title: Inaccurate identification of rotavirus genotype G9 as genotype G3 strains due to primer mismatch.
abstract: Reverse transcription (RT)-PCR is now the standard method for typing group A rotaviruses (RVA) to monitor the circulating genotypes in a population. Selection of primers that can accurately type the circulating genotypes is crucial in the context of vaccine introduction and correctly interpreting the impact of vaccination on strain distribution. To our knowledge this study is the first report from Asia of misidentification of genotype G9 as G3 due to a primer-template mismatch. We tested two published G-genotype specific primers sets, designed by Gouvea and colleagues (Set A) and Iturriza-Gomara and colleagues (Set B) on RVA from Hong Kong and Sri Lanka. Among 52 rotaviruses typed as G3 by set A primers, 36 (69.2%) were identified as G9 by nucleotide sequencing and set B primers. Moreover, of 300 rotaviruses tested, 28.3% were untypable by set A primers whereas only 12.3% were untypable by set B primers. Our findings reinforce the need to periodically monitor the primers used for RVA genotyping.
authors.affiliation: Department of Microbiology, School of Medicine, Oita University, Yufu, Oita, Japan.
authors.forename: Marcelo Takahiro
authors.initials: MT
authors.lastname: Mitui
authors.forename: Tga Nilmini
authors.initials: TN
authors.lastname: Chandrasena
authors.forename: Paul Ks
authors.initials: PK
authors.lastname: Chan
authors.forename: Shaman
authors.initials: S
authors.lastname: Rajindrajith
authors.forename: E Anthony S
authors.initials: EA
authors.lastname: Nelson
authors.forename: Ting Fan
authors.initials: TF
authors.lastname: Leung
authors.forename: Akira
authors.initials: A
authors.lastname: Nishizono
authors.forename: Kamruddin
authors.initials: K
authors.lastname: Ahmed
mesh_terms: D002675:Child, Preschool; D017931:DNA Primers / Q000235:genetics*; D003951:Diagnostic Errors; D005838:Genotype; D006723:Hong Kong; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D012401:Rotavirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D012400:Rotavirus Infections / Q000821:virology*; D013188:Sri Lanka
chemical_list: D017931:DNA Primers