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

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, G1 P [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 G1 P[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 (R) and Rotarix (TM) vaccines administered on demand in our country, Rota Teq (R) is considered the vaccine that has the widest coverage for the genotypes observed in our country and region. ROTASIIL (R) 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

Detection of rotavirus, adenovirus, norovirus,and determination of rotavirus genotype in patients with acute gastroenteritis

Akut enfeksiyöz gastroenterit, tüm dünyada görülen yaygın bir hastalıktır ve çoğu vakaya viral patojenler neden olur. Rotavirus (RV), Norovirus, Adenovirus (AdV) ve Astrovirusler dahil olmak üzere birçok farklı virus, çoğu akut viral gastroenterit vakasından sorumludur. Centers for Disease Control (CDC) göre, viral gastroenterit enfeksiyonları dünya çapında her yıl 200.000'den fazla çocuk ölümüne neden olmaktadır. Bunlardan RV, aşıyla önlenebilir bir hastalıktır. Ancak aşıların kapsamlarında farklılıklar bulunduğundan, bölgelere göre yerleşik genotipler için uygun aşı seçimi önemlidir. Bölgemizde akut gastroenteritli çocuklarda RV, AdV ve Norovirus infeksiyonlarının tespiti ve RV genotip tayini yapmak amacıyla hastanemiz çocuk hastalıklarına ait birimlere başvuran çocuklara ait toplam 341 dışkı örneği çalışmaya dahil edildi. ELISA veya immunokromotografik yöntemlerle dışkıda antijen tespiti yapıldı. RV pozitif örneklerden ise genotip tayini yapıldı. Dışkı örneklerinde RV pozitifliği %23.1, Norovirus %7.3, AdV pozitifliği ise %12.9 olarak tespit edildi. Ülkemiz verileriyle karşılaştırıldığında RV görülme oranı ülkemizden bildirilen çalışmalara benzer, AdV görülme oranı daha yüksek ve NoV görülme oranı ise daha düşük bulunmuştur. RV genotip analizinde ise en sık görülen G tipi G2 (%52.5) olarak bulunmuştur. Bunun dışında G1, G9, G3, G4 genotipleri tespit edilmiştir. En sık görülen P tipi ise P4 (%83) olarak bulunmuştur. Ayrıca P9 ve P10 genotipleri tespit edilmiştir. G ve P genotipinin birlikte tespit edildiği numunelerin dağılımına bakıldığında; en sık olarak G1P [4], G2P [9], G9P [4] genotipleri görülmüştür. RV aşılarından Rota Teq®, ülkemiz ve bölgemizde görülen genotipleri en geniş olarak kapsayan aşı olarak görülmektedir. Bölgemizde rastlanan RV genotiplerini %87.5 oranında kapsamaktadır. Genotiplerin ülke ve bölgelere göre değişkenlik göstermesi nedeniyle RV hastalığının mevcut yükünü artırma potansiyeline sahip suşların ortaya çıkışı sürekli olarak izlenmelidir.Acute infectious gastroenteritis is a common disease worldwide and most cases are caused by viral pathogens. Many different viruses are responsible for most cases of acute viral gastroenteritis, including Rotavirus (RV), Norovirus, Adenovirus (AdV), and Astroviruses. According to the Centers for Disease Control (CDC), viral gastroenteritis infections cause more than 200,000 child deaths worldwide each year. of these, RV is a vaccine-preventable disease. However, since there are differences in the scope of the vaccines, it is important to select the appropriate vaccine for the established genotypes according to the regions. A total of 341 stool samples from children who applied to the pediatric units of our hospital in order to detect RV, AdV and Norovirus infections in children with acute gastroenteritis in our region and to determine the RV genotype were included in the study. Antigen detection was performed in stool by ELISA or immunochromatographic methods. Genotype determination was made from RV positive samples. In stool samples, RV positivity was 23.1%, Norovirus 7.3%, and AdV positivity was 12.9%. When compared with the data of our country, the incidence of RV was similar to the studies reported from our country, the incidence of AdV was higher and the rate of NoV incidence was lower. In the RV genotype analysis, the most common G type was found to be G2 (52.5%). Apart from this, G1, G9, G3, G4 genotypes were determined. The most common P type was found to be P4 (83%). In addition, P9 and P10 genotypes were determined. Considering the distribution of the samples in which the G and P genotypes were determined together; the most common genotypes were G1P [4], G2P [9], G9P [4]. Among the RV vaccines, Rota Teq® is seen as the vaccine that covers the most genotypes seen in our country and region. It covers 87.5% of the Rotavirus genotypes found in our region. Because genotypes vary by country and region, emergence of strains with the potential to increase the current burden of RV disease should be continuously monitored