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222 base pairs in NS5B region and the determination of hepatitis C virus genotype 6.
Intervirology. 2006; 49(4):224-9.I

Abstract

OBJECTIVE

The present study was performed to genotype hepatitis C virus (HCV) by direct sequencing of a 222-bp nucleotide in the NS5B region and comparing the results with those of direct sequencing in the core region. We investigated a new region for HCV genotyping which gave the best performance to discriminate HCV genotype 6a, the unique genotype found in Southeast Asia.

METHODS

Plasma samples taken from 57 HCV-infected blood donors were used in this study. RT-PCR products were amplified using primers located in the NS5B region. The 222-bp PCR products were purified and sequenced. The genotype of HCV isolates were obtained by phylogenetic analysis and compared with HCV reference strains stored in the GenBank database. The HCV sequences clustering in the same node were considered to be of the same genotype.

RESULTS

Thirty-one, 22 and 4 samples of HCV genotype 3a, 1a and 1b, respectively, were analyzed by this method. Upon comparison with genotyping in the core region, 86 and 14% of the samples yielded concordant and discordant genotype results, respectively. The majority of discordant results (63%; 5 of 8) was observed with HCV genotype 6a which yielded 6a upon core sequencing as opposed to 1a or 3a upon NS5B sequencing.

CONCLUSION

HCV genotype 6a obtained by direct sequencing in the core region could not be unequivocally arrived at by sequencing 222 bp in the NS5B region. Hence, sequencing in the core region is preferable for genotyping our specimens, even though longer PCR products are required as this method enables discrimination between genotype 6a and the remaining genotypes.

Authors+Show Affiliations

Department of Microbiology, Faculty of Medicine, Srinakharinwirot University, Bangkok, Thailand.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

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

Language

eng

PubMed ID

16491017

Citation

Chinchai, Teeraporn, et al. "222 Base Pairs in NS5B Region and the Determination of Hepatitis C Virus Genotype 6." Intervirology, vol. 49, no. 4, 2006, pp. 224-9.
Chinchai T, Noppornpanth S, Bedi K, et al. 222 base pairs in NS5B region and the determination of hepatitis C virus genotype 6. Intervirology. 2006;49(4):224-9.
Chinchai, T., Noppornpanth, S., Bedi, K., Theamboonlers, A., & Poovorawan, Y. (2006). 222 base pairs in NS5B region and the determination of hepatitis C virus genotype 6. Intervirology, 49(4), 224-9.
Chinchai T, et al. 222 Base Pairs in NS5B Region and the Determination of Hepatitis C Virus Genotype 6. Intervirology. 2006;49(4):224-9. PubMed PMID: 16491017.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - 222 base pairs in NS5B region and the determination of hepatitis C virus genotype 6. AU - Chinchai,Teeraporn, AU - Noppornpanth,Suwanna, AU - Bedi,Kavita, AU - Theamboonlers,Apiradee, AU - Poovorawan,Yong, Y1 - 2006/02/16/ PY - 2005/07/19/received PY - 2005/08/17/accepted PY - 2006/2/24/pubmed PY - 2006/6/17/medline PY - 2006/2/24/entrez SP - 224 EP - 9 JF - Intervirology JO - Intervirology VL - 49 IS - 4 N2 - OBJECTIVE: The present study was performed to genotype hepatitis C virus (HCV) by direct sequencing of a 222-bp nucleotide in the NS5B region and comparing the results with those of direct sequencing in the core region. We investigated a new region for HCV genotyping which gave the best performance to discriminate HCV genotype 6a, the unique genotype found in Southeast Asia. METHODS: Plasma samples taken from 57 HCV-infected blood donors were used in this study. RT-PCR products were amplified using primers located in the NS5B region. The 222-bp PCR products were purified and sequenced. The genotype of HCV isolates were obtained by phylogenetic analysis and compared with HCV reference strains stored in the GenBank database. The HCV sequences clustering in the same node were considered to be of the same genotype. RESULTS: Thirty-one, 22 and 4 samples of HCV genotype 3a, 1a and 1b, respectively, were analyzed by this method. Upon comparison with genotyping in the core region, 86 and 14% of the samples yielded concordant and discordant genotype results, respectively. The majority of discordant results (63%; 5 of 8) was observed with HCV genotype 6a which yielded 6a upon core sequencing as opposed to 1a or 3a upon NS5B sequencing. CONCLUSION: HCV genotype 6a obtained by direct sequencing in the core region could not be unequivocally arrived at by sequencing 222 bp in the NS5B region. Hence, sequencing in the core region is preferable for genotyping our specimens, even though longer PCR products are required as this method enables discrimination between genotype 6a and the remaining genotypes. SN - 0300-5526 UR - https://www.unboundmedicine.com/medline/citation/16491017/222_base_pairs_in_NS5B_region_and_the_determination_of_hepatitis_C_virus_genotype_6_ L2 - https://www.karger.com?DOI=10.1159/000091469 DB - PRIME DP - Unbound Medicine ER -