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Table 1 Primer or probe sequence for intratypic differentiation (ITD)

From: Vaccine-related poliovirus shedding in trivalent polio vaccine and human immunodeficiency virus status: analysis from under five children

Specificity

Primer or probe (polarity)

Primer or probe sequence (5′ → 3′)

Pan-enterovirus

PCR-1(A)

PCR-2 (S)

PanEV probe (S)

GCGATTGTCACCATWAGCAGYCA

GGCCCCTGAATGCGGCTAATCC

FAM-CCGACTACTTTGGGWGTCCGTGT-BHQ1

Pan-poliovirusa

panPV/PCR-1(A)

panPV/PCR-2(S)

panPV Probe21A(A)

AYRTACATIATYTGRTAIAC

CITAITCIMGITTYGAYATG

FAM-TGRTTNARIGCRTGICCRTTRTT-BHQ1

Serotype 1a

seroPV1A(A)

seroPV1,2S(S)

seroPV1 probe 16A(A)

ATCATIYTPTCIARPATYTG

TGCGIGAYACIACICAYAT

FAM-TGCCYAVICCYGIGMIADYGC-BHQ1

Serotype 2

seroPV2A (A)

seroPV1,2S (S)

seroPV2,probe 5S (S)

AYICCYTCIACIRCICCYTC

TGCGIGAYACIACICAYAT

FAM-CARGARGCIATGCCCICARGGIATNGG-BHQ1

Serotype 3a

seroPV3A (A)

sero PV 3S (S)

seroPV3,probe 11S (S)

CCCIAIPTGRTCRTTIKPRTC

AAYCCITCIRTITTYTAYAC

FAM-CCRTAYGTNGGITTRGCVAAYGC-BHQ1

Sabin 1

Sab1/PCR-1(A)

Sab1/PCR-2(S)

Sab1/probe (A)

CCACTGGCTTCAGTGTTT

AGGTCAGATGCTTGAAAGC

CY5-TTGCCGCCCCCACCGTTTCACGGA-BHQ3

Sabin 2

Sab2/PCR-1(A)

Sab2/PCR-2(S)

Sab2/probe (S)

CGGCTTTGTGTCAGGCA

CCGTTGAAGGGATTACTAAA

FAM-ATTGGTTCCCCCGACTTCCACCAAT-BHQ1

Sabin 3

Sab3/PCR-1(A)

Sab3/PCR-2(S)

Sab3/probe (S)

TTAGTATCAGGTAAGCTATC

AGGGCGCCCTAACTTT

ROX-TCACTCCCGAAGCAACAG-BHQ2

  1. Degenerate primers: K=G and T; M=A and C; R=A and G; Y=C and T; I = degenerate base analog, Inosine; P = degenerate base for (TC)
  2. aWe used degenerate PCR conditions with these primer sets