Differentiation of RotaTeq® vaccine strains from wild-type strains using NSP3 gene in reverse transcription polymerase chain reaction assay

•A novel RT-PCR assay was developed to differentiate RotaTeq® vaccine viruses from wild-type rotaviruses.•The developed assay was able to detect rotaviruses in clinical stool samples.•Of 286 rotaviruses, vaccine-derived strains were identified in 39 samples. RotaTeq® is a live attenuated human-bovine reassortant vaccine against rotaviruses that is used worldwide. However, shedding of the virus used in RotaTeq® has been detected in the feces of children following vaccination by the oral route, possibly affecting community immunity. Therefore, a simple and efficient method to discriminate between virulent and RotaTeq® vaccine strains is required. In this study, a novel one-step multiplex reverse-transcription polymerase chain reaction (RT-PCR) assay targeting the NSP3 gene was developed to detect RotaTeq® vaccine strains in fecal samples. RotaTeq® vaccine viruses were successfully distinguished from known wild-type rotavirus genotypes. In addition, the developed assay was able to detect rotaviruses in clinical stool samples obtained from South Korea during the 2011–2013 rotavirus seasons. Of the 1106 stool specimens from children with acute gastroenteritis that were screened, 286 rotaviruses were genotyped. RotaTeq® vaccine strains were identified in 39 samples (13.6%). The novel RT-PCR assay that was developed could be used to detect and discriminate between RotaTeq® vaccine strains that are shed in fecal matter, and to estimate the quantification of virus that has been shed after vaccination.