TABLE 1.

Primer sets for the diagnostic multiplex PCR assay^a

Host	Target gene	Sequence (5′ to 3′)		Reference
		Forward	Reverse
Viruses
Group a rotavirus	dsRNA segment 6	GGCTTTTAAACGAAGTCTTC	GGTCACATCCTCTCACTACG	67
Group a rotavirus	VP7	GCCTTTAAAAGCGAGAATTT	GGTCACATCATACAAYTC TA	68
Group B rotavirus	VP7	GGAAATAATCAGAGATG	CTACTCGTTTGGCTCCCTCC	69
Group C rotavirus	VP6	TCAAGAAATGGWATGCAACC	CATAGCMGCTGGTCTWATCA	70
Bovine coronavirus	N	GCAATCCAGTAGTAGAGCGT	CTTAGTGGCATCCTTGCCAA	71
Bovine coronavirus	S	ATGTTTTTGATACTTTTAATTTCC	ACACCAGTAGATGGTGCTAT	70
Bovine torovirus	M	TTCTTACTACACTTTTTGGA	ACTCAAACTTAACACTAG AC	70
Bovine torovirus	N	TAATGGCACTGAAGACTC	ACATAACATCTTACATGG	72
Bovine norovirus	RdRp	AGTTAYTTTTCCTTYTAYGGBGA	AGTGTCTCTGTCAGTCATCTTCAT	73
Bovine enteric Nebraska-like calicivirus	RdRp-MCP	TTTCTAACYTATGGGGAYGAYG	GTCACTCATGTTTCCTTCTCTAAT	73
Bovine nebovirus	Capsid	CCACCATTATCACCAAATTGC	CATAATCAGAATAGAAGGCGC	74
Bovine viral diarrhea virus	Bsteii	GATTTCAAGGGGACTTTTTT	ACATCTCCTACTAAGTAGTA	75
Bovine viral diarrhea virus	Bvdv1 genotype	GTAGTCGTCAGTGGTTCG	GCCATGTACAGCAGAGAT	75
Bovine viral diarrhea virus	Polyprotein	ACAAACATGGTTGGTGCAACTGGT	CAGACATATTTGCCTAGGTTCCA	76
Bacteria
Clostridium perfringens	16S rRNA gene	AAAGATGGCATCATCATTCAAC	TACCGTCATTATCTTCCCCAAA	77
Clostridium perfringens	Alpha-toxin genes	GCTAATGTTACTGCCGTTGACC	TCTGATACATCGTGTAAG	77
Salmonella enterica	Sefb	AGATTGGGCACTACACGTGT	TGTACTCCACCAGGTAATTG	78
Salmonella enterica Typhimurium	Rfbj	CCAGCACCAGTTCCAACTTGATAC	GGCTTCCGGCTTTATTGGTAAGCA	79
Enterotoxigenic Escherichia coli	K99	GCTATTAGTGGTCATGGCACTGTAG	TTTGTTTTGGCTAGGCAGTCATTA	80
Enterotoxigenic Escherichia coli	LT1	GCTGACTCTAGACCCCCAG	TGTAACCATCCTCTGCCGGA	81
Enterotoxigenic Escherichia coli	LT2	ATATCATTTTCTGTTTCAGCAAA	CAATAAAATCATCTTCGCTCATG	82
Enterotoxigenic Escherichia coli	ST1	TCCCCTCTTTTAGTCAGTCAACTG	GCACAGGCAGGATTACAACAAAGT	83
Enterotoxigenic Escherichia coli	ST2	CTGTGTGAACATTATAGACAAATA	ACCATTATTTGGGCGCCAAAG	81
Shigatoxigenic Escherichia coli	stx1	GACTGCAAAGACGTATGTAGATTCG	ATCTATCCCTCTGACATCAACTGC	84
Shigatoxigenic Escherichia coli	stx2	ATTAACCACACCCCACCG	GTCATGGAAACCGTTGTCAC	84
Shigatoxigenic Escherichia coli	eaeA	GACCCGGCACAAGCATAAGC	CCACCTGCAGCAACAAGAGG	85
Enterohemorrhagic Escherichia coli	hlyA	GCATCATCAAGCGTACGTTCC	AATGAGCCAAGCTGGTTAAGCT	85

^aAbbreviations: dsRNA segment 6, double-stranded RNA genome segment 6; VP, viral protein; N, nucleocapsid protein; S, S glycoprotein; M, membrane protein; RdRp, RNA-dependent RNA polymerase; MCP, major capsid protein; BstEII, restriction enzyme BstEII; sefB, chaperone protein SefB coding gene; rfbJ, CDP-abequose synthase coding gene; K99, K99 region 1 gene; LT1, heat-labile enterotoxin type 1 A subunit; LT2, heat-labile enterotoxin type 2; ST1, heat-stable enterotoxin 1; ST2, heat-stable enterotoxin 2; stx1, Shiga toxin type 1; stx2, Shiga toxin type 2; eaeA, enterohemorrhagic E. coli O157:H7-specific intimin; hlyA, plasmid-encoded enterohemolysin.