Table 1.

Primers and probes of the three qRT-PCR assays.

Assay		Primer/probe	Sequence (5′-3′)	Genomic location*	Amplicon
N gene assay	IPBCAMS assays	Forward	AACACAAGCTTTCGGCAGAC	29083−29102	195 bp
		Reverse	ACCTGTGTAGGTCAACCACG	29278−29259
		Probe	CAGCGCTTCAGCGTTCTTCGGAATGTCGC	29200−29228
	WHO assays	Forward	CACATTGGCACCCGCAATC	28706−28724	127 bp
		Reverse	GAGGAACGAGAAGAGGCTTG	28833−28814
		Probe	ACTTCCTCAAGGAACAACATTGCCA	28753−28777
	CCDC assays	Forward	GGGGAACTTCTCCTGCTAGAAT	28881−28902	98 bp
		Reverse	CAGACATTTTGCTCTCAAGCTG	28979−28958
		Probe	TTGCTGCTGCTTGACAGATT	28934−28953
ORF 1b gene assay	IPBCAMS assays	Forward	ACGGTGACATGGTACCACAT	13760−13779	215 bp
		Reverse	CTAAGTTGGCGTATACGCGT	13975−13956
		Probe	TACACAATGGCAGACCTCGTCTATGC	13804−13829
	WHO assays	Forward	GTGARATGGTCATGTGTGGCGG	15431−15452	99 bp
		Reverse	CARATGTTAAASACACTATTAGCATA	15530−15505
		Probe	CAGGTGGAACCTCATCAGGAGATGC	15470−15494
	CCDC assays	Forward	CCCTGTGGGTTTTACACTTAA	13342−13362	118 bp
		Reverse	ACGATTGTGCATCAGCTGA	13460−13442
		Probe	CCGTCTGCGGTATGTGGAAAGGTTATGG	13377−13404

Numbering according to a reference genome of SARS-CoV-2 (MN908947.3).