Genotyping of VP6 and NSP4 genes and molecular characterization of NSP4 gene of unusual Rotavirus group A isolated from children with acute gastroenteritis

Abstract

Group A Rotavirus (RVA), which causes acute gastroenteritis (AGE) in children worldwide, is categorized mainly based on VP7 (genotype G) and VP4 (genotype P) genes. Genotypes that circulate at < 1% are considered unusual. Important genes are also VP6 (genotype I) and NSP4 (genotype E). VP6 establishes the group and affects immunogenicity, while NSP4, as enterotoxin, is responsible for the clinical symptoms. Aim of this study was to genotype the VP6 and NSP4 genes and molecularly characterize the NSP4 gene of unusual RVA. Unusual RVA strains extracted from fecal samples of children ≤ 16 years with AGE, were genotyped in VP6 and NSP4 genes with Sanger sequencing. Phylogenetics was performed using MEGA 11. In a 15-year period (2007–2021), 54.8% (34/62) of unusual RVA were successfully I and E genotyped. Three different I and E genotypes were identified; I2 (73.5%, 25/34) and E2 (35.3%, 12/34) were the commonest. E3 genotype was detected from 2017 onwards. The uncommon combination of I2-E3 was found in 26.5%(9/34) of the strains and G3-P[9]-I2-E3 was the most frequent G-P-I-E combination (20.6%,7/34). Statistical analysis showed that children infected with E2 strains had a higher relative frequency of dehydration(50%) compared to those with E3 genotype(p = 0.019). Multiple substitutions were detected in NSP4, but their functional effect remains unknown. The results indicate the genetic diversity of RVA strains. Continuous surveillance of the RVA based on the whole genome will provide a better knowledge of its evolution.