Determination and Genotype Distribution of Rotavirus Gastroenteritis in Pediatric Patients Admitted to a Tertiary Care Hospital

Abstract

Acute infectious gastroenteritis is a prevalent disease worldwide, and most of the cases are caused by viral pathogens. Many different viruses, including Rotavirus (RV), Norovirus, Adenovirus, and Astro-viruses, are responsible for most acute viral gastroenteritis cases. According to the Centers for Disease Control and Prevention (CDC), viral gastroenteritis infections cause more than 200 000 child mortalities each year worldwide. One of the best strategies to reduce the global burden of RV gastroenteritis is the development and administration of effective vaccines. However, since there are differences in the coverage of the vaccines, the choice of appropriate vaccine for localized genotypes based on regions is important. The aim of this study was to detect the RV infections in our region and to perform genotyping using real time polymerase chain reaction (Rt-PCR) and high resolution melting (HRM) analysis. A total of 341 stool samples collected from pediatric patients were tested. Lateral flow immunochromatographic assay principle based assay was used for antigen detection. RT-PCR and HRM were applied for genotype analysis. Similar to the data from our country and Eastern Mediterranean region, RV positivity in stool samples was 23.1%. The majority of the patients (51%) were aged 0-2 years and the vast majority of the patients, with a rate of 77%, were between the ages of 0-5. Most of the cases were detected in the winter months, especially in February. The distribution of 40 samples, whose G genotype could be detected, was as follows: G2, 21 (52.5%); G1, 11 (27.5%); G9, 5 (12.5%); G3, 2 (5%); G4, 1 (2.5%). The distribution of 53 samples, whose P genotype could be detected, was as follows: P4, 44 (83.0%); P9, 8 (15.1%); P10, 1 (1.9%). Among those whose genotype could be detected, the most prevalent genotypes were G2 with 52.5% and P4 with 83%. When the distribution of 25 samples was evaluated, in which RV G and P genotypes were detected simultaneously, G1P [4] 11 (44%), G2P[9] 5 (20%), G9P[4] 5 (20%), G2P[4] 2 (8%), G3P[10] 1 (4%), and G4P[4] 1 (4%) genotypes were determined, respectively. The most commonly observed genotype was G1P[4]. In the HRM analysis, it was observed that the melting curve peaks were at different temperatures in nine of the G2 genotype samples and 16 of the P4 and P9 genotype samples. Thus, genotyping with HRM analysis could not be fully finalized, especially for G2 and P. Of the Rota Teq® and RotarixTM vaccines administered on demand in our country, Rota Teq® is considered the vaccine that has the widest coverage for the genotypes observed in our country and region. ROTASIIL® vaccine, which covers all the genotypes in our region (G1, G2, G3, G4, G9) is not available in our country. The emergence of the strains with the potential to increase the current burden of RV disease should be continuously monitored, as different results are obtained by region and year, even within the same country. Thus, the emergence of vaccine-resistant strains can be followed up, especially in countries with higher viral diversity.