Analysis of genetic variations of hepatitis C virus 5'untranslated regions gene in human immunodeficiency virus-1/hepatitis C virus co-infected patients in Xinjiang

Abstract

Objective To investigate the genetic dynamics of hepatitis C virus (HCV) 5'untranslated regions (UTR) gene in human immunodeficiency virus (HIV-1)/HCV co-infected patients in Xinjiang. Methods Anti-HCV was tested using enzyme linked immunosorbent assay in 212 HIV-1 infected patients in Xinjiang. RNA was extracted from HIV-1/HCV co-infected samples. Then HCV 5'UTR gene was amplified after reverse transcription using PrimeScript™ Ⅱ 1st Strand cDNA Synthesis kit. The sequences were then compared with HCV international standard strains to determine the HCV gene types. The gene distance of 4 sampling virus strains was calculated and the phylogenetic analysis was performed to establish the cladogram. Results One hundred and fifty-seven among the 212 HIV-infected patients were HCV antibody positive. Of them, 2 patients were infected through heterosexual transmission and the remaining 155 patients were injection drug users (IDU). HCV 5'UTR was amlipicated and geno-typed successfully in 131 samples. Five HCV genotypes were identified, including 3a (40/131, 30.53%), 3b (23/131, 17.56%), 1a (11/131, 8.40%), 1b (56/131, 42.75%), and 6a (1/131, 0.76%). The general homology was 87.5%-99.3% in 38 patients, and there were differences in homology in different subtypes. The homology of the 4 sampling sequences from the same sample was 99.3%-100.0%, with the variation of 0-0.7%. The intragroup gene deviation and deviation with the first sample tended to increase with time. The mean evolutionary rate of HCV 5'UTR in HIV-1 infected patients in Xinjiang was 1.62×10-3(95%CI: 1.52×10-3-5.38×10-3). The similarity and homology of several sequences obtained from the one participant were the highest. Conclusions The prevalence of HCV co-infection among HIV-1 infected patients in Xinjiang is high, especially among IDU. Subtype 1b of HCV is prevalent strain. Key words: Human immunodeficiency virus-1; Hepacivirus; 5'UTR; Genetic distance; Evolutionary rate