TABLE 2.

Primers and probes used in real-time PCRs for the detection of 9 canonical subgenomic RNAs (sgRNAs)

Subgenome	Type	Positiona	Sequence (5′–3′)	Primer length	%GC	Amplicon length
All sgRNAs	DNA probe	49–73	FAM-TCTTGTAGATCTGTTCTCTAAACGA-BHQ1	25	36.0	-
All sgRNAs	Forward Primer	27–46	ACAAACCAACCAACTTTCGA	20	40.0	-
S	Reverse Primer	21642–21623	GCAGGGGGTAATTGAGTTCT	20	50.0	130
ORF3a	Reverse Primer	25457–25437	TCCTTGATTTCACCTTGCTTC	21	42.9	116
E	Reverse Primer	26326–26307	GCAAGAATACCACGAAAGCA	20	45.0	133
M	Reverse Primer	26544–26525	TAGTACCGTTGGAATCTGCC	20	50.0	115
ORF6	Reverse Primer	27113–27094	ACTGTATGCAGCAAAACCTG	20	45.0	116
ORF7a	Reverse Primer	27444–27425	AAGCTCACAAGTAGCGAGTG	20	50.0	100
ORF7b	Reverse Primer	27818–27798	AACAAGGAATAGCAGAAAGGC	21	42.9	102
ORF8	Reverse Primer	27949–27929	TCTTGGTGAAATGCAGCTACA	21	42.9	105
N	Reverse Primer	28341–28322	GAATCTGAGGGTCCACCAAA	20	50.0	125

^aPosition refers to the prototype sequence (NC_045512).