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Accurate genotyping of hepatitis C virus through nucleotide sequencing and identification of new HCV subtypes in China population.
Clin Microbiol Infect. 2015 Sep; 21(9):874.e9-874.e21.CM

Abstract

Nucleotide sequencing of the phylogenetically informative region of NS5B remains the gold standard for hepatitis C virus (HCV) genotyping. Here we developed a new methodology for sequencing new NS5B regions to increase the accuracy and sensitivity of HCV genotyping and subtyping. The eight new primers were identified by scanning the full-length NS5B regions from 1127 HCV genomic sequences found in HCV databases. The ability of each pair of primers to amplify HCV subtypes was scored, and the new primers were able to amplify the NS5B region better than the previously used primers, therefore more accurately subtyping HCV strains. Sequencing the DNA amplified by the new primer pairs can specifically and correctly detect the five standard HCV subtypes (1a, 2a, 3b, 6a and 1b). We further examined patient samples and found that the new primers were able to identify HCV subtypes in clinical samples with high sensitivity. This method was able to detect all subtypes of HCV in 567 clinical samples. Importantly, three novel HCV subtypes (1b-2a, 1b-2k and 6d-6k) were identified in the samples, which have not been previous reported in China. In conclusion, sequencing the NS5B region amplified by the new NS5B primers is a more reliable method of HCV genotyping and a more sensitive diagnostic tool than sequencing using the previously described primers, and could identify new HCV subtypes. Our research is useful for clinical diagnosis, guidance of clinical treatment, management of clinical patients, and studies on the epidemiology of HCV.

Authors+Show Affiliations

Department of Clinical Laboratory, China; Clinical Molecular Diagnostic Centre, Renmin Hospital of Wuhan University, Wuhan, China.Department of Pathology, Affiliated Tianyou Hospital of Wuhan University of Science and Technology, Wuhan, China.Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China.Clinical Molecular Diagnostic Centre, Renmin Hospital of Wuhan University, Wuhan, China.Department of Clinical Laboratory, China.Clinical Molecular Diagnostic Centre, Renmin Hospital of Wuhan University, Wuhan, China.Pennsylvania State University College of Medicine and Hershey Medical Center, Hershey, PA, USA.Pennsylvania State University College of Medicine and Hershey Medical Center, Hershey, PA, USA. Electronic address: csong@hmc.psu.edu.Department of Clinical Laboratory, China; Clinical Molecular Diagnostic Centre, Renmin Hospital of Wuhan University, Wuhan, China. Electronic address: climdc@163.com.

Pub Type(s)

Evaluation Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

26055416

Citation

Tong, Y-Q, et al. "Accurate Genotyping of Hepatitis C Virus Through Nucleotide Sequencing and Identification of New HCV Subtypes in China Population." Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases, vol. 21, no. 9, 2015, pp. 874.e9-874.e21.
Tong YQ, Liu B, Liu H, et al. Accurate genotyping of hepatitis C virus through nucleotide sequencing and identification of new HCV subtypes in China population. Clin Microbiol Infect. 2015;21(9):874.e9-874.e21.
Tong, Y. Q., Liu, B., Liu, H., Zheng, H. Y., Gu, J., Liu, H., Song, E. J., Song, C., & Li, Y. (2015). Accurate genotyping of hepatitis C virus through nucleotide sequencing and identification of new HCV subtypes in China population. Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases, 21(9), e9-e21. https://doi.org/10.1016/j.cmi.2015.05.034
Tong YQ, et al. Accurate Genotyping of Hepatitis C Virus Through Nucleotide Sequencing and Identification of New HCV Subtypes in China Population. Clin Microbiol Infect. 2015;21(9):874.e9-874.e21. PubMed PMID: 26055416.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Accurate genotyping of hepatitis C virus through nucleotide sequencing and identification of new HCV subtypes in China population. AU - Tong,Y-Q, AU - Liu,B, AU - Liu,H, AU - Zheng,H-Y, AU - Gu,J, AU - Liu,H, AU - Song,E J, AU - Song,C, AU - Li,Y, Y1 - 2015/06/06/ PY - 2015/01/07/received PY - 2015/05/10/revised PY - 2015/05/26/accepted PY - 2015/6/10/entrez PY - 2015/6/10/pubmed PY - 2016/8/5/medline KW - Genotype KW - hepatitis C virus KW - ns5b KW - sequencing KW - subtype SP - 874.e9 EP - 874.e21 JF - Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases JO - Clin Microbiol Infect VL - 21 IS - 9 N2 - Nucleotide sequencing of the phylogenetically informative region of NS5B remains the gold standard for hepatitis C virus (HCV) genotyping. Here we developed a new methodology for sequencing new NS5B regions to increase the accuracy and sensitivity of HCV genotyping and subtyping. The eight new primers were identified by scanning the full-length NS5B regions from 1127 HCV genomic sequences found in HCV databases. The ability of each pair of primers to amplify HCV subtypes was scored, and the new primers were able to amplify the NS5B region better than the previously used primers, therefore more accurately subtyping HCV strains. Sequencing the DNA amplified by the new primer pairs can specifically and correctly detect the five standard HCV subtypes (1a, 2a, 3b, 6a and 1b). We further examined patient samples and found that the new primers were able to identify HCV subtypes in clinical samples with high sensitivity. This method was able to detect all subtypes of HCV in 567 clinical samples. Importantly, three novel HCV subtypes (1b-2a, 1b-2k and 6d-6k) were identified in the samples, which have not been previous reported in China. In conclusion, sequencing the NS5B region amplified by the new NS5B primers is a more reliable method of HCV genotyping and a more sensitive diagnostic tool than sequencing using the previously described primers, and could identify new HCV subtypes. Our research is useful for clinical diagnosis, guidance of clinical treatment, management of clinical patients, and studies on the epidemiology of HCV. SN - 1469-0691 UR - https://www.unboundmedicine.com/medline/citation/26055416/Accurate_genotyping_of_hepatitis_C_virus_through_nucleotide_sequencing_and_identification_of_new_HCV_subtypes_in_China_population_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1198-743X(15)00566-2 DB - PRIME DP - Unbound Medicine ER -