Development and evaluation of a one-step multiplex real-time TaqMan® RT-qPCR assay for the detection and genotyping of equine G3 and G14 rotaviruses in fecal samples

Table 3 Primers and probe combinations for the detection of rotavirus A (pan-rotavirus A, targeting the NSP3 gene) and specific amplification of the VP7 gene of equine rotavirus A G3 and G14 genotypes

Name	Target	Nucleotide Position	Sequence (5′ to 3′)
NVP3-FDeg¹	NSP3	963-982^a	ACCATCTWCACRTRACCCTC
NVP3-R1¹	NSP3	1053-1,034^a	GGTCACATAACGCCCCTATA
NVP3-Probe¹	NSP3	984-1,026^a	Cy5-ATGAGCACAATAGTTAAAAGCTAACACTGTCAA-BHQ2
RVA-G3-756F	VP7 (G3)^b	756–777	GATGTTACCACGACCACTTGTA
RVA-G3-872R	VP7 (G3)^b	872–854	AGTTGGATCGGCCGTTATG
RVA-G3-779P	VP7 (G3)^b	779–823	FAM-TGGGACCACGAGAGAATGTAGCTGT-TAMRA
RVA-G14-ARG869F	VP7 (G14)^c	869–885	ATCCGACTACGGCTCCA
RVA-G14-ARG1011R	VP7 (G14)^c	1011–990	TGCAGCAGAATTTAATGATCGC
RVA-G14-ARG886P	VP7 (G14)^c	886–915	HEX-CAGATTGGACGAATGATGCGTATAAATTGG-MGB

¹Primers and probe name and sequences derived from Freeman et al., 2008
^anucleotide position based on GenBank Accession number X81436
^bnucleotide position based on GenBank Accession number KM454497.1
^cnucleotide position based on GenBank Accession number KM454508.1
Cy5, cyanine 5; BHQ2, black hole quencher 2; FAM, 6-carboxyfluorescein; TAMRA, tetramethylrhodamine; HEX, hexachloro-fluorescein; MGB, minor groove binder

ISSN: 1743-422X