Table 1.

Primer and probe sequences for detection and quantification of SARS-CoV-2 (E and N1 genes), Murine hepatitis virus (MHV), and CrAssphage by RT-qPCR.

Target	Name	Sequence (5′-3′)
E gene	E Sarbeco F	ACAGGTACGTTAATAGTTAATAGCGT
	E Sarbeco R	ATATTGCAGCAGTACGCACACA
	E Sarbeco P	[6FAM]-ACACTAGCCATCCTTACTGCGCTTCG-[BHQ1]
N1 gene	N1 Forward	GACCCCAAAATCAGCGAAT
	N1 Reverse	TCTGGTTACTGCCAGTTGAATCTG
	N1 Probe	[6FAM]-ACCCCGCATTACGTTTGGTGGACC[BHQ1]
MHV	Forward	GGAACTTCTCGTTGGGCATTATACT
	Reverse	ACCACAAGATTATCATTTTCACAACATA
	Probe	[Cyanine5]-ACATGCTACGGCTCGTGTAACCGAACTGT [BHQ3]
CrAssphage	CPQ56 Forward	CAGAAGTACAAACTCCTAAAAAACGTAGAG
	CPQ65 Reverse	GATGACCAATAAACAAGCCATTAGC
	CPQ65 Probe	[6FAM]-AATAACGATTTACGTGATGTAAC[BHQ1]