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https://doi.org/10.1186/1743-422X-2-24
Title: | Typing of human rotaviruses: Nucleotide mismatches between the VP7 gene and primer are associated with genotyping failure | Authors: | Rahman, M Sultana, R Podder, G Faruque, A.S.G Matthijnssens, J Zaman, K Breiman, R.F Sack, D.A Van Ranst, M Azim, T |
Keywords: | glycoprotein glycoprotein vp7 unclassified drug amino acid substitution article base mispairing binding site gene sequence genotype Human rotavirus nonhuman nucleotide sequence open reading frame sequence analysis virus strain virus typing Antigens, Viral Base Sequence Capsid Proteins DNA Primers Genetic Variation Genotype Humans Molecular Sequence Data Rotavirus Rotavirus |
Issue Date: | 2005 | Publisher: | BMC | Citation: | Rahman, M, Sultana, R, Podder, G, Faruque, A.S.G, Matthijnssens, J, Zaman, K, Breiman, R.F, Sack, D.A, Van Ranst, M, Azim, T (2005). Typing of human rotaviruses: Nucleotide mismatches between the VP7 gene and primer are associated with genotyping failure. Virology Journal 2 : 24. ScholarBank@NUS Repository. https://doi.org/10.1186/1743-422X-2-24 | Rights: | Attribution 4.0 International | Abstract: | Background: Rotavirus genotyping is performed by using reverse transcription PCR with type-specific-primers. Because the high rotavirus mutation rate generates an extensive genomic variation, different G-type-specific primer sets are applied in different geographical locations. In Bangladesh, a significant proportion (36.9%) of the rotavirus strains isolated in 2002 could not be G-typed using the routinely used primer set. To investigate the reason why the strains were untypeable, nucleotide sequencing of the VP7 genes was performed. Results: Four nucleotide substitutions at the G1 primer-binding site of the VP7 gene of Bangladeshi G1 rotaviruses rendered a major proportion of circulating strains untypeable using the routine primer set. Using an alternative primer set, we could identify G1 rotaviruses as the most prevalent genotype (44.8%), followed by G9 (21.7%), G2 (15.0%) and G4 (13.8%). Conclusion: Because of the natural variation in the rotaviral gene sequences, close monitoring of rotavirus genotyping methods is important. © 2005 Rahman et al; licensee BioMed Central Ltd. | Source Title: | Virology Journal | URI: | https://scholarbank.nus.edu.sg/handle/10635/178368 | ISSN: | 1743-422X | DOI: | 10.1186/1743-422X-2-24 | Rights: | Attribution 4.0 International |
Appears in Collections: | Staff Publications Elements |
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