Investigation of rotavirus infection incidence and genotypes in children with acute gastroenteritis

Rotavirus is the most common cause of severe acute gastroenteritis in newborns and young children worldwide. The aim of this study is to determine the incidence and genotypes of rotavirus infection in children under and 5 years of age who were admitted to hospital due to acute gastroenteritis. Between January and December 2017, stool samples were collected from 400 children with acute gastroenteritis. The presence of rotavirus antigen was investigated by the Ridascreen Rotavirus ELISA test (R-Biopharm AG, Germany). Viral RNA extraction from rotavirus positive samples was performed using High Pure Viral RNA kit (Roche Diagnostics, Germany). The RT-PCR test for identification of rotavirus G and P genotypes was carried out using consensus primers specific for the VP7 and VP4 regions. Then, seven rotavirus specific G genotypes (G1-4, G8-10) and six rotavirus specific P genotypes (P[4], P[6], P[8]-[11]) were detected by semi-nested multiplex PCR test. The rate of rotavirus antigen positivity was 22.7% (91). Rotavirus antigen positivity was higher (76.9%) in 0-24 months age group. Rotavirus infection was most prevalent during the autumn, especially in November (38.5%). Out of 91 rotavirus antigen positive samples, 89 (22.2%) were found to be positive by RT-PCR test. Rotavirus G1 genotype was the most common (50.5%) G genotype in 89 stool specimens, followed by G2 (21.3%), G3 (14.6%) and G9 (3.4%). The most predominant P genotype was P[8] (36%), followed by P[6] (22.5%), P[4] (19%), P[9] (4.5%), P[10] (3.4%) and P[11] (1%). The most common G/P combination was G1P[8] with 21.3%, followed by G2P[4] (12.4%), G1P[6] (6.7%), G2P[8] (4.5%) and G3P[8] (3.3%). The incidence of mixed rotavirus infection was detected in 7.9% (7). As a result, the rotavirus P and G genotypes identified in this study were found to be compatible with the genotypes of the existing rotavirus vaccines. Identification and annual surveillance of rotavirus genotypes in our region are important to widespread rotavirus vaccination, to determine vaccine efficacy and to develop alternative rotavirus vaccines in the future. Key Words: Acute gastroenteritis, rotavirus, RT-PCR, semi-nested multiplex PCR, genotyping