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

Fingerprint

Rotavirus
Nucleotides
Genes
Bangladesh
Mutation Rate
Reverse Transcription
Binding Sites
Genotype
Polymerase Chain Reaction

ASJC Scopus subject areas

  • Virology
  • Genetics(clinical)

Cite this

Rahman, M., Sultana, R., Podder, G., Faruque, A. S. G., Matthijnssens, J., Zaman, K., ... 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

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

In: Virology Journal, Vol. 2, 24, 24.03.2005.

Research output: Contribution to journalArticle

Rahman, M, Sultana, R, Podder, G, Faruque, ASG, Matthijnssens, J, Zaman, K, Breiman, RF, Sack, DA, 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, vol. 2, 24. https://doi.org/10.1186/1743-422X-2-24
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. / Typing of human rotaviruses : Nucleotide mismatches between the VP7 gene and primer are associated with genotyping failure. In: Virology Journal. 2005 ; Vol. 2.
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