Quadruplex Real-Time TaqMan® RT-qPCR Assay for Differentiation of Equine Group A and B Rotaviruses and Identification of Group A G3 and G14 Genotypes

• Published in: Viruses Vol. 15; no. 8; p. 1626
• Main Authors: Carossino, Mariano, Balasuriya, Udeni B. R, Thieulent, Côme J, Barrandeguy, Maria E, Vissani, Maria Aldana, Parreño, Viviana
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 26-07-2023; MDPI
• Subjects: Acids; Animals; Comparative analysis; Diarrhea; DNA sequencing; Epidemics; Epidemiology; equine rotavirus A; equine rotavirus B; ERVA; ERVB; Feces; Genes; Genetic aspects; Genomes; Genotypes; Horses; Laboratories; Microscopy; Nucleotide sequencing; Polymerase chain reaction; Proteins; Public health; RNA polymerase; Rotavirus; rotavirus A; rotavirus B; Strains (organisms); Vaccine development; Vaccines; Viruses; Massachusetts; Kentucky; United States > US
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v15081626

Equine rotavirus A (ERVA) is the leading cause of diarrhea in foals, with G3P[12] and G14P[12] genotypes being the most prevalent. Recently, equine G3-like RVA was recognized as an emerging infection in children, and a group B equine rotavirus (ERVB) was identified as an emergent cause of foal diarrhea in the US. Thus, there is a need to adapt molecular diagnostic tools for improved detection and surveillance to identify emerging strains, understand their molecular epidemiology, and inform future vaccine development. We developed a quadruplex TaqMan® RT-qPCR assay for differentiation of ERVA and ERVB and simultaneous G-typing of ERVA strains, evaluated its analytical and clinical performance, and compared it to (1) a previously established ERVA triplex RT-qPCR assay and (2) standard RT-PCR assay and Sanger sequencing of PCR products. This quadruplex RT-qPCR assay demonstrated high sensitivity (>90%)/specificity (100%) for every target and high overall agreement (>96%). Comparison between the triplex and quadruplex assays revealed only a slightly higher sensitivity for the ERVA NSP3 target using the triplex format (p-value 0.008) while no significant differences were detected for other targets. This quadruplex RT-qPCR assay will significantly enhance rapid surveillance of both ERVA and ERVB circulating and emerging strains with potential for interspecies transmission.