Full-length sequencing and baseline resistance-associated substitution of hepatitis C virus subtype 3b / 临床肝胆病杂志

ABSTRACT

ObjectiveTo investigate the application of next-generation sequencing (NGS) in determining the full-length sequence and baseline resistance-associated substitution (RAS) of hepatitis C virus (HCV) subtype 3b. MethodsNucleic acid was extracted from plasma of a HCV RNA-positive blood donor, and after sequence-independent amplification, a sequencing library was constructed and NGS was performed using Illumina Hiseq. Bioinformatics methods were used to analyze full-length HCV sequence, viral genotype, and baseline RAS to direct-acting antivirals (DAAs). ResultsA total of 8.4 Gb data with more than 56 million reads were obtained. The full-length HCV sequence was obtained by bioinformatics analysis, with an average sequencing depth of 488 007 and a genotype of 3b subtype. A total of 12 RASs were identified in HCV amino acid sequence, i.e., Y56H, Q80K, Q80R, and A156G located in NS3, M28G, Q/A30G, Q/A30K, L31F, L31M, and Y93H located in NS5A, and S282T and V321A located in NS5B, among which Q/A30K and L31M located in NS5A had high frequencies of 99.16% and 98.37%, respectively, while the other 10 RASs had low frequencies of ＜0.5%. ConclusionNGS can be used to determine the full-length sequence and genotype of HCV subtype 3b and identify baseline RASs, which has great significance in the epidemiological study of HCV subtype 3b and the development of DAA treatment regimens.