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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.
J Clin Lab Anal. 2017 May; 31(3)JC

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.

CONCLUSION

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+Show Affiliations

Department of Clinical Virology, Christian Medical College, Vellore, India.Department of Clinical Virology, Christian Medical College, Vellore, India.Department of Clinical Virology, Christian Medical College, Vellore, India.Department of Clinical Virology, Christian Medical College, Vellore, India.Department of Gastrointestinal Sciences, Christian Medical College, Vellore, India.Department of Clinical Virology, Christian Medical College, Vellore, India.Department of Clinical Virology, Christian Medical College, Vellore, India.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

27580956

Citation

Daniel, Hubert D-J, et al. "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." Journal of Clinical Laboratory Analysis, vol. 31, no. 3, 2017.
Daniel HD, David J, Raghuraman S, et al. 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. J Clin Lab Anal. 2017;31(3).
Daniel, H. D., David, J., Raghuraman, S., Gnanamony, M., Chandy, G. M., Sridharan, G., & Abraham, P. (2017). 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. Journal of Clinical Laboratory Analysis, 31(3). https://doi.org/10.1002/jcla.22045
Daniel HD, et al. 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. J Clin Lab Anal. 2017;31(3) PubMed PMID: 27580956.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - 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. AU - Daniel,Hubert D-J, AU - David,Joel, AU - Raghuraman,Sukanya, AU - Gnanamony,Manu, AU - Chandy,George M, AU - Sridharan,Gopalan, AU - Abraham,Priya, Y1 - 2016/09/01/ PY - 2016/05/06/received PY - 2016/07/28/accepted PY - 2016/9/2/pubmed PY - 2017/12/28/medline PY - 2016/9/2/entrez KW - 5′NCR PCR-RFLP KW - HCV core type-specific PCR KW - HCV genotype KW - HCV subtype KW - NS5b sequencing JF - Journal of clinical laboratory analysis JO - J Clin Lab Anal VL - 31 IS - 3 N2 - 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. CONCLUSION: 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. SN - 1098-2825 UR - https://www.unboundmedicine.com/medline/citation/27580956/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_ L2 - https://doi.org/10.1002/jcla.22045 DB - PRIME DP - Unbound Medicine ER -