TABLE 2

List of primers and probes used in the ITD 5.0 rRT-PCR assays by assay, primer and probe sequences, and binding regions

Assay type and targetPrimer or probe (dye)aOligonucleotide sequence (5′→3′)nt positionb
Quadruplex
    Sabin 1Sabin 1 2SAGG TCA GAT GCT TGA AAG C2505–2523
Sabin 1 probe A4 (Cy5)CGC CCC CAC CGT TTC ACG GA2540–2559
Sabin 1 1ACCA CTG GCT TCA GTG TTT2600–2583
    Sabin 2Sabin 2 2SCCG TTG AAG GGA TTA CTA AA2525–2544
Sabin 2 probe (FAM)ATT GGT TCC CCC GAC TTC CAC CAA T2550–2572
Sabin 2 1ACGG CTT TGT GTC AGG CA2595–2579
    Sabin 3Sabin 3 2SAGG GCG CCC TAA CTT T2537–2552
Sabin 3 probe (ROX)TCA CTC CCG AAG CAA CAG2554–2571
Sabin 3 1ATTA GTA TCA GGT AAG CTA TC2591–2572
    PanEV (any EV)PAN-EV SGGC CCC TGA ATG CGG CTA ATC C458–480
PAN-EV probe (VIC)CCG ACT ACT TTG GGW GTC CGT GT546–568
PAN-EV AGCG ATT GTC ACC ATW AGC AGY CA603–581
PanPV (any poliovirus)PanPV/PCR-S1TTG GAG TTC TTC ACI TAI TCI MGI TTY GAY ATG2832–2864
PanPV PCR-probe 1A (FAM)TGR TTN ARI GCR TGI CCR TTR TT2926–2904
PanPV PCR-1AGGA GCT CCG GGT GGG AYR TAC ATI ATY TGR TAI AC2962–2928
WPV1 (wild PV1)WEAF WPV1 SGTA CAA ACC AGT CAY GTN AT2661–2680
SOAS WPV1 SCGT ACA GAC TAG RCA YGT NAT2660–2680
WPV1 probe S (FAM)CAT WAT GGT TAC RCA MGC ACC T2729–2750
WPV1 AGAG AAT AAY TTG TCY TTK GAY GT2800–2778
PV2 (any serotype 2)PV Type 2 SGAT GCA AAY AAC GGI CAT GC2911–2930
PV Type 2 probe S (FAM)ATG ACT ATA CGT GGC AGA C2993–3011
PV Type 2 probe 1D S (FAM)CRC CKA TIC CTG GYA2972–2986
PV Type 2 ATCA TAA AAG TGG GAR TAC GCR TT3110–3088
PV Type 2 A 1CTCG TAA AAA TGA GAA TAT GCA TT3110–3088
AFR WPV3
    WPV3-ISOAS WPV3 SCAG GGA GTA GAT GAY CTN AT2443–2462
    WEAF genotypeWEAF WPV3 SCAG GGG GTT GAT GAY TTR AT2443–2462
WPV3 probe S (Cy5)CNC ARA ACA GYC TTC CGG ATA CC2504–2526
WPV3 AACK GTG TCT GAY GGN AC2623–2607
SOAS WPV3
    WPV3-IISOAS 6SGTY RTA CAR CGR CGY AGY AGR A2671–2692
    SOAS genotypeSOAS WPV3 probe S (FAM)TTC TTY GCA AGI GGR GCR TGY GT2713–2735
SOAS 5ATCY TTR TAI GTR ATG CGC CAA G2816–2795
  • a Probes labeled with 6-carboxyfluorescein (FAM) were quenched with black hole quencher 1 (BHQ1), those labeled with ROX were quenched with BHQ2, those labeled with Cy5 were quenched with BHQ3, and those labeled with VIC were quenched with 6-carboxytetramethylrhodamine (TAMRA).

  • b All nucleotide positions are relative to those described by Toyoda et al. (34), except PanPV GenBank accession no. AY184219.1 and SOAS WPV3 GenBank accession no. AJ293918.1.