222 Base Pairs in NS5B Region and the Determination of Hepatitis C Virus Genotype 6
| Autor: | Kavita Bedi, Apiradee Theamboonlers, Yong Poovorawan, Teeraporn Chinchai, Suwanna Noppornpanth |
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| Rok vydání: | 2006 |
| Předmět: |
Genes
Viral Genotype Base pair viruses Hepatitis C virus Hepacivirus Blood Donors Viral Nonstructural Proteins medicine.disease_cause chemistry.chemical_compound Virology medicine Humans Base Pairing NS5B Phylogeny Genetics Base Sequence biology Sequence Analysis RNA Nucleic acid sequence virus diseases Hepatitis C Thailand medicine.disease biology.organism_classification digestive system diseases Infectious Diseases chemistry GenBank |
| Zdroj: | Intervirology. 49:224-229 |
| ISSN: | 1423-0100 0300-5526 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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