Open Access Short report

Inaccurate identification of rotavirus genotype G9 as genotype G3 strains due to primer mismatch

Marcelo Takahiro Mitui1, TGA Nilmini Chandrasena2, Paul KS Chan3, Shaman Rajindrajith4, E Anthony S Nelson5, Ting Fan Leung5, Akira Nishizono1 and Kamruddin Ahmed6*

Author Affiliations

1 Department of Microbiology, School of Medicine, Oita University, Yufu, Oita, Japan

2 Department of Parasitology, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka

3 Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, People’s Republic of China

4 Department of Pediatrics, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka

5 Department of Paediatrics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, People’s Republic of China

6 Research Promotion Institute, Oita University, Yufu, Oita, Japan

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Virology Journal 2012, 9:144  doi:10.1186/1743-422X-9-144

Published: 3 August 2012

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.

Keywords:
Group a rotavirus; Genotyping; Primer mismatch; Genotype G3; Genotype G9; Hong Kong; Sri Lanka