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 coul

SUBMITTER: Rahman M 

PROVIDER: S-EPMC1079962 | biostudies-literature | 2005 Mar

REPOSITORIES: biostudies-literature