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Typing of human rotaviruses: nucleotide mismatches between the VP7 gene and primer are associated with genotyping failure.


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.

SUBMITTER: Rahman M 

PROVIDER: S-EPMC1079962 | biostudies-literature | 2005

REPOSITORIES: biostudies-literature

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Typing of human rotaviruses: nucleotide mismatches between the VP7 gene and primer are associated with genotyping failure.

Rahman Mustafizur M   Sultana Rasheda R   Podder Goutam G   Faruque Abu S G AS   Matthijnssens Jelle J   Zaman Khalequz K   Breiman Robert F RF   Sack David A DA   Van Ranst Marc M   Azim Tasnim T  

Virology journal 20050324


<h4>Background</h4>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, nucleot  ...[more]

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