Table 1.

Genotype-specific oligonucleotides used in CCoV fluorogenic and conventional RT-PCR assays

Primer/probe	Sequence 5′ to 3′	Sense	Position	Amplicon size (bp)	Specificity
CCoV1aa	GTGCTTCCTCTTGAAGGTACA	+	502–522c	239	CCoV type I
CCoV2a	TCTGTTGAGTAATCACCAGCT	−	720–740c
CCoVI-Fb	CGTTAGTGCACTTGGAAGAAGCT	+	478–499c	111
CCoVI-Rb	ACCAGCCATTTTAAATCCTTCA	−	567–588c
CCoVI-Pbb	FAM-CCTCTTGAAGGTACACCAA-TAMRA	+	508–526c
Can1Fa	TAACATTGCTCTCAGGGAATTTG	+	6937–6959d	202	CCoV type II
CCoV2a	TCTGTTGAGTAATCACCAGCT	−	7118–7138d
CCoVII-Fb	TAGTGCATTAGGAAGAAGCT	+	6878–6897d	105
CCoVII-Rb	AGCAATTTTGAACCCTTC	−	6966–6982d
CCoVII-Pbb	FAM-CCTCTTGAAGGTGTGCC-TAMRA	+	6906–6922d

FAM, 6-carboxyfluorescein; TAMRA, 6-carboxytetramethylrhodamine.

^aConventional RT-PCR (Pratelli et al., 2002a, Pratelli et al., 2004).

^bFluorogenic RT-PCR.

^cOligonucleotide position is referred to the sequence of CCoV type I strain 259/01 (accession: AF502583).

^dOligonucleotide position is referred to the sequence of CCoV type II strain Insavc-1 (accession: D13096).