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. 2021 Mar 2;6(2):e00816-20. doi: 10.1128/mSystems.00816-20

TABLE 1.

Primer sets for the diagnostic multiplex PCR assaya

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
a

Abbreviations: 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.