Table 1.

Assay targets under investigation and their alignment position in the SARS-CoV-2 reference genome sequence (NC 045512.2).

Assay design	Forward primer (5′–3′)	Reverse primer (5′–3′)	Probe (5′–3′)	SARS-CoV-2 gene (alignment position)	# of mutated templates	References
C3 ORF3a	GTTACGACTATTGTATACCTTACAATAGTGTA	CACAGTCTTTTACTCCAGATTCCCATTTTTCA	AGGACTTGTTGTGCCATCACCTGAAG	ORF3a (25,830–26,013)	1	Unpublished (DNASoftware, Inc.)
C4 ORF8	CGTGTCCTATTCACTTCTATTCTAAA	ACTGTATAATTACCGATATCGATGTACTGA	TGGATGAGGCTGGTTCTAAATCACCC	ORF8 (27,980–28,155)	18	Unpublished (DNASoftware, Inc.)
CHAN S	CCTACTAAATTAAATGATCTCTGCTTTACT	CAAGCTATAACGCAGCCTGTA	CGCTCCAGGGCAAACTGGAAAG	S (22,692–22,889)	1	24
China N	GGGGAACTTCTCCTGCTAGAAT	CAGACATTTTGCTCTCAAGCTG	TTGCTGCTGCTTGACAGATT	N (28,861–28,999)	55	25
France IP2	ATGAGCTTAGTCCTGTTG	CTCCCTTTGTTGTGTTGT	AGATGTCTTGTGCTGCCGGTA	ORF1ab (12,670–12,817)	1	26
HKU ORF1b	TGGGGYTTTACRGGTAACCT	AACRCGCTTAACAAAGCACTC	TAGTTGTGATGCWATCATGACTAG	ORF1ab (18,758–18,929)	1	27
Young ORF1ab	TCATTGTTAATGCCTATATTAACC	CACTTAATGTAAGGCTTTGTTAAG	AACTGCAGAGTCACATGTTGACA	ORF1ab (14,135–14,263)	1	28
Young S	TATACATGTCTCTGGGACCA	ATCCAGCCTCTTATTATGTTAGAC	CTAAGAGGTTTGATAACCCTGTCCTACC	S (21,743–21,896)	10	28
NCOV N GENE	CACATTGGCACCCGCAATC	GAGGAACGAGAAGAGGCTTG	ACTTCCTCAAGGAACAACATTGCCA	N (28,686–28,853)	1	29
Noblis 40	GCCGCTGTTGATGCACTATG	TGTCGTCTCAGGCAATGCAT	ACGTGCTCGTGTAGAGTGTTTTGAT	ORF1ab (17,150–17,357)	1	30
Japan N2	AAATTTTGGGGACCAGGAAC	TGGCAGCTGTGTAGGTCAAC	ATGTCGCGCATTGGCATGGA	N (29,125–29,282)	16	31
BVP 501Y	CGGTAGCACACCTTGTAATG	ACTACTACTCTGTATGGTTGGTAA	CCCACTTATGGTG	S (22,986–23,096)	10	32
CDC N1	GACCCCAAAATCAGCGAAAT	TCTGGTTACTGCCAGTTGAATCTG	ACCCCGCATTACGTTTGGTGGACC	N (28,267–28,377)	51	33
CDC N2	TTACAAACATTGGCCGCAAA	GCGCGACATTCCGAAGAA	ACAATTTGCCCCCAGCGCTTCAG	N (29,144–29,249)	57	33
Yale 69/70 del	TCAACTCAGGACTTGTTCTTACCT	TGGTAGGACAGGGTTATCAAAC	TTCCATGCTATACATGTCTCTGGGA	S (21,700–21,839)	4	34