Protein sequence features of H1N1 swine influenza A viruses detected on commercial swine farms in Serbia

1. Bálint A., Kiss I., Bányai K., Biksi I., Szentpáli-Gavallér K., Magyar T., Jankovics I., Rózsa M., Szalai B., Takács M., Tóth A.G., Dán A.: Emergence and characterisation of pandemic H1N1 influenza viruses in Hungarian swine herds. Acta Vet Hung 2013, 61, 125–134, doi: 10.1556/AVet.2012.059. Bálint A. Kiss I. Bányai K. Biksi I. Szentpáli-Gavallér K. Magyar T. Jankovics I. Rózsa M. Szalai B. Takács M. Tóth A.G. Dán A. : Emergence and characterisation of pandemic H1N1 influenza viruses in Hungarian swine herds . Acta Vet Hung 2013 , 61 , 125 – 134 , doi: 10.1556/AVet.2012.059 . Open DOISearch in Google Scholar

2. Bouvier M.N., Palese P.: The biology of influenza viruses. Vaccine 2008, 26, D49–D53, doi: 10.1016/j.vaccine.2008.07.039. Bouvier M.N. Palese P. : The biology of influenza viruses . Vaccine 2008 , 26 , D49 – D53 , doi: 10.1016/j.vaccine.2008.07.039 . Open DOISearch in Google Scholar

3. Burke D.F., Smith D.J.: A recommended numbering scheme for influenza A HA subtypes. PLoS One 2014, 9, e112302, doi: 10.1371/journal.pone.0112302. Burke D.F. Smith D.J. : A recommended numbering scheme for influenza A HA subtypes . PLoS One 2014 , 9 , e112302 , doi: 10.1371/journal.pone.0112302 . Open DOISearch in Google Scholar

4. Bussey K.A., Bousse T.L., Desmet E.A., Kim B., Takimoto T.: PB2 residue 271 plays a key role in enhanced polymerase activity of influenza A viruses in mammalian host cells. J Virol 2010, 84, 4395–4406, doi: 10.1128/JVI.02642-09. Bussey K.A. Bousse T.L. Desmet E.A. Kim B. Takimoto T. : PB2 residue 271 plays a key role in enhanced polymerase activity of influenza A viruses in mammalian host cells . J Virol 2010 , 84 , 4395 – 4406 , doi: 10.1128/JVI.02642-09 . Open DOISearch in Google Scholar

5. Cai M., Zhong R., Qin C., Yu Z., Wen X., Xian J., Chen Y., Cai Y., Yi H., Gong L., Zhang G.: The R251K Substitution in Viral Protein PB2 Increases Viral Replication and Pathogenicity of Eurasian Avian-like H1N1 Swine Influenza Viruses. Viruses 2020, 12, 52, doi: 10.3390/v12010052. Cai M. Zhong R. Qin C. Yu Z. Wen X. Xian J. Chen Y. Cai Y. Yi H. Gong L. Zhang G. : The R251K Substitution in Viral Protein PB2 Increases Viral Replication and Pathogenicity of Eurasian Avian-like H1N1 Swine Influenza Viruses . Viruses 2020 , 12 , 52 , doi: 10.3390/v12010052 . Open DOISearch in Google Scholar

6. Cao Z., Zeng W., Hao X., Huang J., Cai M., Zhou P., Zhang I.G.: Continuous evolution of influenza A viruses of swine from 2013 to 2015 in Guangdong, China. PLoS One 2019, 14, e0217607, doi: 10.1371/journal.pone.0217607. Cao Z. Zeng W. Hao X. Huang J. Cai M. Zhou P. Zhang I.G. : Continuous evolution of influenza A viruses of swine from 2013 to 2015 in Guangdong, China . PLoS One 2019 , 14 , e0217607 , doi: 10.1371/journal.pone.0217607 . Open DOISearch in Google Scholar

7. Caton A.J., Brownlee G.G., Yewdell J.W., Gerhard W.: The antigenic structure of the influenza virus A/PR/8/34 hemagglutinin (H1 subtype). Cell 1982, 31, 417–427, doi: 10.1016/0092-8674(82)90135-0. Caton A.J. Brownlee G.G. Yewdell J.W. Gerhard W. : The antigenic structure of the influenza virus A/PR/8/34 hemagglutinin (H1 subtype) . Cell 1982 , 31 , 417 – 427 , doi: 10.1016/0092-8674(82)90135-0 . Open DOISearch in Google Scholar

8. Cauldwell A.V., Long J.S., Moncorgé O., Barclay W.S.: Viral determinants of influenza A virus host range. J Gen Virol 2014, 95, 1193–1210, doi: 10.1099/vir.0.062836-0. Cauldwell A.V. Long J.S. Moncorgé O. Barclay W.S. : Viral determinants of influenza A virus host range . J Gen Virol 2014 , 95 , 1193 – 1210 , doi: 10.1099/vir.0.062836-0 . Open DOISearch in Google Scholar

9. Chen W., Calvo P.A., Malide D., Gibbs J., Schubert U., Bacik I., Basta S., O’Neill R., Schickli J., Palese P., Henklein P., Bennink J.R., Yewdell J.W.: A novel influenza A virus mitochondrial protein that induces cell death. Nat Med 2001, 7, 1306–1312, doi: 10.1038/nm1201-1306. Chen W. Calvo P.A. Malide D. Gibbs J. Schubert U. Bacik I. Basta S. O’Neill R. Schickli J. Palese P. Henklein P. Bennink J.R. Yewdell J.W. : A novel influenza A virus mitochondrial protein that induces cell death . Nat Med 2001 , 7 , 1306 – 1312 , doi: 10.1038/nm1201-1306 . Open DOISearch in Google Scholar

10. Danilenko D.M., Komissarov A.B., Fadeev A.V., Bakaev M.I., Ivanova A.A., Petrova P.A., Vassilieva A.D., Komissarova K.S., Zheltukhina A.I., Konovalova N.I., Vasin A.V.: Antigenic and Genetic Characterization of Swine Influenza Viruses Identified in the European Region of Russia, 2014–2020. Front Microbiol 2021, 12, 662028, doi: 10.3389/fmicb.2021.662028. Danilenko D.M. Komissarov A.B. Fadeev A.V. Bakaev M.I. Ivanova A.A. Petrova P.A. Vassilieva A.D. Komissarova K.S. Zheltukhina A.I. Konovalova N.I. Vasin A.V. : Antigenic and Genetic Characterization of Swine Influenza Viruses Identified in the European Region of Russia, 2014–2020 . Front Microbiol 2021 , 12 , 662028 , doi: 10.3389/fmicb.2021.662028 . Open DOISearch in Google Scholar

11. Dong G., Peng C., Luo J., Wang C., Han L., Wu B., Ji G., He H.: Adamantane-resistant influenza A viruses in the world (1902–2013): frequency and distribution of M2 gene mutations. PLoS One 2015, 10, e0119115, doi: 10.1371/journal.pone.0119115. Dong G. Peng C. Luo J. Wang C. Han L. Wu B. Ji G. He H. : Adamantane-resistant influenza A viruses in the world (1902–2013): frequency and distribution of M2 gene mutations . PLoS One 2015 , 10 , e0119115 , doi: 10.1371/journal.pone.0119115 . Open DOISearch in Google Scholar

12. Dunagan M.M., Hardy K., Takimoto T.: Impact of Influenza A Virus Shutoff Proteins on Host Immune Responses. Vaccines 2021, 9, 629, doi: 10.3390/vaccines9060629. Dunagan M.M. Hardy K. Takimoto T. : Impact of Influenza A Virus Shutoff Proteins on Host Immune Responses . Vaccines 2021 , 9 , 629 , doi: 10.3390/vaccines9060629 . Open DOISearch in Google Scholar

13. Dürrwald R., Wedde M., Biere B., Oh D.Y., Heßler-Klee M., Geidel C., Volmer R., Hauri A.M., Gerst K., Thürmer A., Appelt S., Reiche J., Duwe S., Buda S., Wolff T., Haas W.: Zoonotic infection with swine A/H1avN1 influenza virus in a child, Germany, June 2020. Euro Surveill 2020, 25, 2001638, doi: 10.2807/1560-7917.ES.2020.25.42.2001638. Dürrwald R. Wedde M. Biere B. Oh D.Y. Heßler-Klee M. Geidel C. Volmer R. Hauri A.M. Gerst K. Thürmer A. Appelt S. Reiche J. Duwe S. Buda S. Wolff T. Haas W. : Zoonotic infection with swine A/H1avN1 influenza virus in a child, Germany, June 2020 . Euro Surveill 2020 , 25 , 2001638 , doi: 10.2807/1560-7917.ES.2020.25.42.2001638 . Open DOISearch in Google Scholar

14. Garten R.J., Davis C.T., Russell C.A., Shu B., Lindstrom S., Balish A., Sessions W.M., Xu X., Skepner E., Deyde V., Okomo-Adhiambo M., Gubareva L., Barnes J., Smith C.B., Emery S.L., Hillman M.J., Rivailler P., Smagala J, de Graaf M., Burke D.F., Fouchier R.A., Pappas C., Alpuche-Aranda C.M., López-Gatell H., Olivera H., López I., Myers C.A., Faix D., Blair P.J., Yu C., Keene K.M., Dotson P.D. Jr, Boxrud D., Sambol A.R., Abid S.H., St George K., Bannerman T., Moore A.L., Stringer D.J., Blevins P., Demmler-Harrison G.J., Ginsberg M., Kriner P., Waterman S., Smole S., Guevara H.F., Belongia E.A., Clark P.A., Beatrice S.T., Donis R., Katz J., Finelli L., Bridges C.B., Shaw M., Jernigan D.B., Uyeki T.M., Smith D.J., Klimov A.I., Cox N.J.: Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 2009, 325, 197–201, doi: 10.1126/science.1176225. Garten R.J. Davis C.T. Russell C.A. Shu B. Lindstrom S. Balish A. Sessions W.M. Xu X. Skepner E. Deyde V. Okomo-Adhiambo M. Gubareva L. Barnes J. Smith C.B. Emery S.L. Hillman M.J. Rivailler P. Smagala J de Graaf M. Burke D.F. Fouchier R.A. Pappas C. Alpuche-Aranda C.M. López-Gatell H. Olivera H. López I. Myers C.A. Faix D. Blair P.J. Yu C. Keene K.M. Dotson P.D. Jr Boxrud D. Sambol A.R. Abid S.H. St George K. Bannerman T. Moore A.L. Stringer D.J. Blevins P. Demmler-Harrison G.J. Ginsberg M. Kriner P. Waterman S. Smole S. Guevara H.F. Belongia E.A. Clark P.A. Beatrice S.T. Donis R. Katz J. Finelli L. Bridges C.B. Shaw M. Jernigan D.B. Uyeki T.M. Smith D.J. Klimov A.I. Cox N.J. : Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans . Science 2009 , 325 , 197 – 201 , doi: 10.1126/science.1176225 . Open DOISearch in Google Scholar

15. Graef K.M., Vreede F.T., Lau Y.F., McCall A.W., Carr S.M., Subbarao K., Fodor E.: The PB2 subunit of the influenza virus RNA polymerase affects virulence by interacting with the mitochondrial antiviral signaling protein and inhibiting expression of beta interferon. J Virol 2010, 84, 8433–8445, doi: 10.1128/JVI.00879-10. Graef K.M. Vreede F.T. Lau Y.F. McCall A.W. Carr S.M. Subbarao K. Fodor E. : The PB2 subunit of the influenza virus RNA polymerase affects virulence by interacting with the mitochondrial antiviral signaling protein and inhibiting expression of beta interferon . J Virol 2010 , 84 , 8433 – 8445 , doi: 10.1128/JVI.00879-10 . Open DOISearch in Google Scholar

16. Harder T.C., Grosse Beilage E., Lange E., Meiners C., Döhring S., Pesch S., Noé T., Grund C., Beer M., Starick E.: Expanded cocirculation of stable subtypes, emerging lineages, and new sporadic reassortants of porcine influenza viruses in swine populations in Northwest Germany. J Virol 2013, 87, 10460–10476, doi: 10.1128/JVI.00381-13. Harder T.C. Grosse Beilage E. Lange E. Meiners C. Döhring S. Pesch S. Noé T. Grund C. Beer M. Starick E. : Expanded cocirculation of stable subtypes, emerging lineages, and new sporadic reassortants of porcine influenza viruses in swine populations in Northwest Germany . J Virol 2013 , 87 , 10460 – 10476 , doi: 10.1128/JVI.00381-13 . Open DOISearch in Google Scholar

17. Howden K.J., Brockhoff E.J., Caya F.D., McLeod L.J., Lavoie M., Ing J.D., Bystrom J.M., Alexandersen S., Pasick J.M., Berhane Y., Morrison M.E., Keenliside J.M., Laurendeau S., Rohonczy E.B.: An investigation into human pandemic influenza virus (H1N1) 2009 on an Alberta swine farm. Can Vet J 2009, 50, 1153–1161. Howden K.J. Brockhoff E.J. Caya F.D. McLeod L.J. Lavoie M. Ing J.D. Bystrom J.M. Alexandersen S. Pasick J.M. Berhane Y. Morrison M.E. Keenliside J.M. Laurendeau S. Rohonczy E.B. : An investigation into human pandemic influenza virus (H1N1) 2009 on an Alberta swine farm . Can Vet J 2009 , 50 , 1153 – 1161 . Search in Google Scholar

18. Hu J., Ma C., Liu X.: PA-X: a key regulator of influenza A virus pathogenicity and host immune responses. Med Microbiol Immunol 2018, 207, 255–269, doi: 10.1007/s00430-018-0548-z. Hu J. Ma C. Liu X. : PA-X: a key regulator of influenza A virus pathogenicity and host immune responses . Med Microbiol Immunol 2018 , 207 , 255 – 269 , doi: 10.1007/s00430-018-0548-z . Open DOISearch in Google Scholar

19. Hussain M., Galvin H.D., Haw T.Y., Nutsford A.N., Husain M.: Drug resistance in influenza A virus: the epidemiology and management. Infect Drug Resist 2017, 10, 121–134, doi: 10.2147/IDR.S105473. Hussain M. Galvin H.D. Haw T.Y. Nutsford A.N. Husain M. : Drug resistance in influenza A virus: the epidemiology and management . Infect Drug Resist 2017 , 10 , 121 – 134 , doi: 10.2147/IDR.S105473 . Open DOISearch in Google Scholar

20. Jagger B.W., Wise H.M., Kash J.C., Walters K.A., Wills N.M., Xiao Y.L., Dunfee R.L., Schwartzman L.M., Ozinsky A., Bell G.L., Dalton R.M., Lo A., Efstathiou S., Atkins J.F., Firth A.E., Taubenberger J.K., Digard P.: An overlapping protein-coding region in influenza A virus segment 3 modulates the host response. Science 2012, 337, 199–204, doi: 10.1126/science.1222213. Jagger B.W. Wise H.M. Kash J.C. Walters K.A. Wills N.M. Xiao Y.L. Dunfee R.L. Schwartzman L.M. Ozinsky A. Bell G.L. Dalton R.M. Lo A. Efstathiou S. Atkins J.F. Firth A.E. Taubenberger J.K. Digard P. : An overlapping protein-coding region in influenza A virus segment 3 modulates the host response . Science 2012 , 337 , 199 – 204 , doi: 10.1126/science.1222213 . Open DOISearch in Google Scholar

21. Kamal R.P., Alymova I.V., York I.A.: Evolution and Virulence of Influenza A Virus Protein PB1-F2. Int J Mol Sci 2017, 19, 96, doi: 10.3390/ijms19010096. Kamal R.P. Alymova I.V. York I.A. : Evolution and Virulence of Influenza A Virus Protein PB1-F2 . Int J Mol Sci 2017 , 19 , 96 , doi: 10.3390/ijms19010096 . Open DOISearch in Google Scholar

22. Koel B.F., Mögling R., Chutinimitkul S., Fraaij P.L., Burke D.F., van der Vliet S., de Wit E., Bestebroer T.M., Rimmelzwaan G.F., Osterhaus A.D., Smith D.J., Fouchier R.A., de Graaf M.: Identification of amino acid substitutions supporting antigenic change of influenza A(H1N1)pdm09 viruses. J Virol 2015, 89, 3763–3775, doi: 10.1128/JVI.02962-14. Koel B.F. Mögling R. Chutinimitkul S. Fraaij P.L. Burke D.F. van der Vliet S. de Wit E. Bestebroer T.M. Rimmelzwaan G.F. Osterhaus A.D. Smith D.J. Fouchier R.A. de Graaf M. : Identification of amino acid substitutions supporting antigenic change of influenza A(H1N1)pdm09 viruses . J Virol 2015 , 89 , 3763 – 3775 , doi: 10.1128/JVI.02962-14 . Open DOISearch in Google Scholar

23. Kumar S., Stecher G., Tamura K.: MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 2016, 33, 1870–1874, doi: 10.1093/molbev/msw054. Kumar S. Stecher G. Tamura K. : MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets . Mol Biol Evol 2016 , 33 , 1870 – 1874 , doi: 10.1093/molbev/msw054 . Open DOISearch in Google Scholar

24. Lefkowitz E.J., Dempsey D.M., Hendrickson R.C., Orton R.J., Siddell S.G., Smith D.B.: Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Res 2018, 46, D708–D717, doi: 10.1093/nar/gkx932. Lefkowitz E.J. Dempsey D.M. Hendrickson R.C. Orton R.J. Siddell S.G. Smith D.B. : Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV) . Nucleic Acids Res 2018 , 46 , D708 – D717 , doi: 10.1093/nar/gkx932 . Open DOISearch in Google Scholar

25. Liu Q., Qiao C., Marjuki H., Bawa B., Ma J., Guillossou S., Webby R.J., Richt J.A., Ma W.: Combination of PB2 271A and SR polymorphism at positions 590/591 is critical for viral replication and virulence of swine influenza virus in cultured cells and in vivo. J Virol 2012, 86, 1233–1237, doi: 10.1128/JVI.05699-11. Liu Q. Qiao C. Marjuki H. Bawa B. Ma J. Guillossou S. Webby R.J. Richt J.A. Ma W. : Combination of PB2 271A and SR polymorphism at positions 590/591 is critical for viral replication and virulence of swine influenza virus in cultured cells and in vivo . J Virol 2012 , 86 , 1233 – 1237 , doi: 10.1128/JVI.05699-11 . Open DOISearch in Google Scholar

26. Long J.S., Mistry B., Haslam S.M., Barclay W.S.: Host and viral determinants of influenza A virus species specificity. Nat Rev Microbiol 2019, 17, 67–81, doi: 10.1038/s41579-018-0115-z. Long J.S. Mistry B. Haslam S.M. Barclay W.S. : Host and viral determinants of influenza A virus species specificity . Nat Rev Microbiol 2019 , 17 , 67 – 81 , doi: 10.1038/s41579-018-0115-z . Open DOISearch in Google Scholar

27. Maksimovic Zoric J., Milicevic V., Stevancevic O., Chiapponi C., Potkonjak A., Stojanac N., Kureljušic B., Veljovic Lj., Radosavljevic V., Savic B.:Phylogenetic analysis of HA and NA genes of swine influenza viruses in Serbia in 2016-2018. Acta Vet-Beograd 2020, 70, 110–125, doi: 10.2478/acve-2020-0008. Maksimovic Zoric J. Milicevic V. Stevancevic O. Chiapponi C. Potkonjak A. Stojanac N. Kureljušic B. Veljovic Lj. Radosavljevic V. Savic B. : Phylogenetic analysis of HA and NA genes of swine influenza viruses in Serbia in 2016-2018 . Acta Vet-Beograd 2020 , 70 , 110 – 125 , doi: 10.2478/acve-2020-0008 . Open DOISearch in Google Scholar

28. Maksimovic Zoric J., Milicevic V., Veljovic L.J., Radosavljevic V., Kureljusic B., Stevancevic O., Chiapponi C.: Genetic analysis of influenza A viruses of swine from commercial farms in Serbia. Vet It, doi: 10.12834/VetIt.2712.17810.2 (in print). Maksimovic Zoric J. Milicevic V. Veljovic L.J. Radosavljevic V. Kureljusic B. Stevancevic O. Chiapponi C. : Genetic analysis of influenza A viruses of swine from commercial farms in Serbia . Vet It , doi: 10.12834/VetIt.2712.17810.2 (in print). Open DOISearch in Google Scholar

29. Mancera Gracia J.C., Pearce D.S., Masic A., Balasch M.: Influenza A Virus in Swine: Epidemiology, Challenges and Vaccination Strategies. Front Vet Sci 2020, 7, 647, doi: 10.3389/fvets.2020.00647. Mancera Gracia J.C. Pearce D.S. Masic A. Balasch M. : Influenza A Virus in Swine: Epidemiology, Challenges and Vaccination Strategies . Front Vet Sci 2020 , 7 , 647 , doi: 10.3389/fvets.2020.00647 . Open DOISearch in Google Scholar

30. Moncorgé O., Long J.S, Cauldwell A.V., Zhou H., Lycett S.J., Barclay W.S.: Investigation of Influenza Virus Polymerase Activity in Pig Cells. J Virol 2013, 87, 384–394, doi: 10.1128/JVI.01633-12. Moncorgé O. Long J.S Cauldwell A.V. Zhou H. Lycett S.J. Barclay W.S. : Investigation of Influenza Virus Polymerase Activity in Pig Cells . J Virol 2013 , 87 , 384 – 394 , doi: 10.1128/JVI.01633-12 . Open DOISearch in Google Scholar

31. Muramoto Y., Noda T., Kawakami E., Akkina R., Kawaoka Y.: Identification of novel influenza A virus proteins translated from PA mRNA. J Virol 2013, 87, 2455–2462, doi: 10.1128/JVI.02656-12. Muramoto Y. Noda T. Kawakami E. Akkina R. Kawaoka Y. : Identification of novel influenza A virus proteins translated from PA mRNA . J Virol 2013 , 87 , 2455 – 2462 , doi: 10.1128/JVI.02656-12 . Open DOISearch in Google Scholar

32. Noronha J.M., Liu M., Squires R.B., Pickett B.E., Hale B.G., Air G.M., Galloway S.E., Takimoto T., Schmolke M., Hunt V., Klem E., García-Sastre A., McGee M., Scheuermann R.H.: Influenza virus sequence feature variant type analysis: evidence of a role for NS1 in influenza virus host range restriction. J Virol 2012, 86, 5857–5866, doi: 10.1128/JVI.06901-11. Noronha J.M. Liu M. Squires R.B. Pickett B.E. Hale B.G. Air G.M. Galloway S.E. Takimoto T. Schmolke M. Hunt V. Klem E. García-Sastre A. McGee M. Scheuermann R.H. : Influenza virus sequence feature variant type analysis: evidence of a role for NS1 in influenza virus host range restriction . J Virol 2012 , 86 , 5857 – 5866 , doi: 10.1128/JVI.06901-11 . Open DOISearch in Google Scholar

33. Novel Swine-Origin Influenza A (H1N1) Virus Investigation Team: Emergence of a Novel Swine-Origin Influenza A (H1N1) Virus in Humans. N Engl J Med 2009, 360, 2605–2615, doi: 10.1056/NEJMoa0903810. Novel Swine-Origin Influenza A (H1N1) Virus Investigation Team : Emergence of a Novel Swine-Origin Influenza A (H1N1) Virus in Humans . N Engl J Med 2009 , 360 , 2605 – 2615 , doi: 10.1056/NEJMoa0903810 . Open DOISearch in Google Scholar

34. Pan C., Cheung B., Tan S., Li C., Li L., Liu S., Jiang S.: Genomic signature and mutation trend analysis of pandemic (H1N1) 2009 influenza A virus. PLoS One 2010, 5, e9549, doi: 10.1371/journal.pone.0009549. Pan C. Cheung B. Tan S. Li C. Li L. Liu S. Jiang S. : Genomic signature and mutation trend analysis of pandemic (H1N1) 2009 influenza A virus . PLoS One 2010 , 5 , e9549 , doi: 10.1371/journal.pone.0009549 . Open DOISearch in Google Scholar

35. Patel M.C., Mishin V.P., De La Cruz J.A., Chesnokov A., Nguyen H.T., Wilson M.M., Barnes J., Kondor R.J.G., Wentworth D.E., Gubareva L.V.: Detection of baloxavir resistant influenza A viruses using next generation sequencing and pyrosequencing methods. Antiviral Res 2020, 182, 104906, doi: 10.1016/j.antiviral.2020.104906. Patel M.C. Mishin V.P. De La Cruz J.A. Chesnokov A. Nguyen H.T. Wilson M.M. Barnes J. Kondor R.J.G. Wentworth D.E. Gubareva L.V. : Detection of baloxavir resistant influenza A viruses using next generation sequencing and pyrosequencing methods . Antiviral Res 2020 , 182 , 104906 , doi: 10.1016/j.antiviral.2020.104906 . Open DOISearch in Google Scholar

36. Pensaert M., Ottis K., Vandeputte J., Kaplan M.M., Bachmann P.A.: Evidence for the natural transmission of influenza A virus from wild ducks to swine and its potential importance for man. Bull World Health Organ 1981, 59, 75–78. Pensaert M. Ottis K. Vandeputte J. Kaplan M.M. Bachmann P.A. : Evidence for the natural transmission of influenza A virus from wild ducks to swine and its potential importance for man . Bull World Health Organ 1981 , 59 , 75 – 78 . Search in Google Scholar

37. Pleschka S.: Chapter 1, Overview of influenza viruses. In: Swine Influenza, edited by J.A. Richt, R.J. Webby, Springer, New York, 2012, pp. 1–20. Pleschka S. : Chapter 1, Overview of influenza viruses . In: Swine Influenza , edited by Richt J.A. Webby R.J. , Springer , New York , 2012 , pp. 1 – 20 . Search in Google Scholar

38. Salvesen H.A., Whitelaw C.B.A.: Current and prospective control strategies of influenza A virus in swine. Porc Health Manag 2021,7, 23, doi: 10.1186/s40813-021-00196-0. Salvesen H.A. Whitelaw C.B.A. : Current and prospective control strategies of influenza A virus in swine . Porc Health Manag 2021 , 7 , 23 , doi: 10.1186/s40813-021-00196-0 . Open DOISearch in Google Scholar

39. Schrauwen E.J.A., Fouchier R.A.M.: Host adaptation and transmission of influenza A viruses in mammals. Emerg Microbes Infect 2014, 3, e9, doi: 10.1038/emi.2014.9. Schrauwen E.J.A. Fouchier R.A.M. : Host adaptation and transmission of influenza A viruses in mammals . Emerg Microbes Infect 2014 , 3 , e9 , doi: 10.1038/emi.2014.9 . Open DOISearch in Google Scholar

40. Selman M., Dankar S.K., Forbes N.E., Jia J.-J., Brown E.G.: Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. Emerg Microbes Infect 2012, 1, e42, doi: 10.1038/emi.2012.38. Selman M. Dankar S.K. Forbes N.E. Jia J.-J. Brown E.G. : Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing . Emerg Microbes Infect 2012 , 1 , e42 , doi: 10.1038/emi.2012.38 . Open DOISearch in Google Scholar

41. Shi M., Jagger B.W., Wise H.M., Digard P., Holmes E.C., Taubenberger J.K.: Evolutionary conservation of the PA-X open reading frame in segment 3 of influenza A virus. J Virol 2012, 86, 12411–12413, doi: 10.1128/JVI.01677-12. Shi M. Jagger B.W. Wise H.M. Digard P. Holmes E.C. Taubenberger J.K. : Evolutionary conservation of the PA-X open reading frame in segment 3 of influenza A virus . J Virol 2012 , 86 , 12411 – 12413 , doi: 10.1128/JVI.01677-12 . Open DOISearch in Google Scholar

42. Sriwilaijaroen N., Suzuki Y.: Molecular basis of the structure and function of H1 hemagglutinin of influenza virus. Proc Jpn Acad Ser B Phys Biol Sci 2012, 88, 226–249, doi: 10.2183/pjab.88.226. Sriwilaijaroen N. Suzuki Y. : Molecular basis of the structure and function of H1 hemagglutinin of influenza virus . Proc Jpn Acad Ser B Phys Biol Sci 2012 , 88 , 226 – 249 , doi: 10.2183/pjab.88.226 . Open DOISearch in Google Scholar

43. Sun H., Xiao Y., Liu J., Wang D., Li F., Wang C., Li C., Zhu J., Song J., Sun H., Jiang Z., Liu L., Zhang X., Wei K., Hou D., Pu J., Sun Y., Tong Q., Bi Y., Chang K.-C., Liu S., Gao G.F., Liu J.: Prevalent Eurasian avian-like H1N1 swine influenza virus with 2009 pandemic viral genes facilitating human infection. Proc Natl Acad Sci USA 2020, 117, 17204–17210, doi: 10.1073/pnas.1921186117. Sun H. Xiao Y. Liu J. Wang D. Li F. Wang C. Li C. Zhu J. Song J. Sun H. Jiang Z. Liu L. Zhang X. Wei K. Hou D. Pu J. Sun Y. Tong Q. Bi Y. Chang K.-C. Liu S. Gao G.F. Liu J. : Prevalent Eurasian avian-like H1N1 swine influenza virus with 2009 pandemic viral genes facilitating human infection . Proc Natl Acad Sci USA 2020 , 117 , 17204 – 17210 , doi: 10.1073/pnas.1921186117 . Open DOISearch in Google Scholar

44. Suttie A., Deng Y.-M., Greenhill A.R., Dussart P., Horwood P.F., Karlsson E.A.: Inventory of molecular markers affecting biological characteristics of avian influenza A viruses. Virus Genes 2019, 55, 739–768, doi: 10.1007/s11262-019-01700-z. Suttie A. Deng Y.-M. Greenhill A.R. Dussart P. Horwood P.F. Karlsson E.A. : Inventory of molecular markers affecting biological characteristics of avian influenza A viruses . Virus Genes 2019 , 55 , 739 – 768 , doi: 10.1007/s11262-019-01700-z . Open DOISearch in Google Scholar

45. Thippamom N., Sreta D., Kitikoon P., Thanawongnuwech R., Poovorawan Y., Theamboonlers A., Suwannakarn K., Parchariyanon S., Damrongwatanapokin S., Amonsin A.: Genetic variations of nucleoprotein gene of influenza A viruses isolated from swine in Thailand. Virol J 2010, 7, 185, doi: 10.1186/1743-422X-7-185. Thippamom N. Sreta D. Kitikoon P. Thanawongnuwech R. Poovorawan Y. Theamboonlers A. Suwannakarn K. Parchariyanon S. Damrongwatanapokin S. Amonsin A. : Genetic variations of nucleoprotein gene of influenza A viruses isolated from swine in Thailand . Virol J 2010 , 7 , 185 , doi: 10.1186/1743-422X-7-185 . Open DOISearch in Google Scholar

46. Trock S.C., Burke S.A., Cox N.J.: Development of framework for assessing influenza virus pandemic risk. Emerg Infect Dis 2015, 21, 1372–1378, doi: 10.3201/eid2108.141086. Trock S.C. Burke S.A. Cox N.J. : Development of framework for assessing influenza virus pandemic risk . Emerg Infect Dis 2015 , 21 , 1372 – 1378 , doi: 10.3201/eid2108.141086 . Open DOISearch in Google Scholar

47. Vasin A.V., Temkina O.A., Egorov V.V., Klotchenko S.A., Plotnikova M.A., Kiselev O.I.: Molecular mechanisms enhancing the proteome of influenza A viruses: an overview of recently discovered proteins. Virus Res 2014, 185, 53–63, doi: 10.1016/j.virusres.2014.03.015. Vasin A.V. Temkina O.A. Egorov V.V. Klotchenko S.A. Plotnikova M.A. Kiselev O.I. : Molecular mechanisms enhancing the proteome of influenza A viruses: an overview of recently discovered proteins . Virus Res 2014 , 185 , 53 – 63 , doi: 10.1016/j.virusres.2014.03.015 . Open DOISearch in Google Scholar

48. Welsh M.D., Baird P.M., Guelbenzu-Gonzalo M.P., Hanna A., Reid S.M., Essen S., Russell C., Thomas S., Barrass L., McNeilly F., McKillen J., Todd D., Harkin V., McDowell S., Choudhury B., Irvine R.M., Borobia J., Grant J., Brown I.H.: Initial incursion of pandemic (H1N1) 2009 influenza A virus into European pigs. Vet Rec 2010, 166, 642–645, doi: 10.1136/vr.4851. Welsh M.D. Baird P.M. Guelbenzu-Gonzalo M.P. Hanna A. Reid S.M. Essen S. Russell C. Thomas S. Barrass L. McNeilly F. McKillen J. Todd D. Harkin V. McDowell S. Choudhury B. Irvine R.M. Borobia J. Grant J. Brown I.H. : Initial incursion of pandemic (H1N1) 2009 influenza A virus into European pigs . Vet Rec 2010 , 166 , 642 – 645 , doi: 10.1136/vr.4851 . Open DOISearch in Google Scholar

49. Wise H.M., Foeglein A., Sun J., Dalton R.M., Patel S., Howard W., Anderson E.C., Barclay W.S., Digard P.: A complicated message: Identification of a novel PB1-related protein translated from influenza A virus segment 2 mRNA. J Virol 2009, 83, 8021–8031, doi: 10.1128/JVI.00826-09. Wise H.M. Foeglein A. Sun J. Dalton R.M. Patel S. Howard W. Anderson E.C. Barclay W.S. Digard P. : A complicated message: Identification of a novel PB1-related protein translated from influenza A virus segment 2 mRNA . J Virol 2009 , 83 , 8021 – 8031 , doi: 10.1128/JVI.00826-09 . Open DOISearch in Google Scholar

50. Zhang Y., Aevermann B.D., Anderson T.K., Burke D.F., Dauphin G., Gu Z., He S., Kumar S., Larsen C.N., Lee A.J., Li X., Macken C., Mahaffey C., Pickett B.E., Reardon B., Smith T., Stewart L., Suloway C., Sun G., Tong L., Vincent A.L., Walters B., Zaremba S., Zhao H., Zhou L., Zmasek C., Klem E.B., Scheuermann R.H.: Influenza Research Database: An integrated bioinformatics resource for influenza virus research. Nucleic Acids Res 2017, 45, D466–D474, doi: 10.1093/nar/gkw857. Zhang Y. Aevermann B.D. Anderson T.K. Burke D.F. Dauphin G. Gu Z. He S. Kumar S. Larsen C.N. Lee A.J. Li X. Macken C. Mahaffey C. Pickett B.E. Reardon B. Smith T. Stewart L. Suloway C. Sun G. Tong L. Vincent A.L. Walters B. Zaremba S. Zhao H. Zhou L. Zmasek C. Klem E.B. Scheuermann R.H. : Influenza Research Database: An integrated bioinformatics resource for influenza virus research . Nucleic Acids Res 2017 , 45 , D466 – D474 , doi: 10.1093/nar/gkw857 . Open DOISearch in Google Scholar