title: Discrepancy between Hepatitis C Virus Genotypes and NS4-Based Serotypes: Association with Their Subgenomic Sequences.
abstract: Determination of hepatitis C virus (HCV) genotypes plays an important role in the direct-acting agent era. Discrepancies between HCV genotyping and serotyping assays are occasionally observed. Eighteen samples with discrepant results between genotyping and serotyping methods were analyzed. HCV serotyping and genotyping were based on the HCV nonstructural 4 (NS4) region and 5'-untranslated region (5'-UTR), respectively. HCV core and NS4 regions were chosen to be sequenced and were compared with the genotyping and serotyping results. Deep sequencing was also performed for the corresponding HCV NS4 regions. Seventeen out of 18 discrepant samples could be sequenced by the Sanger method. Both HCV core and NS4 sequences were concordant with that of genotyping in the 5'-UTR in all 17 samples. In cloning analysis of the HCV NS4 region, there were several amino acid variations, but each sequence was much closer to the peptide with the same genotype. Deep sequencing revealed that minor clones with different subgenotypes existed in two of the 17 samples. Genotyping by genome amplification showed high consistency, while several false reactions were detected by serotyping. The deep sequencing method also provides accurate genotyping results and may be useful for analyzing discrepant cases. HCV genotyping should be correctly determined before antiviral treatment.
authors.affiliation: Department of Molecular Virology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan. nannwewin@gmail.com.
authors.forename: Nan Nwe
authors.initials: NN
authors.lastname: Win
authors.affiliation: Department of Molecular Virology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan. nakamotoer@faculty.chiba-u.jp.
authors.forename: Shingo
authors.initials: S
authors.lastname: Nakamoto
authors.affiliation: Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan. kandat-cib@umin.ac.jp.
authors.forename: Tatsuo
authors.initials: T
authors.lastname: Kanda
authors.affiliation: Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan. hiroki.takahashi@chiba-u.jp.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Takahashi
authors.affiliation: Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan. azusan_takahashi@faculty.chiba-u.jp.
authors.forename: Azusa
authors.initials: A
authors.lastname: Takahashi-Nakaguchi
authors.affiliation: Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan. ntcph863@yahoo.co.jp.
authors.forename: Shin
authors.initials: S
authors.lastname: Yasui
authors.affiliation: Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan. nkmr.chiba@gmail.com.
authors.forename: Masato
authors.initials: M
authors.lastname: Nakamura
authors.affiliation: Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan. gosyou100@yahoo.co.jp.
authors.forename: Shuang
authors.initials: S
authors.lastname: Wu
authors.affiliation: Safety and Health Organization, Chiba University, Chiba 263-8522, Japan. imazekif@faculty.chiba-u.jp.
authors.forename: Fumio
authors.initials: F
authors.lastname: Imazeki
authors.affiliation: Department of Gastroenterology, Kikkoman General Hospital, Noda 278-0005, Japan. smikami@mail.kikkoman.co.jp.
authors.forename: Shigeru
authors.initials: S
authors.lastname: Mikami
authors.affiliation: Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan. yokosukao@faculty.chiba-u.jp.
authors.forename: Osamu
authors.initials: O
authors.lastname: Yokosuka
authors.affiliation: Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan. gonoi@faculty.chiba-u.jp.
authors.forename: Tohru
authors.initials: T
authors.lastname: Gonoi
authors.affiliation: Department of Molecular Virology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan. sirasawa@faculty.chiba-u.jp.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Shirasawa
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics*; D000368:Aged; D000369:Aged, 80 and over; D000595:Amino Acid Sequence; D000998:Antiviral Agents / Q000627:therapeutic use; D005260:Female; D016679:Genome, Viral / Q000235:genetics*; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods; D016174:Hepacivirus / Q000145:classification / Q000235:genetics* / Q000502:physiology; D006526:Hepatitis C / Q000097:blood / Q000188:drug therapy / Q000821:virology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008297:Male; D008875:Middle Aged; D015203:Reproducibility of Results; D065288:Serogroup; D012703:Serotyping / Q000379:methods; D016896:Treatment Outcome; D014758:Viral Core Proteins / Q000235:genetics; D017361:Viral Nonstructural Proteins / Q000235:genetics*
chemical_list: D020121:5' Untranslated Regions; D000998:Antiviral Agents; C093542:NS4 protein, hepatitis C virus; D014758:Viral Core Proteins; D017361:Viral Nonstructural Proteins; C069130:nucleocapsid protein, Hepatitis C virus
keywords: discrepancy; genotypes; genotyping; hepatitis C virus; serotyping