A Real-Time RT-PCR Assay for Genotyping of Rotavirus

Authors
Seyed Dawood Mousavi-Nasab 1
Farzaneh Sabahi 2
Hooman Kaghazian 1
Mahdi Paryan 1
Siamak Mirab Samiee 3
Mostafa Ghaderi 4
Fatemeh Zali 5
Manoochehr Makvandi 6
1 Department of Research and Development, Production and Research Complex, Pasteur Institute of Iran, Tehran, Iran
2 Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
3 Reference Health Laboratories Research Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran
4 Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran
5 Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
6 Infectious and Tropical Diseases Research Center, Health research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
10.29252/ibj.24.6.394
Abstract
Background: HRV is the causative agent of severe gastroenteritis in children and responsible for two million hospitalizations and more than a half-million deaths annually. Sequence characteristics of the gene segments encoding the VP7 and VP4 proteins are used for the genotype classification of rotavirus. A wide variety of molecular methods are available, mainly based on reverse transcription PCR for rapid, specific and sensitive genotyping of rotaviruses. This study describes an alternative real-time PCR assay for genotyping of rotavirus. Methods: The samples of stools studied in this research have been collected from patients referred to Children's Medical Centers, Tehran, Iran. Rotavirus detection and genotyping were performed using the RT-PCR and semi-nested RT-PCR, respectively. Samples were then genotyped with a new real-time PCR. Results: The real-time PCR was able to genotype all positive samples with a mean Ct of 28.2. Besides, a concordance rate of 100% was detected between real-time PCR and semi-nested RT-PCR. Conclusion: In this study, the genotyping of rotavirus with real-time PCR showed that this method can provide several favorable features, including high sensitivity and specificity, and a wide dynamic range for rotavirus genotyping.
Keywords
Gastroenteritis
Genotype
Real-Time Polymerase Chain Reaction
Rotavirus
Iranian Biomedical Journal
Volume 24, Issue 6 - Serial Number 94
November and December 2020
Pages 399-404