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 |