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Table 6 Performance of real-time RT-PCR assays targeting the H1av, H1hu, H3, N1 and N2 genes in porcine clinical samples containing European swIAVs

From: Molecular subtyping of European swine influenza viruses and scaling to high-throughput analysis

Clinical samplesa (Panel 3) M gene RT-qPCR (Cq-value) Real-time RT-PCRs for molecular subtypingc (Cq-value)
swIAV lineage known from conventional RT-PCRs and commercial H1N1pdm RT-qPCRs Identification HA subtyping NA subtyping
HA NAb H1av H1hu H3 N1 N2
H1av N1av 120137–4 20.6 19.19 no Cq no Cq 19.85 no Cq
120183–5 18.1 19.33 no Cq no Cq 19.25 no Cq
130004–5 17.59 19.08 no Cq no Cq 17.75 no Cq
130020–4 26.43 31.38 no Cq no Cq 26.83 no Cq
130028–3 26.43 22.13 no Cq no Cq 26.98 no Cq
130065–5 17 23.08 no Cq no Cq 20.73 no Cq
130144–4 22.26 22.20 no Cq no Cq 22.46 no Cq
130153–6 22.46 32.33 no Cq no Cq 22.49 no Cq
130157–6 27.46 24.22 no Cq no Cq 24.25 no Cq
140014–4 17.56 nt nt nt 17.45 no Cq
140016–5 19.09 nt nt nt 19.73 no Cq
H1av N2 120057–3 17.89 17.25 no Cq no Cq no Cq 19.72
120345–2 17.51 21.51 no Cq no Cq no Cq 20.35
130133–3 21.18 21.67 no Cq no Cq no Cq 23.54
110214–1 28.92 27.82 no Cq no Cq nt nt
H1hu N2 100231-1c 18.57 no Cq 24.79 no Cq no Cq 21.86
120037–4 23.88 no Cq 27.79 no Cq no Cq 27.04
120285–6 23.37 no Cq 25.58 no Cq no Cq 24.45
120424–5 21.32 no Cq 25.43 no Cq no Cq 24.96
130039–2 22.5 no Cq 22.66 no Cq no Cq 22.08
130111–5 21 no Cq 22.79 no Cq no Cq 22.06
130111–6 19.6 nt nt nt no Cq 22.04
130129–4 18.29 no Cq 26.63 no Cq no Cq 22.58
130193–6 21.95 no Cq 25.36 no Cq no Cq 24.11
130129–5 17.86 no Cq 27.63 nt no Cq 22.63
130140–5 13.74 no Cq 20.21 nt no Cq 16.36
130285–4 29.54 nt nt nt no Cq 27.57
130420–4 22.31 no Cq 23.90 nt no Cq 24.12
130429–6 22.42 no Cq 24.26 nt no Cq 21.40
130431–4 15.82 no Cq 18.31 nt no Cq 17.41
H1hu N1av 110619–8 17.28 no Cq 21.86 no Cq 18.74 no Cq
120067–3 27.47 no Cq 33.08 no Cq 27.47 no Cq
H1av/H1hu N2 130103–2 21.46 28.36 23.42 no Cq 22.72 24.56
H1pdm N1pdm 110578–1 22.16 no Cq no Cq no Cq 24.09 no Cq
120158–7 16.97 no Cq no Cq no Cq 19.37 no Cq
120333–1 20.08 no Cq no Cq no Cq 21.70 no Cq
130116–1 25.21 no Cq no Cq no Cq 28.01 no Cq
H3 N2 120031–1 21.83 no Cq no Cq 22.68 no Cq 24.46
H1av N? 130044–2 32.18 no Cq no Cq nt 30.37 no Cq
130113–2 33.24 no Cq no Cq nt no Cq no Cq
130120–3 33.91 41.43 no Cq nt 31.64 no Cq
130135–6 30.77 28.13 no Cq nt 27.85 no Cq
130175–2 34.36 no Cq no Cq nt no Cq no Cq
130185–6 27.41 no Cq no Cq nt 24.76 no Cq
130188–3 30.5 27.73 no Cq nt 28.30 no Cq
130236–1 32.88 no Cq no Cq nt no Cq no Cq
130259–2 33.26 32.05 no Cq nt 31.22 no Cq
130282–4 27.53 37.19 no Cq nt 27.45 no Cq
130392–3 31.53 34.52 no Cq nt 32.07 no Cq
130300–4 31.22 no Cq no Cq nt no Cq no Cq
130319–5 34.2 no Cq no Cq nt no Cq no Cq
130336–4 33.7 no Cq no Cq nt no Cq no Cq
130387–5 23.93 28.20 no Cq nt 25.70 no Cq
130391–4 34.75 no Cq no Cq nt no Cq no Cq
130419–6 27.43 no Cq no Cq nt 28.53 no Cq
130439–5 29.97 no Cq no Cq nt no Cq no Cq
H? N2 130023–4 25.43 no Cq 27.58 nt no Cq 26.27
130034–3 23.05 no Cq 26.51 nt no Cq 25.68
130277–3 22 nt nt nt no Cq 24.52
nt nt 130133–5 23.02 22.90 31.53 nt no Cq 24.76
  1. aAll samples were nasal swab supernatants except the marked one that was a lung sample. bN1av means that the conventional N1 RT-PCR was positive but the N1pdm commercial RT-qPCR was negative. Call RT-qPCRs were run as monoplex procedures except N1 and N2 that were run in a duplex. Cq: quantification cycle; nt = not tested. Bold data correspond to additional results obtained with the novel RT-qPCRs as compared to conventional RT-PCRs