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Table 2 Primers and probes used for sequencing-independent pathotyping of Eurasian avian influenza A subtype H7 viruses by real time RT-PCR

From: Real-time reverse transcription PCR-based sequencing-independent pathotyping of Eurasian avian influenza A viruses of subtype H7

Primer/Probe ID

Sequence (5′ to 3′)

Location

Amplicon size

Accession numbera

H7_CS-F1

TGMTGCTRGCAACAGGAAT

989–1007

107b

KX979524

H7_CS-F2 N

TGCTACTRGCAACAGGGAT

989–1007

H7_CS-F3

TGMTGCTGGCAACWGGRAT

968–986

H7_CS-R1N

CGTCAATKAGRCCTTCCCA

1096–1078

H7_CS-R2N

TCCATTTTCWATRAAACCYGC

1056–1036

H7_CS-R3

CATCAAYCAGACCYTCCCA

1056–1076

H7_CS-LP-FAM

C + C + AAAG + GGA + A + GAG + GC

1026–1040

KY676327.1

H7_CS-HP_EMS-FAM

CCAAAGAGAAAGAGAAGAGGCC

1027–1046

120c

AB438941

H7_CS-HP_IT-FAM

TTCCAAAAGGATCGCGTGTGAGGA

1004–1027

KF493066

  1. aAccession number of sequence/virus used to position the oligonucleotide along the HA gene
  2. bsize applied to LP sequences
  3. csize applied to HP sequences
  4. + indicates that the following position constituted a “locked” nucleotide (LNA)