title: Comparison of Three Different Hepatitis C Virus Genotyping Methods: 5'NCR PCR-RFLP, Core Type-Specific PCR, and NS5b Sequencing in a Tertiary Care Hospital in South India.
abstract: BACKGROUND
  Based on genetic heterogeneity, hepatitis C virus (HCV) is classified into seven major genotypes and 64 subtypes. In spite of the sequence heterogeneity, all genotypes share an identical complement of colinear genes within the large open reading frame. The genetic interrelationships between these genes are consistent among genotypes. Due to this property, complete sequencing of the HCV genome is not required. HCV genotypes along with subtypes are critical for planning antiviral therapy. Certain genotypes are also associated with higher progression to liver cirrhosis.
  
  
  METHODS
  In this study, 100 blood samples were collected from individuals who came for routine HCV genotype identification. These samples were used for the comparison of two different genotyping methods (5'NCR PCR-RFLP and HCV core type-specific PCR) with NS5b sequencing.
  
  
  RESULTS
  Of the 100 samples genotyped using 5'NCR PCR-RFLP and HCV core type-specific PCR, 90% (κ = 0.913, P < 0.00) and 96% (κ = 0.794, P < 0.00) correlated with NS5b sequencing, respectively. Sixty percent and 75% of discordant samples by 5'NCR PCR-RFLP and HCV core type-specific PCR, respectively, belonged to genotype 6. All the HCV genotype 1 subtypes were classified accurately by both the methods.
  
  
  CONCLUSIONS
  This study shows that the 5'NCR-based PCR-RFLP and the HCV core type-specific PCR-based assays correctly identified HCV genotypes except genotype 6 from this region. Direct sequencing of the HCV core region was able to identify all the genotype 6 from this region and serves as an alternative to NS5b sequencing.
authors: Department of Clinical Virology, Christian Medical College, Vellore, India.
authors: Hubert D-J
authors: HD
authors: Daniel
authors: Department of Clinical Virology, Christian Medical College, Vellore, India.
authors: Joel
authors: J
authors: David
authors: Department of Clinical Virology, Christian Medical College, Vellore, India.
authors: Sukanya
authors: S
authors: Raghuraman
authors: Department of Clinical Virology, Christian Medical College, Vellore, India.
authors: Manu
authors: M
authors: Gnanamony
authors: Department of Gastrointestinal Sciences, Christian Medical College, Vellore, India.
authors: George M
authors: GM
authors: Chandy
authors: Department of Clinical Virology, Christian Medical College, Vellore, India.
authors: Gopalan
authors: G
authors: Sridharan
authors: Department of Clinical Virology, Christian Medical College, Vellore, India.
authors: Priya
authors: P
authors: Abraham
mesh_terms: D060005:Genotyping Techniques / Q000379:methods*; D016174:Hepacivirus / Q000235:genetics*; D006526:Hepatitis C / Q000175:diagnosis* / Q000821:virology*; D006801:Humans; D007194:India; D016133:Polymerase Chain Reaction / Q000379:methods*; D012150:Polymorphism, Restriction Fragment Length / Q000235:genetics; D012367:RNA, Viral / Q000032:analysis / Q000235:genetics; D017423:Sequence Analysis, RNA; D062606:Tertiary Care Centers; D014758:Viral Core Proteins / Q000235:genetics; D017361:Viral Nonstructural Proteins / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase
chemical_list: D012367:RNA, Viral; D014758:Viral Core Proteins; D017361:Viral Nonstructural Proteins; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase
keywords: 5′NCR PCR-RFLP; HCV core type-specific PCR; HCV genotype; HCV subtype; NS5b sequencing