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

Mustafizur Rahman, Rasheda Sultana, Goutam Podder, Abu S.G. Faruque, Jelle Matthijnssens, Khalequz Zaman, Robert F. Breiman, David A. Sack, Marc Van Ranst, Tasnim Azim

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number24
JournalVirology Journal
Volume2
DOIs
StatePublished - Mar 24 2005
Externally publishedYes

ASJC Scopus subject areas

  • Virology
  • Infectious Diseases

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    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]. https://doi.org/10.1186/1743-422X-2-24