Reemergence of new variant G3 rotavirus in Japanese pediatric patients, 2009–2011

► Epidemiological study of rotavirus in children with diarrhea in Japan was conducted. ► Rotavirus was detected in 19.9%, of which G3P[8] was the most prevalent genotype. ► We examined the changes of rotavirus genotypes in Japanese population. ► G3 rotaviruses were emerged as the most predominant genotype and replaced G1 rotavirus. ► Rotavirus G3 strain is the major cause of infection in five geographical areas of Japan. The molecular epidemiology and characterization of rotaviruses obtained from non-hospitalized children with acute gastroenteritis in five different prefectures (Hokkaido, Saga, Tokyo, Osaka, and Kyoto) from July 2009 to June 2011 was investigated. Among 831 fecal specimens tested, rotavirus was found in 165 specimens (19.9%). The rotavirus detection rate in 2010–2011 (23.3%) was higher than those in 2009–2010 (16.0%). The highest prevalence of rotavirus was found in children aged 12 to 23months. Rotavirus could be detected throughout the 8month period with a peak in April. We found that G3P[8] was the most prevalent genotype (54.5%), followed by G1P[8] (29.1%), G9P[8] (9.1%), G3P[4] (3.0%), G2P[4] (2.5%), G1P[4] (1.2%), and G4P[8] (0.6%), respectively. Interestingly, G3 strains emerged as the most predominant genotype and replaced G1 rotavirus which had been reported as the most predominant genotype in the previous studies. Phylogenetic analysis revealed that G3 rotavirus strains were closely related to the “new variant G3” 5091 strain, which emerged in Japan in 2003–2004. A significant increase in the prevalence of rotavirus G3 found in this study indicates that rotavirus G3 strain is the major cause of infection in five geographical areas of Japan and may distribute globally in the near future.