title: 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%).
  
  
  CONCLUSIONS
  Because of the natural variation in the rotaviral gene sequences, close monitoring of rotavirus genotyping methods is important.
authors.affiliation: ICDDR,B: Centre for Health and Population Research, Mohakhali, Dhaka-1212, Bangladesh. mustafizur.rahman@uz.kuleuven.ac.be
authors.forename: Mustafizur
authors.initials: M
authors.lastname: Rahman
authors.forename: Rasheda
authors.initials: R
authors.lastname: Sultana
authors.forename: Goutam
authors.initials: G
authors.lastname: Podder
authors.forename: Abu S G
authors.initials: AS
authors.lastname: Faruque
authors.forename: Jelle
authors.initials: J
authors.lastname: Matthijnssens
authors.forename: Khalequz
authors.initials: K
authors.lastname: Zaman
authors.forename: Robert F
authors.initials: RF
authors.lastname: Breiman
authors.forename: David A
authors.initials: DA
authors.lastname: Sack
authors.forename: Marc
authors.initials: M
authors.lastname: Van Ranst
authors.forename: Tasnim
authors.initials: T
authors.lastname: Azim
mesh_terms: D000956:Antigens, Viral / Q000235:genetics*; D001483:Base Sequence; D036022:Capsid Proteins / Q000235:genetics*; D017931:DNA Primers; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D012401:Rotavirus / Q000235:genetics*
chemical_list: D000956:Antigens, Viral; D036022:Capsid Proteins; D017931:DNA Primers; C050779:VP7 protein, Rotavirus