Please use this identifier to cite or link to this item: 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
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