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Title: Typing of human rotaviruses: nucleotide mismatches between the VP7 gene and primer are associated with genotyping failure
Authors: Rahman, Mustafizur ×
Sultana, Rasheda
Podder, Goutam
Faruque, Abu S G
Matthijnssens, Jelle
Zaman, Khalequz
Breiman, Robert F
Sack, David A
Van Ranst, Marc
Azim, Tasnim #
Issue Date: Jan-2005
Publisher: BioMed Central
Series Title: Virology Journal vol:2 pages:24-28
Article number: 24
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.
ISSN: 1743-422X
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Laboratory of Clinical and Epidemiological Virology (Rega Institute)
Laboratory of Clinical Bacteriology and Mycology
× corresponding author
# (joint) last author

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