Table 2.

Primers and probes used for ddPCR

Virus	Sequence (5′–3′)	PCR reaction profile	Reference
MS2	TGCTCGCGGATACCCG	25 °C, 3 min; 47 °C, 60 min; 95 °C, 10 min; 40 cycles of 95 °C, 30 s; 55 °C, 1 min with ramp rate of 2 °C s-1; 98 °C, 10 min; held at 4 °C	Trojnar et al. (2020)
	AACTTGCGTTCTCGAGCGAT
	[FAM]ACCTCGGGTTTCCGTCTTGCTCGT[BHQ1]
Phi6	TGGCGGCGGTCAAGAGC	25 °C, 3 min; 50 °C, 60 min; 95 °C, 10 min; 40 cycles of 95 °C, 30 s; 60 °C, 1 min with ramp rate of 2 °C s-1; 98 °C, 10 min; held at 4 °C	Flood et al. (2021)
	GGATGATTCTCCAGAAGCTGCTG
	[FAM]CGGTCGTCGCAGGTCTGACACTCGC[BHQ1]
Coronavirus OC43	CGATGAGGCTATTCCGACTAGGT	25 °C, 3 min; 50 °C, 1 h; 95 °C, 10 min; 40 cycles of 95 °C, 30 s; 55 °C, 1 min with ramp rate of 2 °C s-1; 98 °C, 10 min; held at 4 °C	Pecson et al. (2021)
	CCTTCCTGAGCCTTCAATATAGTAACC
	[FAM]TCCGCCTGGCACGGTACTCCCT[BHQ1]
Adenovirus	GGACGCCTCGGAGTACCTGAG	95 °C, 10 min; 39 cycles of 94 °C, 30 s; 55 °C, 1 min with ramp rate of 2 °C s-1; 98 °C, 10 min; held at 4 °C	Jothikumar et al. (2005)
	ACIGTGGGGTTTCTGAACTTGTT
	[FAM]CTGGTGCAGTTCGCCCGTGCCA[BHQ1]
CDV	CTGTCRGTAATCGAGRATTCGA	25 °C, 3 min; 42 °C, 1 h; 95 °C, 10 min; 40 cycles of 95 °C, 30 s; 55 °C, 1 min with ramp rate of 2 °C s-1; 98 °C, 10 min; then held at 4 °C	Halecker et al. (2021)
	GCCGAAAGAATATCCCCAGTTAG
	[FAM]ATCTTCGCCAGARTCYTCAGTGCT[BHQ1]