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. 2018 Jan 24;56(2):e01624-17. doi: 10.1128/JCM.01624-17

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 target Primer or probe (dye)a Oligonucleotide sequence (5′→3′) nt positionb
Quadruplex
    Sabin 1 Sabin 1 2S AGG TCA GAT GCT TGA AAG C 2505–2523
Sabin 1 probe A4 (Cy5) CGC CCC CAC CGT TTC ACG GA 2540–2559
Sabin 1 1A CCA CTG GCT TCA GTG TTT 2600–2583
    Sabin 2 Sabin 2 2S CCG TTG AAG GGA TTA CTA AA 2525–2544
Sabin 2 probe (FAM) ATT GGT TCC CCC GAC TTC CAC CAA T 2550–2572
Sabin 2 1A CGG CTT TGT GTC AGG CA 2595–2579
    Sabin 3 Sabin 3 2S AGG GCG CCC TAA CTT T 2537–2552
Sabin 3 probe (ROX) TCA CTC CCG AAG CAA CAG 2554–2571
Sabin 3 1A TTA GTA TCA GGT AAG CTA TC 2591–2572
    PanEV (any EV) PAN-EV S GGC CCC TGA ATG CGG CTA ATC C 458–480
PAN-EV probe (VIC) CCG ACT ACT TTG GGW GTC CGT GT 546–568
PAN-EV A GCG ATT GTC ACC ATW AGC AGY CA 603–581
PanPV (any poliovirus) PanPV/PCR-S1 TTG GAG TTC TTC ACI TAI TCI MGI TTY GAY ATG 2832–2864
PanPV PCR-probe 1A (FAM) TGR TTN ARI GCR TGI CCR TTR TT 2926–2904
PanPV PCR-1A GGA GCT CCG GGT GGG AYR TAC ATI ATY TGR TAI AC 2962–2928
WPV1 (wild PV1) WEAF WPV1 S GTA CAA ACC AGT CAY GTN AT 2661–2680
SOAS WPV1 S CGT ACA GAC TAG RCA YGT NAT 2660–2680
WPV1 probe S (FAM) CAT WAT GGT TAC RCA MGC ACC T 2729–2750
WPV1 A GAG AAT AAY TTG TCY TTK GAY GT 2800–2778
PV2 (any serotype 2) PV Type 2 S GAT GCA AAY AAC GGI CAT GC 2911–2930
PV Type 2 probe S (FAM) ATG ACT ATA CGT GGC AGA C 2993–3011
PV Type 2 probe 1D S (FAM) CRC CKA TIC CTG GYA 2972–2986
PV Type 2 A TCA TAA AAG TGG GAR TAC GCR TT 3110–3088
PV Type 2 A 1C TCG TAA AAA TGA GAA TAT GCA TT 3110–3088
AFR WPV3
    WPV3-I SOAS WPV3 S CAG GGA GTA GAT GAY CTN AT 2443–2462
    WEAF genotype WEAF WPV3 S CAG GGG GTT GAT GAY TTR AT 2443–2462
WPV3 probe S (Cy5) CNC ARA ACA GYC TTC CGG ATA CC 2504–2526
WPV3 A ACK GTG TCT GAY GGN AC 2623–2607
SOAS WPV3
    WPV3-II SOAS 6S GTY RTA CAR CGR CGY AGY AGR A 2671–2692
    SOAS genotype SOAS WPV3 probe S (FAM) TTC TTY GCA AGI GGR GCR TGY GT 2713–2735
SOAS 5A TCY TTR TAI GTR ATG CGC CAA G 2816–2795
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.