Please use this identifier to cite or link to this item: https://ir.swu.ac.th/jspui/handle/123456789/15027
ชื่อเรื่อง: 222 Base pairs in NS5B region and the determination of hepatitis C virus genotype 6
ผู้แต่ง: Chinchai T.
Noppornpanth S.
Bedi K.
Theamboonlers A.
Poovorawan Y.
Keywords: 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
วันที่เผยแพร่: 2006
บทคัดย่อ: 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.
URI: https://ir.swu.ac.th/jspui/handle/123456789/15027
https://www.scopus.com/inward/record.uri?eid=2-s2.0-33646679138&doi=10.1159%2f000091469&partnerID=40&md5=baac5bc280be0421007a941d60428983
ISSN: 3005526
Appears in Collections:Scopus 1983-2021

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