Table 1.

Primer and TaqMan probe sequences used for the detection of SARS-CoV-2 in this study.

Assay	Name	Function	Sequence (5′ → 3′)a, b	Location	Temperature for annealing/extension	Reference
2019-nCoV_N2	CDCN2-F	Forward primer	TTACAAACATTGGCCGCAAA	29,164–29,183	55 °C	CDC (2020)
	CDCN2-R	Reverse primer	GCGCGACATTCCGAAGAA	29,213–29,230
	CDCN2-P	TaqMan Probe	ACAATTTGCCCCCAGCGCTTCAG-	29,188–29,210
2019-nCoV_N3	CDCN3-F	Forward primer	GGGAGCCTTGAATACACCAAAA	28,681–28,702	55 °C	CDC (2020)
	CDCN3-R	Reverse primer	TGTAGCACGATTGCAGCATTG	28,732–28,752
	CDCN3-P	TaqMan Probe	AYCACATTGGCACCCGCAATCCTG-	28,704–28,727
NIID_2019-nCoV_N	NIID-F	Forward primer	AAATTTTGGGGACCAGGAAC	29,125–29,144	60 °C	Shirato et al. (2020)
	NIID-R	Reverse primer	TGGCACCTGTGTAGGTCAAC	29,263–29,282
	NIID-P	TaqMan Probe	ATGTCGCGCATTGGCATGGA	29,222–29,241
MNV	MKMNVF	Forward primer	CGGTGAAGTGCTTCTGAGGTT	6330–6350	56 °C	Kitajima et al. (2008)
	MKMNVR	Reverse primer	GCAGCGTCAGTGCTGTCAA	6371–6389
	MKMNVP	TaqMan Probe	CGAACCTACATGCGTCAG	6352–6369

^aAll TaqMan probes were labeled with 5′-FAM and 3′-TAMRA.

^bThe corresponding nucleotide positions of SARS-CoV-2 Wuhan-Hu-1 strain and MNV strain S7-PP3 (GenBank acc. No. MN908947.3 and AB435515.1, respectively).