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. 2020 Nov 10;758:143578. doi: 10.1016/j.scitotenv.2020.143578

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
a

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

b

The 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).