1b, and 2000~2007 period for HCV-3a. HCV population genetic characteristics was as follows: HCV-1b, 3a, 3b and 6a experienced population expansion, among which 3a and 3b were the most obvious. As to the analysis of HCV selection pressure, two positive selection sites (235 and 243)were found in the 339 nucleotide fragment of the NS5B sequence in injecting drug users, but mutation only occurred at position 316 [mutation rate 1.24% (14/1 130)] among 5 direct antiviral drug (DAA) sites in this gene. 【Conclusion】 The evolution of HCV-3b in Guangdong has showed an obvious trend of population expansion, with a high proportion and homology especially in the local IDUs. HCV-3b should be the focus of HCV prevention and control in this region. Given that the positively selected sites of the HCV NS5B gene region of IDUs in Guangdong are non-DAA binding sites, DAA is expected to demonstrate a good effect on these patients.
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),lb (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 lb 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.
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),lb (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 lb 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.