S. No.  Swine Sample Types  Methods Used for Influenza Virus Detection  Virus Types/Subtypes Detected  References
1.  Nasal swab  RNA extraction, real-time RT-PCR, reverse transcription PCR, multiplex RT-PCR, ligation, partial/whole genome Sanger sequencing, Next-generation sequencing, phylogenetic analysis, virus isolation (MDCK cells/Caco-2 cells/HRT18 cells/SPF chicken eggs), transmission electron microscopy, HI assay, NI assay, ultracentrifugation  H1N1, H1N2,H3N2, H4N6, A(H1N1)pdm09, Reassortant H1N1, Reassortant A(H1N1)pdm09, Triple-reassortant H3N2, H1N7, H5N2, IBV, IDV  [5,37,43,45,46,61,74,88,137,157,171,176,188,191,199,207,215,219,220,221,241,243,248,250,263,289,290,301,306,307,326,334]
2.  Tracheal swab  RNA extraction, real-time RT-PCR, reverse transcription PCR, Sanger sequencing, virus isolation (MDCK cells, SPF chicken eggs)  H5N1, IAV, ICV, H1N1, A(H1N1)pdm09,  [38,59,103,321,331]
3.  Nasal wipe  Real-time RT-PCR  H3N2  [289]
4.  Snout wipe  RNA extraction, real-time RT-PCR, virus isolation  IAV  [286]
5.  Oropharyngeal swab  RNA extraction, real-time RT-PCR, Sanger sequencing  IAV, A(H1N1)pdm09  [211,276]
6.  Nasopharyngeal swab  RNA extraction, real-time RT-PCR, virus isolation (SPF chicken eggs), Sanger sequencing  H3N2, A(H1N1)pdm09, IBV, ICV  [38,141,211,277]
7.  Oral fluid  RNA extraction, real-time RT-PCR, virus isolation, Sanger sequencing, Next-generation sequencing (MiSeq)  IAV, IDV, H1N1, H1N2, H3N2, A(H1N1)pdm09  [45,192,227,282,285,287,302,322]
8.  Blood/ serum  IDEXX Ab test, ELISA, HI assay, NI assay, VN assay, MN assay, western blot, virus isolation (MDCK cells)  H1N1, H1N2, H3N2, A(H1N1)pdm09, H5N1, H5N2, H5N3, H9N2, H7N9, H3N1, H4N8, H6N6, H6N2, H7N2, IBV, ICV, IDV  [37,38,46,52,59,70,79,96,97,135,138,153,186,195,200,215,291,306]
9.  Lung/liver/internal organ tissues  RNA extraction, real-time RT-PCR, reverse transcription-PCR, ligation, HI assay, virus isolation (MDCK cells/SPF chicken eggs), Sanger and Next-generation sequencing, hematoxylin-eosin staining, immunohistochemistry, Immunofluorescence  H1N1, H1N2, Reassortant H1N1, H3N2, H2N3, A(H1N1)pdm09, H7N2, IDV  [45,121,127,128,130,201,203,243,245,248,274,314,320,325,327]
10.  Lung homogenate  RNA extraction, real-time RT-PCR, multiplex RT-PCR, single step RT-PCR, virus isolation (MDCK cells/Caco-2 cells/SPF chicken eggs), Sanger sequencing, membrane enzyme immunoassay, HI assay  H1N1, H1N2, H3N2, Reassortant H1N2, A(H1N1)pdm09  [130,213,218,292]
11.  Fecal slurry  RNA extraction, qRT-PCR  IAV  [88]
12.  Rectal swab  Nucleic acid extraction, reverse transcription, metagenomic sequencing  IAV  [300]