TABLE 4.

Published PCR primer and probe sequences for detection of viral pathogens associated with bovine respiratory disease complex. F′ forward; P′ probe, R’ reverse sequences.

Pathogen	Target Gene	Sequence (5’—3′)	References
Bovine Adenovirus 3	Hexon	F′ ATT​ACC​AGC​GTC​AAC​CTC​TAC	Kishimoto et al. (2017)
		P′ TCC​ACT​TTG​GAA​GCT​ATG​CTC​CGC
		R′ CCG​CCG​AGA​GAT​AGT​CAT​TAA​A
Bovine Adenovirus 7	Hexon	F′ CRAGGGAATAYYTGTCTGAAAATC	Kishimoto et al. (2017)
		P′ TTCATCWCTGCCACWCAAAGCTTTTTT
		R′ AAGGATCTCTAAATTTYTCTCCAAGA
Bovine Coronavirus	N (nucleocapsid protein)	F′ GGA​CCC​AAG​TAG​CGA​TGA​G	(Kishimoto et al., 2017; Goto et al., 2020)
		P′ ATT​CCG​ACT​AGG​TTT​CCG​CCT​GG
		R′ GAC​CTT​CCT​GAG​CCT​TCA​ATA
	N	F′ GCC​GAT​CAG​TCC​GAC​CAA​TC	Thanthrige-Don et al. (2018)
		R′ AGA​ATG​TCA​GCC​GGG​GTA​T
Bovine Herpes Virus 1	gE (glycoprotein E)	F′ CAA​TAA​CAG​CGT​AGA​CCT​GGT​C	(Kishimoto et al., 2017; Goto et al., 2020)
		P′ TGC​GGC​CTC​CGG​GCT​TTA​CGT​CT
		R′ GCT​GTA​GTC​CCA​AGC​TTC​CAC
	gC	F′ ATG​TTA​GCG​CTC​TGG​AAC​C	Horwood and Mahony, (2011)
		P′ ACG​GAC​GTG​CGC​GAA​AAG​A
		R′ CTT​TAC​GGT​CGA​CGA​CTC​C
	Glycoprotein B gene	F′ TGA​GGC​CTA​TGT​ATG​GGC​AGT​T	Thanthrige-Don et al. (2018)
		R′ GGA​CAC​AAC​AAA​CAA​TGC​GG
	Glycoprotein B gene	F′ TGT​GGA​CCT​AAA​CCT​CAC​GGT	Thonur et al. (2012)
		P′ AGG​ACC​GCG​AGT​TCT​TGC​CGC
		R′ GTA​GTC​GAG​CAG​ACC​CGT​GTC
	gB	F′ GCG​TCA​TTT​ACA​AGG​AGA​ACA​TC	Fan et al. (2017)
		R′ ATCTCGCCCATGCCCAC
Bovine Influenza D Virus	PB1	F′ CAG​CTG​CGA​TGT​CTG​TCA​TAA​G	(Kishimoto et al., 2017; Goto et al., 2020)
		P′ AAT​GGA​CTT​TCT​CCT​GGG​ACT​GCT
		R′ ACA​AAT​TCG​CAG​GGC​CAT​TA
Bovine Parainfluenza Virus 3	M (membrane protein)	F′ TGT​CTT​CCA​CTA​GAT​AGA​GGG​ATA​AAA​TT	(Horwood and Mahony, 2011; Kishimoto et al., 2017; Goto et al., 2020)
		P′ ACA​GCA​ATT​GGA​TCA​ATA​A
		R′ GCA​ATG​ATA​ACA​ATG​CCA​TGG​A
	M gene	F′ TGTCTTCCACTMGATAGAGGGATAAAATT	Thanthrige-Don et al. (2018)
		R′ CCTTTCTCATCTAAGATCTGGACMACC
		R′ CCT​TTT​TCA​TCT​AGA​ATC​TGA​ACT​ACT​CC
	Nucleoprotein gene	F′ GGT​AGG​AGC​ACC​TCC​ACG​ATT	Thonur et al. (2012)
		P′ AAG​ATC​TTG​TTC​ACA​CAT​TC
		R′ GCT​CCA​AGG​CAT​GCT​GGA​TA
	Nucleoprotein gene	F′ TGA​TTG​GAT​GTT​CGG​GAG​TGA	Thonur et al. (2012)
		P′ TAC​AAT​CGA​GGA​TCT​TGT​TCA
		R′ AGA​ATC​CTT​TCC​TCA​ATC​CTG​ATA​TAC​T
Bovine Respiratory Syncytial Virus	N (nucleocapsid protein)	F′ GCA​ATG​CTG​CAG​GAC​TAG​GTA​TAA​T	(Kishimoto et al., 2017; Goto et al., 2020)
		P′ ACC​AAG​ACT​TGT​ATG​ATG​CTG​CCA​AAG​CA
		R′ ACA​CTG​TAA​TTG​ATG​ACC​CCA​TTC​T
	N gene	F′ TAT​GCT​ATG​TCC​CGA​TTG​G	Liu et al. (2019)
		R′ ACT​GAT​TTG​GCT​AGT​ACA​CCC
	G attachment glycoprotein	F′ ACACATCAATYCAAAGCACCACAC	Thanthrige-Don et al. (2018)
		R′ GCTRGTTCTGTGGTGGRTTGTTGTC
	Nucleocapsid	F′ GGT​CAA​ACT​AAA​TGA​CAC​TTT​CAA​CAA​G	Thonur et al. (2012)
		P′ TAGTACAGGTGACAA + CA + T + TG
		R′ AGC​ATA​CCA​CAC​AAC​TTA​TTG​AGA​TG
	Glycoprotein F	F′ AAT​CAA​CAT​GCA​GTG​CAG​TTA​G	Socha and Rola, (2011)
		R′ TTTGGTCATTCGTFATAGGCAT
	Glycoprotein G	F′ CAT​CAA​TCC​AAA​GCA​CCA​CAC​TGT​C	Socha and Rola, (2011)
		R′ GCT​AGT​TCT​GTG​GTG​GAT​TGT​TGT​C
	N4	F′ GTTGCTGCTTTGGTTAT	Socha and Rola, (2011)
		R′ AGACTTGTATGATGCTGC
	N protein	F′ GTC​AGC​TTA​ACA​TCA​GAA​GTT​CAA​G	Socha and Rola, (2011)
		R′ ACA​TAG​CAC​TAT​CAT​ACC​ACA​ATC​A