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Table 2 Specificity of the real-time RT-PCR assays developed for the identification of swIAV HA and NA genes originating from the European enzootic lineages H1avN1, H1huN2, H1N1pdm and H3N2

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

Virus strains (Panel 1) M gene RT-qPCRb (Cq- value) Real-time RT-PCRs for molecular subtypingc (Cq-value)
Subtype and lineage Name HA subtyping NA subtyping
HA lineage of the most antigenically related reference strain (from HI tests) Lineage known from conventional RT-PCRs and commercial H1pdm and N1pdm RT-qPCRsb
HA NAa H1av H1hu H3 N1 N2
H1av H1av N1av A/Sw/Aisne/0054/10 25.48 24.16 no Cq no Cq 24.61 no Cq
A/Sw/Ille et Vilaine/0187/11 26.87 26.92 no Cq no Cq 24.45 no Cq
A/Sw/Ille et Vilaine/0208/11 24.6 23.45 no Cq no Cq 19.05 no Cq
A/Sw/Morbihan/0294/11 27 25.88 no Cq no Cq 24.86 no Cq
A/Sw/Finistere/0307/11 27.12 30.23 no Cq no Cq 28.64 no Cq
A/Sw/LoireAtlantique/0405/11 26.9 29.84 no Cq no Cq 28.03 no Cq
A/Sw/France/41–120137/12 24.33 19.84 no Cq no Cq 27.55 no Cq
A/Sw/France/72–120183/12 25.12 25.16 no Cq no Cq 25.27 no Cq
A/Sw/France/29–120326/12 26.34 36.15 no Cq no Cq 27.68 no Cq
A/Sw/France/22–120340/12 24.29 23.40 no Cq no Cq 22.70 no Cq
A/Sw/France/56–120452/12 25.75 30.63 no Cq no Cq 25.91 no Cq
A/Sw/France/53–130065/13 26.65 33.03 no Cq no Cq 30.16 no Cq
H1av H1av N2 A/Sw/Cotes d’Armor/0102/08 25.38 23.13 no Cq no Cq no Cq 23.62
A/Sw/Cotes d’Armor/0186/10 26.56 24.92 no Cq no Cq no Cq 26.69
A/Sw/Morbihan/0213/11 24.26 24.37 no Cq no Cq no Cq 23.98
A/Sw/Morbihan/0599/11 24.6 26.17 no Cq no Cq no Cq 24.06
A/Sw/France/37–120,345/12 24.34 27.26 no Cq no Cq no Cq 24.91
H1hu H1hu N2 A/Sw/Cotes d’Armor/0074/11 26.81 no Cq 30.80 no Cq no Cq 29.33
A/Sw/France/22–110,153/11 26.87 no Cq 32.06 no Cq no Cq 28.08
A/Sw/Finistere/0186/11 26.63 no Cq 31.08 no Cq no Cq 29.74
A/Sw/Ille et Vilaine/0346/11 25.6 no Cq 26.83 no Cq no Cq 25.26
A/Sw/Ille et Vilaine/0415/11 24.05 no Cq 28.07 no Cq no Cq 26.43
A/Sw/Maine et Loire/0589/11 24.65 no Cq 23.19 no Cq no Cq 23.27
A/Sw/France/56–120177/12 25.05 no Cq 30.97 no Cq no Cq 30.66
A/Sw/France/22–120255/12 25.68 no Cq 29.93 no Cq no Cq 27.52
A/Sw/France/29–120,258/12 27.17 no Cq 31.01 no Cq no Cq 29.21
A/Sw/France/22–130032/13 24.54 no Cq 23.30 no Cq no Cq 25.82
H1hu H1hu N1av A/Sw/Cotes d’Armor/0046/08 25.85 no Cq 28.06 no Cq 24.46 no Cq
A/Sw/Cotes d’Armor/0070/10 24.59 no Cq 28.80 no Cq 24.54 no Cq
A/Sw/Morbihan/0163/10 26.12 no Cq 32.22 no Cq 26.53 no Cq
A/Sw/France/56–110525/10 25.63 no Cq 29.24 no Cq 32.04 no Cq
A/Sw/France/22–120067/12 26.46 no Cq 31.69 no Cq 26.66 no Cq
H1pdm H1pdm N1pdm A/California/04/09 25.92 no Cq no Cq no Cq 27.76 no Cq
A/Sw/Sarthe/0255/10 26.26 no Cq no Cq no Cq 26.51 no Cq
A/Sw/Sarthe/0262/10 25.32 no Cq no Cq no Cq 26.02 no Cq
A/Sw/Cotes d’Armor/110466/10 25.15 no Cq no Cq no Cq 27.35 no Cq
A/Sw/Haute-Loire/0578/11 26.42 no Cq no Cq no Cq 28.44 no Cq
A/Sw/France/18–120158/12 27.29 no Cq no Cq no Cq 29.73 no Cq
A/Sw/France/18–120333/12 24.04 no Cq no Cq no Cq 24.37 no Cq
A/Sw/France/71–130116/13 24.68 no Cq no Cq no Cq 28.93 no Cq
H3 H3 N2 A/Sw/Flandres/1/98 24.98 no Cq no Cq 24.39 no Cq 25.58
A/Sw/France/59–120031/12 26.1 no Cq no Cq 27.47 no Cq 26.68
  1. aN1av means that the conventional N1 RT-qPCR was positive but the N1pdm commercial RT-qPCR was negative; bCommercial kits [21]; cHA RT-qPCRs were run as monoplex procedures whereas NA RT-qPCRs were run in duplex; Cq: quantification cycle
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