Table 1. List of primers/probe for virus detection.

	Target	Name used in this study	Name	Sequence 5’ to 3’
USA CDC,	N Gene	N1	2019-nCoV_N1-F	GACCCCAAAATCAGCGAAAT
			2019-nCoV_N1-R	TCTGGTTACTGCCAGTTGAATCTG
			2019-nCoV_N1-P	ACCCCGCATTACGTTTGGTGGACC
	N Gene	N2	2019-nCoV_N2-F	TTACAAACATTGGCCGCAAA
			2019-nCoV_N2-R	GCGCGACATTCCGAAGAA
			2019-nCoV_N2-P	ACAATTTGCCCCCAGCGCTTCAG
	N Gene	N3	2019-nCoV_N3-F	ATCACATTGGCACCCGCAATCCTG
			2019-nCoV_N3-R	AGATTTGGACCTGCGAGCG
			2019-nCoV_N3-P	TTCTGACCTGAAGGCTCTGCGCG
Charité, Germany	E gene	E	E_Sarbeco_F1	ACAGGTACGTTAATAGTTAATAGCGT
			E_Sarbeco_R2	ATATTGCAGCAGTACGCACACA
			E_Sarbeco_P1	ACACTAGCCATCCTTACTGCGCTTCG
China, CDC	Orf1 / Rdrp gene	ORF1ab	ORF1ab-F	CCCTGTGGGTTTTACACTTAA
			ORF1ab-R	ACGATTGTGCATCAGCTGA
			ORF1ab-P	CCGTCTGCGGTATGTGGAAAGGTTATGG
Japan	N Gene	N	NIID_2019-nCOV_N_F2	AAATTTTGGGGACCAGGAAC
			NIID_2019-nCOV_N_R2	TGGCAGCTGTGTAGGTCAAC
			NIID_2019-nCOV_N_P2	ATGTCGCGCATTGGCATGGA
Variants detection (this study)	Wild type S gene	Spike-F	Spike-F	TCAACTCAGGACTTGTTCTTAC
		Spike-R	Spike-R	TGGTAGGACAGGGTTATCAAAC
		WT-Spike	Wild type Spike-P	TGGTCCCAGAGACATGTATAGCAT
	Mutant S gene	Mutant spike 1	Mutant S-Probe 1	CCATTGGTCCCAGAGATAGCATGG
		Mutant spike 2	Mutant S-Probe 2	CAGAGATAGCATGGAACCAAGTAA
		Mutant spike 3	Mutant S-probe 3	CCCAGAGATAGCATGGAACCAAGT
	Orf1ab / Wild type NSP6 gene	NSP6-F	NSP6-F	CTAGTTGGGTGATGCGTATT
		NSP6-R	NSP6-R	ACACAGTTCTTGCTGTCATAA
		Wild type NSP6	Wild type NSP6-P	AGTCTTTTAGCTTAAAACCAGACAAACTAGT
	Orf1ab / NSP6 mutant gene	Mutant NSP6	Mutant NSP6	AACACAGTCTTTTAGCTTCAAACTAGTATCAA

TaqMan probes are labeled at the 5’-end with the reporter molecule 6-carboxyfluorescein (FAM) and with the quencher, Blackhole Quencher 1 (BHQ1) at the 3’-end.