Publication:
222 Base pairs in NS5B region and the determination of hepatitis C virus genotype 6

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Issued Date

2006

Resource Type

Article

File Type

application/pdf

ISSN

3005526

DOI

10.1159/000091469

Other identifier(s)

2-s2.0-33646679138

Rights Holder(s)

Scopus

Bibliographic Citation

Intervirology. Vol 49, No.4 (2006), p.224-229

Suggested Citation

Chinchai T., Noppornpanth S., Bedi K., Theamboonlers A., Poovorawan Y. 222 Base pairs in NS5B region and the determination of hepatitis C virus genotype 6. Intervirology. Vol 49, No.4 (2006), p.224-229. doi:10.1159/000091469 Retrieved from: https://hdl.handle.net/20.500.14740/5781

Title

222 Base pairs in NS5B region and the determination of hepatitis C virus genotype 6

Author(s)

Chinchai T.
 Noppornpanth S.
 Bedi K.
 Theamboonlers A.
 Poovorawan Y.

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 or3a 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. Copyright © 2006 S. Karger AG.

Subject(s)

Protein ns5b
 Unclassified drug
 Virus protein
 Article
 Base pairing
 Blood donor
 GenBank
 Gene sequence
 Genotype
 Hepatitis C virus
 Nonhuman
 Nucleotide sequence
 Phylogeny
 Priority journal
 Reverse transcription polymerase chain reaction
 Southeast Asia
 Virus isolation
 Base Pairing
 Base Sequence
 Blood Donors
 Genes, Viral
 Genotype
 Hepacivirus
 Hepatitis C
 Humans
 Phylogeny
 Sequence Analysis, RNA
 Thailand
 Viral Nonstructural Proteins
 Hepatitis C virus
 Hepatitis C virus genotype 6

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https://hdl.handle.net/20.500.14740/5781

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Scopus: Year 1983-2021

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