1 Lamb, R.A., Choppin, P.W., 1983. The gene structure and replication of influenza virus. Annu Rev Biochem 52, 467-506.
2 Hause, B.M., Ducatez, M., Collin, E.A., Ran, Z., Liu, R., Sheng, Z., Armien, A., Kaplan, B., Chakravarty, S., Hoppe, A.D., Webby, R.J., Simonson, R.R., Li, F., 2013. Isolation of a novel swine influenza virus from Oklahoma in 2011 which is distantly related to human influenza C viruses. PLoS Pathog 9, e1003176.
3 World health organization, 1980. A revision of the system of nomenclature for influenza viruses: a WHO memorandum. Bull. World Health Organ 58, 585-591.
4 Hinshaw, V.S., Air, G.M., Gibbs, A.J., Graves, L., Prescott, B., Karunakaran, D., 1982. Antigenic and genetic characterization of a novel hemagglutinin subtype of influenza A viruses from gulls. J Virol 42, 865-872.
5 Kawaoka, Y., Yamnikova, S., Chambers, T.M., Lvov, D.K., Webster, R.G., 1990. Molecular characterization of a new hemagglutinin, subtype H14, of influenza A virus. Virology 179, 759-767.
6 Rohm, C., Zhou, N., Suss, J., Mackenzie, J., Webster, R.G., 1996. Characterization of a novel influenza hemagglutinin, H15: criteria for determination of influenza A subtypes. Virology 217, 508-516.
7 Fouchier, R.A., Munster, V., Wallensten, A., Bestebroer, T.M., Herfst, S., Smith, D., Rimmelzwaan, G.F., Olsen, B., Osterhaus, A.D., 2005. Characterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black- headed gulls. J Virol 79, 2814-2822.
8 Ma, W., Lager, K.M., Vincent, A.L., Janke, B.H., Gramer, M.R., Richt, J.A., 2009. The role of swine in the generation of novel influenza viruses. Zoonoses Public Health 56, 326-337.
9 Kitikoon, P., Vincent, A.L., Jones, K.R., Nilubol, D., Yu, S., Janke, B.H., Thacker, B.J., Thacker, E.L., 2009. Vaccine efficacy and immune response to swine influenza virus challenge in pigs infected with porcine reproductive and respiratory syndrome virus at the time of SIV vaccination. Vet Microbiol 139, 235-244.
10 Vincent, A., Awada, L., Brown, I., Chen, H., Claes, F., Dauphin, G., Donis, R., Culhane, M., Hamilton, K., Lewis, N., Mumford, E., Nguyen, T., Parchariyanon, S., Pasick, J., Pavade, G., Pereda, A., Peiris, M., Saito, T., Swenson, S., Van Reeth, K., Webby, R., Wong, F., Ciacci-Zanella, J., 2014. Review of influenza A virus in swine worldwide: a call for increased surveillance and research. Zoonoses Public Health 61, 4-17.
11 Bennett, R., Ijpelaar, J., 2005. Updated estimates of the costs associated with thirty four endemic livestock diseases in Great Britain: A note. J Agr Econ 56, 135-144.
12 World organization for animal health, 2009. The human influenza due to a novel subtype H1N1. http://www.fao.org/3/a-ak061e.pdf Accessed 26 January 2016.
13 Ito, T., Couceiro, J.N., Kelm, S., Baum, L.G., Krauss, S., Castrucci, M.R., Donatelli, I., Kida, H., Paulson, J.C., Webster, R.G., Kawaoka, Y., 1998. Molecular basis for the generation in pigs of influenza A viruses with pandemic potential. J Virol 72, 7367-7373.
14 Brown, I.H., 2000. The epidemiology and evolution of influenza viruses in pigs. Vet Microbiol 74, 29-46.
15 Zell, R., Scholtissek, C., Ludwig, S., 2013. Genetics, evolution, and the zoonotic capacity of European swine influenza viruses. Curr Top Microbiol Immunol 370, 29-55.
16 Zhu, H., Webby, R., Lam, T.T., Smith, D.K., Peiris, J.S., Guan, Y., 2013. History of swine influenza viruses in Asia. Curr Top Microbiol Immunol 370, 57-68.
17 Guan, Y., Shortridge, K.F., Krauss, S., Li, P.H., Kawaoka, Y., Webster, R.G., 1996. Emergence of avian H1N1 influenza viruses in pigs in China. J Virol 70, 8041-8046.
18 Takemae, N., Parchariyanon, S., Damrongwatanapokin, S., Uchida, Y., Ruttanapumma, R., Watanabe, C., Yamaguchi, S., Saito, T., 2008. Genetic diversity of swine influenza viruses isolated from pigs during 2000 to 2005 in Thailand. Influenza Other Respir Viruses 2, 181-189.
19 Poonsuk, S., Sangthong, P., Petcharat, N., Lekcharoensuk, P., 2013. Genesis and genetic constellations of swine influenza viruses in Thailand. Vet Microbiol 167, 314-326.
20 Nonthabenjawan, N., Chanvatik, S., Chaiyawong, S., Jairak, W., Boonyapisusopha, S., Tuanudom, R., Thontiravong, A., Bunpapong, N., Amonsin, A., 2015. Genetic diversity of swine influenza viruses in Thai swine farms, 2011-2014. Virus Genes 50, 221-230.
21 Abe, H., Mine, J., Parchariyanon, S., Takemae, N., Boonpornprasert, P., Ubonyaem, N., Patcharasinghawut, P., Nuansrichay, B., Tanikawa, T., Tsunekuni, R., Saito, T., 2015. Co-infection of influenza A viruses of swine contributes to effective shuffling of gene segments in a naturally reared pig. Virology 484, 203-212.
22 Lee, J.H., Pascua, P.N., Decano, A.G., Kim, S.M., Park, S.J., Kwon, H.I., Kim, E.H., Kim, Y.I., Kim, H., Kim, S.Y., Song, M.S., Jang, H.K., Park, B.K., Choi, Y.K., 2015. Evaluation of the zoonotic potential of a novel reassortant H1N2 swine influenza virus with gene constellation derived from multiple viral sources. Infect Genet Evol 34, 378-393.
23 Takemae, N., Nguyen, P.T., Le, V.T., Nguyen, T.N., To, T.L., Nguyen, T.D., Pham, V.P., Vo, H.V., Le, Q.V.T., Do, H.T., Nguyen, D.T., Uchida, Y., Saito, T., 2018. Appearance of reassortant European avian-origin H1 influenza A viruses of swine in Vietnam. Transbound Emerg Dis 65, 1110-1116.
24 Kundin, W.D., 1970. Hong Kong A-2 influenza virus infection among swine during a human epidemic in Taiwan. Nature 228, 857.
25 Tumova, B., Mensik, J., Stumpa, A., Fedova, D., Pospisil, Z., 1976. Serological evidence and isolation of a virus closely related to the human A/Hong Kong/68 (H3N2) strain in swine populations in Czechoslovakia in 1969-1972. Zentralbl Veterinarmed B 23, 590-563.
26 Shortridge, K.F., Webster, R.G., 1979. Geographical distribution of swine (Hsw1N1) and Hong Kong (H3N2) influenza virus variants in pigs in Southeast Asia. Intervirology 11, 9-15.
27 Nerome, K., Ishida, M., Nakayama, M., Oya, A., Kanai, C., Suwicha, K., 1981. Antigenic and genetic analysis of A/Hong Kong (H3N2) influenza viruses isolated from swine and man. J Gen Virol 56, 441-445.
28 Ottis, K., Sidoli, L., Bachmann, P.A., Webster, R.G., Kaplan, M.M., 1982. Human influenza A viruses in pigs: isolation of a H3N2 strain antigenically related to A/England/42/72 and evidence for continuous circulation of human viruses in the pig population. Arch Virol 73, 103-108.
29 Zhou, N.N., Senne, D.A., Landgraf, J.S., Swenson, S.L., Erickson, G., Rossow, K., Liu, L., Yoon, K., Krauss, S., Webster, R.G., 1999. Genetic reassortment of avian, swine, and human influenza A viruses in American pigs. J Virol 73, 8851- 8856.
30 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., Lopez-Gatell, H., Olivera, H., Lopez, 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., 2009. Antigenic and genetic characteristics of swine- origin 2009 A(H1N1) influenza viruses circulating in humans. Science 325, 197- 201.
31 Smith, G.J., Vijaykrishna, D., Bahl, J., Lycett, S.J., Worobey, M., Pybus, O.G., Ma, S.K., Cheung, C.L., Raghwani, J., Bhatt, S., Peiris, J.S., Guan, Y., Rambaut, A., 2009. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459, 1122-1125.
32 Sreta, D., Tantawet, S., Na Ayudhya, S.N., Thontiravong, A., Wongphatcharachai, M., Lapkuntod, J., Bunpapong, N., Tuanudom, R., Suradhat, S., Vimolket, L., Poovorawan, Y., Thanawongnuwech, R., Amonsin, A., Kitikoon, P., 2010. Pandemic (H1N1) 2009 virus on commercial swine farm, Thailand. Emerg Infect Dis 16, 1587-1590.
33 Vijaykrishna, D., Poon, L.L., Zhu, H.C., Ma, S.K., Li, O.T., Cheung, C.L., Smith, G.J., Peiris, J.S., Guan, Y., 2010. Reassortment of pandemic H1N1/2009 influenza A virus in swine. Science 328, 1529.
34 Ducatez, M.F., Hause, B., Stigger-Rosser, E., Darnell, D., Corzo, C., Juleen, K., Simonson, R., Brockwell-Staats, C., Rubrum, A., Wang, D., Webb, A., Crumpton, J.C., Lowe, J., Gramer, M., Webby, R.J., 2011. Multiple reassortment between pandemic (H1N1) 2009 and endemic influenza viruses in pigs, United States. Emerg Infect Dis 17, 1624-1629.
35 Howard, W.A., Essen, S.C., Strugnell, B.W., Russell, C., Barass, L., Reid, S.M., Brown, I.H., 2011. Reassortant pandemic (H1N1) 2009 virus in pigs, United Kingdom. Emerg Infect Dis 17, 1049-1052.
36 Kitikoon, P., Sreta, D., Na Ayudhya, S.N., Wongphatcharachai, M., Lapkuntod, J., Prakairungnamthip, D., Bunpapong, N., Suradhat, S., Thanawongnuwech, R., Amonsin, A., 2011. Brief report: molecular characterization of a novel reassorted pandemic H1N1 2009 in Thai pigs. Virus Genes 43, 1-5.
37 Lam, T.T., Zhu, H., Wang, J., Smith, D.K., Holmes, E.C., Webster, R.G., Webby, R., Peiris, J.M., Guan, Y., 2011. Reassortment events among swine influenza A viruses in China: implications for the origin of the 2009 influenza pandemic. J Virol 85, 10279-10285.
38 Moreno, A., Di Trani, L., Faccini, S., Vaccari, G., Nigrelli, D., Boniotti, M.B., Falcone, E., Boni, A., Chiapponi, C., Sozzi, E., Cordioli, P., 2011. Novel H1N2 swine influenza reassortant strain in pigs derived from the pandemic H1N1/2009 virus. Vet Microbiol 149, 472-477.
39 Hiromoto, Y., Parchariyanon, S., Ketusing, N., Netrabukkana, P., Hayashi, T., Kobayashi, T., Takemae, N., Saito, T., 2012. Isolation of the pandemic (H1N1) 2009 virus and its reassortant with an H3N2 swine influenza virus from healthy weaning pigs in Thailand in 2011. Virus Res 169, 175-181.
40 Kirisawa, R., Ogasawara, Y., Yoshitake, H., Koda, A., Furuya, T., 2014. Genomic reassortants of pandemic A (H1N1) 2009 virus and endemic porcine H1 and H3 viruses in swine in Japan. J Vet Med Sci 76, 1457-1470.
41 Kanehira, K., Takemae, N., Uchida, Y., Hikono, H., Saito, T., 2014. Reassortant swine influenza viruses isolated in Japan contain genes from pandemic A(H1N1) 2009. Microbiol Immunol 58, 327-341.
42 Diaz, A., Marthaler, D., Culhane, M., Sreevatsan, S., Alkhamis, M., Torremorell, M., 2017. Complete genome sequencing of influenza A viruses within swine farrow-to-wean farms reveals the emergence, persistence, and subsidence of diverse viral genotypes. J Virol 91, e00745-17
43 Gao S, Anderson TK, Walia RR, Dorman KS, Janas-Martindale A, Vincent AL. 2017. The genomic evolution of H1 influenza A viruses from swine detected in the United States between 2009 and 2016. J Gen Virol 98, 2001-2010.
44 Xu, X., Subbarao, Cox, N.J., Guo, Y., 1999. Genetic characterization of the pathogenic influenza A/Goose/Guangdong/1/96 (H5N1) virus: similarity of its hemagglutinin gene to those of H5N1 viruses from the 1997 outbreaks in Hong Kong. Virology 261, 15-19.
45 Mase, M., Tsukamoto, K., Imada, T., Imai, K., Tanimura, N., Nakamura, K., Yamamoto, Y., Hitomi, T., Kira, T., Nakai, T., Kiso, M., Horimoto, T., Kawaoka, Y., Yamaguchi, S., 2005. Characterization of H5N1 influenza A viruses isolated during the 2003-2004 influenza outbreaks in Japan. Virology 332, 167-176.
46 Shivakoti, S., Ito, H., Otsuki, K., Ito, T., 2010. Characterization of H5N1 highly pathogenic avian influenza virus isolated from a mountain hawk eagle in Japan. J Vet Med Sci 72, 459-463.
47 Sakoda, Y., Ito, H., Uchida, Y., Okamatsu, M., Yamamoto, N., Soda, K., Nomura, N., Kuribayashi, S., Shichinohe, S., Sunden, Y., Umemura, T., Usui, T., Ozaki, H., Yamaguchi, T., Murase, T., Ito, T., Saito, T., Takada, A., Kida, H., 2012. Reintroduction of H5N1 highly pathogenic avian influenza virus by migratory water birds, causing poultry outbreaks in the 2010-2011 winter season in Japan. J Gen Virol 93, 541-550.
48 Uchida, Y., Suzuki, Y., Shirakura, M., Kawaguchi, A., Nobusawa, E., Tanikawa, T., Hikono, H., Takemae, N., Mase, M., Kanehira, K., Hayashi, T., Tagawa, Y., Tashiro, M., Saito, T., 2012. Genetics and infectivity of H5N1 highly pathogenic avian influenza viruses isolated from chickens and wild birds in Japan during 2010-11. Virus Res 170, 109-117.
49 Saito, T., Tanikawa, T., Uchida, Y., Takemae, N., Kanehira, K., Tsunekuni, R., 2015. Intracontinental and intercontinental dissemination of Asian H5 highly pathogenic avian influenza virus (clade 2.3.4.4) in the winter of 2014-2015. Rev Med Virol 25, 388-405.
50 Tanikawa, T., Kanehira, K., Tsunekuni, R., Uchida, Y., Takemae, N., Saito, T., 2016. Pathogenicity of H5N8 highly pathogenic avian influenza viruses isolated from a wild bird fecal specimen and a chicken in Japan in 2014. Microbiol Immunol 60, 243-252.
51 Lee, Y.J., Kang, H.M., Lee, E.K., Song, B.M., Jeong, J., Kwon, Y.K., Kim, H.R., Lee, K.J., Hong, M.S., Jang, I., Choi, K.S., Kim, J.Y., Lee, H.J., Kang, M.S., Jeong, O.M., Baek, J.H., Joo, Y.S., Park, Y.H., Lee, H.S., 2014. Novel reassortant influenza A(H5N8) viruses, South Korea, 2014. Emerg Infect Dis 20, 1087-1089.
52 Lee, D.H., Torchetti, M.K., Winker, K., Ip, H.S., Song, C.S., Swayne, D.E., 2015. Intercontinental spread of Asian-origin H5N8 to North America through Beringia by migratory birds. J Virol 89, 6521-6524.
53 Si, Y.J., Lee, I.W., Kim, E.H., Kim, Y.I., Kwon, H.I., Park, S.J., Nguyen, H.D., Kim, S.M., Kwon, J.J., Choi, W.S., Beak, Y.H., Song, M.S., Kim, C.J., Webby, R.J., Choi, Y.K., 2017. Genetic characterisation of novel, highly pathogenic avian influenza (HPAI) H5N6 viruses isolated in birds, South Korea, November 2016. Euro Surveill 22, 30434
54 Takemae, N., Tsunekuni, R., Sharshov, K., Tanikawa, T., Uchida, Y., Ito, H., Soda, K., Usui, T., Sobolev, I., Shestopalov, A., Yamaguchi, T., Mine, J., Ito, T., Saito, T., 2017. Five distinct reassortants of H5N6 highly pathogenic avian influenza A viruses affected Japan during the winter of 2016-2017. Virology 512, 8-20.
55 Tsunekuni, R., Yaguchi, Y., Kashima, Y., Yamashita, K., Takemae, N., Mine, J., Tanikawa, T., Uchida, Y., Saito, T., 2018. Spatial transmission of H5N6 highly pathogenic avian influenza viruses among wild birds in Ibaraki Prefecture, Japan, 2016-2017. Arch Virol 163, 1195-1207.
56 Ozawa, M., Matsuu, A., Khalil, A.M., Nishi, N., Tokorozaki, K., Masatani, T., Horie, M., Okuya, K., Ueno, K., Kuwahara, M., Toda, S., 2018. Phylogenetic variations of highly pathogenic H5N6 avian influenza viruses isolated from wild birds in the Izumi plain, Japan, during the 2016-17 winter season. Transbound Emerg Dis 66, 797-806
57 Food and agriculture organization, 2015. FAOSTAT data, Available from http://faostat.fao.org/. Accessed 4 October 2018 for Chapter II and 1 March 2020 for Chapter I.
58 Yamane, N., Arikawa, J., Odagiri, T., Ishida, N., 1979. Annual examination of influenza virus infection among pigs in Miyagi prefecture, Japan: the appearance of Hsw1N1 virus. Acta Virol 23, 240-248.
59 Sugimura, T., Yonemochi, H., Ogawa, T., Tanaka, Y., Kumagai, T., 1980. Isolation of a recombinant influenza virus (Hsw 1 N2) from swine in Japan. Arch Virol 66, 271-274.
60 Ozawa, M., Matsuu, A., Yonezawa, K., Igarashi, M., Okuya, K., Kawabata, T., Ito, K., Tsukiyama-Kohara, K., Taneno, A., Deguchi, E., 2015. Efficient isolation of swine influenza viruses by age-targeted specimen collection. J Clin Microbiol 53, 1331-1338.
61 Okuya, K., Matsuu, A., Kawabata, T., Koike, F., Ito, M., Furuya, T., Taneno, A., Akimoto, S., Deguchi, E., Ozawa, M., 2018. Distribution of gene segments of the pandemic A(H1N1) 2009 virus lineage in pig populations. Transbound Emerg Dis 65, 1502-1513.
62 Ito, T., Kawaoka, Y., Vines, A., Ishikawa, H., Asai, T., Kida, H., 1998. Continued circulation of reassortant H1N2 influenza viruses in pigs in Japan. Arch Virol 143, 1773-1782.
63 Saito, T., Suzuki, H., Maeda, K., Inai, K., Takemae, N., Uchida, Y., Tsunemitsu, H., 2008. Molecular characterization of an H1N2 swine influenza virus isolated in Miyazaki, Japan, in 2006. J Vet Med Sci 70, 423-427.
64 Yoneyama, S., Hayashi, T., Kojima, H., Usami, Y., Kubo, M., Takemae, N., Uchida, Y., Saito, T., 2010. Occurrence of a pig respiratory disease associated with swine influenza A (H1N2) virus in Tochigi Prefecture, Japan. J Vet Med Sci 72, 481-488.
65 Takemae, N., Parchariyanon, S., Ruttanapumma, R., Hiromoto, Y., Hayashi, T., Uchida, Y., Saito, T., 2011. Swine influenza virus infection in different age groups of pigs in farrow-to-finish farms in Thailand. Virol J 8, 537.
66 Huddleston, J.A., Brownlee, G.G., 1982. The sequence of the nucleoprotein gene of human influenza A virus, strain A/NT/60/68. Nucleic Acids Res 10, 1029- 1038.
67 Ngo, L.T., Hiromoto, Y., Pham, V.P., Le, H.T., Nguyen, H.T., Le, V.T., Takemae, N., Saito, T., 2012. Isolation of novel triple-reassortant swine H3N2 influenza viruses possessing the hemagglutinin and neuraminidase genes of a seasonal influenza virus in Vietnam in 2010. Influenza Other Respir Viruses 6, 6-10.
68 Heine, H.G., Trinidad, L., Selleck, P., Lowther, S., 2007. Rapid detection of highly pathogenic avian influenza H5N1 virus by TaqMan reverse transcriptase- polymerase chain reaction. Avian diseases 51, 370-372.
69 Heine, H.G., Foord, A.J., Wang, J., Valdeter, S., Walker, S., Morrissy, C., Wong, F.Y., Meehan, B., 2015. Detection of highly pathogenic zoonotic influenza virus H5N6 by reverse-transcriptase quantitative polymerase chain reaction. Virol J 12, 18.
70 Takemae, N., Nguyen, T., Ngo, L.T., Hiromoto, Y., Uchida, Y., Pham, V.P., Kageyama, T., Kasuo, S., Shimada, S., Yamashita, Y., Goto, K., Kubo, H., Le, V.T., Van Vo, H., Do, H.T., Nguyen, D.H., Hayashi, T., Matsuu, A., Saito, T., 2013. Antigenic variation of H1N1, H1N2 and H3N2 swine influenza viruses in Japan and Vietnam. Arch Virol 158, 859-876.
71 Takemae, N., Shobugawa, Y., Nguyen, P.T., Nguyen, T., Nguyen, T.N., To, T.L., Thai, P.D., Nguyen, T.D., Nguyen, D.T., Nguyen, D.K., Do, H.T., Le, T.Q., Hua, P.T., Van Vo, H., Nguyen, D.T., Nguyen, D.H., Uchida, Y., Saito, R., Saito, T., 2016. Effect of herd size on subclinical infection of swine in Vietnam with influenza A viruses. BMC Vet Res 12, 227.
72 World health organization, 2002. The human influenza due to a novel subtype H1N1. Available from http://www.who.int/csr/resources/publications/influenza/whocdscsrncs20025rev. pdf Accessed 10 March 2016.
73 Hall, T.A., 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser.41:95–98
74 Katoh, K., Standley, D.M., 2016. A simple method to control over-alignment in the MAFFT multiple sequence alignment program. Bioinformatics 32, 1933- 1942.
75 Price, M.N., Dehal, P.S., Arkin, A.P., 2010. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One 5, e9490.
76 Drummond, A.J., Suchard, M.A., Xie, D., Rambaut, A., 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29, 1969-1973.
77 Fu, L., Niu, B., Zhu, Z., Wu, S., Li, W., 2012. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150-3152.
78 Matsuu, A., Uchida, Y., Takemae, N., Mawatari, T., Yoneyama, S.K., Kasai, T., Nakamura, R., Eto, M., Saito, T., 2012. Genetic characterization of swine influenza viruses isolated in Japan between 2009 and 2012. Microbiol Immunol 56, 792-803.
79 Ma, J., Shen, H., McDowell, C., Liu, Q., Duff, M., Lee, J., Lang, Y., Hesse, D., Richt, J.A., Ma, W., 2019. Virus survival and fitness when multiple genotypes and subtypes of influenza A viruses exist and circulate in swine. Virology 532, 30-38.
80 Mancera Gracia, J.C., Van den Hoecke, S., Richt, J.A., Ma, W., Saelens, X., Van Reeth, K., 2017. A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. Sci Rep 7, 1323.
81 Ryt-Hansen, P., Pedersen, A.G., Larsen, I., Krog, J.S., Kristensen, C.S., Larsen, L.E., 2019. Acute Influenza A virus outbreak in an enzootic infected sow herd: impact on viral dynamics, genetic and antigenic variability and effect of maternally derived antibodies and vaccination. PLoS One 14, e0224854.
82 Sun, H., Cunningham, F.L., Harris, J., Xu, Y., Long, L.P., Hanson-Dorr, K., Baroch, J.A., Fioranelli, P., Lutman, M.W., Li, T., Pedersen, K., Schmit, B.S., Cooley, J., Lin, X., Jarman, R.G., DeLiberto, T.J., Wan, X.F., 2015. Dynamics of virus shedding and antibody responses in influenza A virus-infected feral swine. J Gen Virol 96, 2569-2578.
83 Both, G.W., Shi, C.H., Kilbourne, E.D., 1983. Hemagglutinin of swine influenza virus: a single amino acid change pleiotropically affects viral antigenicity and replication. Proc Natl Acad Sci U S A 80, 6996-7000.
84 Pulit-Penaloza, J.A., Jones, J., Sun, X., Jang, Y., Thor, S., Belser, J.A., Zanders, N., Creager, H.M., Ridenour, C., Wang, L., Stark, T.J., Garten, R., Chen, L.M., Barnes, J., Tumpey, T.M., Wentworth, D.E., Maines, T.R., Davis, C.T., 2018. Antigenically diverse swine origin H1N1 variant influenza viruses exhibit differential ferret pathogenesis and transmission phenotypes. J Virol 92, e00095- 18
85 Rajao, D.S., Anderson, T.K., Kitikoon, P., Stratton, J., Lewis, N.S., Vincent, A.L., 2018. Antigenic and genetic evolution of contemporary swine H1 influenza viruses in the United States. Virology 518, 45-54.
86 Koel, B.F., Burke, D.F., Bestebroer, T.M., van der Vliet, S., Zondag, G.C., Vervaet, G., Skepner, E., Lewis, N.S., Spronken, M.I., Russell, C.A., Eropkin, M.Y., Hurt, A.C., Barr, I.G., de Jong, J.C., Rimmelzwaan, G.F., Osterhaus, A.D., Fouchier, R.A., Smith, D.J., 2013. Substitutions near the receptor binding site determine major antigenic change during influenza virus evolution. Science 342, 976-979.
87 Santos, J.J.S., Abente, E.J., Obadan, A.O., Thompson, A.J., Ferreri, L., Geiger, G., Gonzalez-Reiche, A.S., Lewis, N.S., Burke, D.F., Rajao, D.S., Paulson, J.C., Vincent, A.L., Perez, D.R., 2019. Plasticity of Amino Acid Residue 145 Near the receptor binding site of H3 swine influenza A viruses and its impact on receptor binding and antibody recognition. J Virol 93, e01413-18
88 Nerome, K., Ishida, M., Oya, A., Kanai, C., Suwicha, K., 1982. Isolation of an influenza H1N1 virus from a pig. Virology 117, 485-489.
89 Chutinimitkul, S., Thippamom, N., Damrongwatanapokin, S., Payungporn, S., Thanawongnuwech, R., Amonsin, A., Boonsuk, P., Sreta, D., Bunpong, N., Tantilertcharoen, R., Chamnanpood, P., Parchariyanon, S., Theamboonlers, A., Poovorawan, Y., 2008. Genetic characterization of H1N1, H1N2 and H3N2 swine influenza virus in Thailand. Arch Virol 153, 1049-1056.
90 Charoenvisal, N., Keawcharoen, J., Sreta, D., Chaiyawong, S., Nonthabenjawan, N., Tantawet, S., Jittimanee, S., Arunorat, J., Amonsin, A., Thanawongnuwech, R., 2013. Genetic characterization of Thai swine influenza viruses after the introduction of pandemic H1N1 2009. Virus Genes 47, 75-85.
91 Arunorat, J., Charoenvisal, N., Woonwong, Y., Kedkovid, R., Thanawongnuwech, R., 2016. Determination of current reference viruses for serological study of swine influenza viruses after the introduction of pandemic 2009 H1N1 (pdmH1N1) in Thailand. J Virol Methods 236, 5-9.
92 Simon-Grife, M., Martin-Valls, G.E., Vilar, M.J., Busquets, N., Mora- Salvatierra, M., Bestebroer, T.M., Fouchier, R.A., Martin, M., Mateu, E., Casal, J., 2012. Swine influenza virus infection dynamics in two pig farms; results of a longitudinal assessment. Vet Res 43, 24.
93 Rose, N., Herve, S., Eveno, E., Barbier, N., Eono, F., Dorenlor, V., Andraud, M., Camsusou, C., Madec, F., Simon, G., 2013. Dynamics of influenza A virus infections in permanently infected pig farms: evidence of recurrent infections, circulation of several swine influenza viruses and reassortment events. Vet Res 44, 72.
94 Thrusfield, M., 1995. Veterinary Epidemiology. Oxford: Blackwell Science Ltd, 2, 117-198
95 Kumar, S., Stecher, G., Peterson, D., Tamura, K., 2012. MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis. Bioinformatics 28, 2685-2686.
96 Bouckaert, R., Heled, J., Kuhnert, D., Vaughan, T., Wu, C.H., Xie, D., Suchard, M.A., Rambaut, A., Drummond, A.J., 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 10, e1003537.
97 Anderson, T.K., Macken, C.A., Lewis, N.S., Scheuermann, R.H., Van Reeth, K., Brown, I.H., Swenson, S.L., Simon, G., Saito, T., Berhane, Y., Ciacci-Zanella, J., Pereda, A., Davis, C.T., Donis, R.O., Webby, R.J., Vincent, A.L., 2016. A Phylogeny-based global nomenclature system and automated annotation tool for H1 hemagglutinin genes from swine influenza A viruses. mSphere 1, e00275-16
98 Caton, A.J., Brownlee, G.G., Yewdell, J.W., Gerhard, W., 1982. The antigenic structure of the influenza virus A/PR/8/34 hemagglutinin (H1 subtype). Cell 31, 417-427.
99 Igarashi, M., Ito, K., Yoshida, R., Tomabechi, D., Kida, H., Takada, A., 2010. Predicting the antigenic structure of the pandemic (H1N1) 2009 influenza virus hemagglutinin. PLoS One 5, e8553.
100 Matsuzaki, Y., Sugawara, K., Nakauchi, M., Takahashi, Y., Onodera, T., Tsunetsugu-Yokota, Y., Matsumura, T., Ato, M., Kobayashi, K., Shimotai, Y., Mizuta, K., Hongo, S., Tashiro, M., Nobusawa, E., 2014. Epitope mapping of the hemagglutinin molecule of A/(H1N1)pdm09 influenza virus by using monoclonal antibody escape mutants. J Virol 88, 12364-12373.
101 Wiley, D.C., Wilson, I.A., Skehel, J.J., 1981. Structural identification of the antibody-binding sites of Hong Kong influenza haemagglutinin and their involvement in antigenic variation. Nature 289, 373-378.
102 Kryazhimskiy, S., Plotkin, J.B., 2008. The population genetics of dN/dS. PLoS Genet 4, e1000304.
103 Murcia, P.R., Hughes, J., Battista, P., Lloyd, L., Baillie, G.J., Ramirez-Gonzalez, R.H., Ormond, D., Oliver, K., Elton, D., Mumford, J.A., Caccamo, M., Kellam, P., Grenfell, B.T., Holmes, E.C., Wood, J.L., 2012. Evolution of an Eurasian avian-like influenza virus in naive and vaccinated pigs. PLoS Pathog 8, e1002730.
104 Diaz, A., Allerson, M., Culhane, M., Sreevatsan, S., Torremorell, M., 2013. Antigenic drift of H1N1 influenza A virus in pigs with and without passive immunity. Influenza Other Respir Viruses 7 Suppl 4, 52-60.
105 Fitch, W.M., Leiter, J.M., Li, X.Q., Palese, P., 1991. Positive Darwinian evolution in human influenza A viruses. Proc Natl Acad Sci U S A 88, 4270- 4274.
106 Rambaut, A., Pybus, O.G., Nelson, M.I., Viboud, C., Taubenberger, J.K., Holmes, E.C., 2008. The genomic and epidemiological dynamics of human influenza A virus. Nature 453, 615-619.
107 Nelson, M.I., Stratton, J., Killian, M.L., Janas-Martindale, A., Vincent, A.L., 2015. Continual reintroduction of human pandemic H1N1 influenza A viruses into swine in the United States, 2009 to 2014. J Virol 89, 6218-6226.
108 Tinoco, Y.O., Montgomery, J.M., Kasper, M.R., Nelson, M.I., Razuri, H., Guezala, M.C., Azziz-Baumgartner, E., Widdowson, M.A., Barnes, J., Gilman, R.H., Bausch, D.G., Gonzalez, A.E., 2016. Transmission dynamics of pandemic influenza A(H1N1)pdm09 virus in humans and swine in backyard farms in Tumbes, Peru. Influenza Other Respir Viruses 10, 47-56.
109 Prachayangprecha, S., Makkoch, J., Vuthitanachot, C., Vuthitanachot, V., Payungporn, S., Chieochansin, T., Theamboonlers, A., Poovorawan, Y., 2011. Epidemiological and serological surveillance of human pandemic influenza A virus infections during 2009-2010 in Thailand. Jpn J Infect Dis 64, 377-381.
110 Prachayangprecha, S., Vichaiwattana, P., Korkong, S., Felber, J.A., Poovorawan, Y., 2015. Influenza activity in Thailand and occurrence in different climates. Springerplus 4, 356.
111 World organization for animal health: Update on avian influenza in animals (types H5 and H7). http://www.oie.int/en/animal-health-in-the-world/update-on- avian-influenza Accessed 5 December 2018.
112 Beerens, N., Koch, G., Heutink, R., Harders, F., Vries, D.P.E., Ho, C., Bossers, A., Elbers, A., 2018. Novel Highly Pathogenic Avian Influenza A(H5N6) Virus in the Netherlands, December 2017. Emerg Infect Dis 24, 770-773
113 Lee, E.K., Lee, Y.N., Kye, S.J., Lewis, N.S., Brown, I.H., Sagong, M., Heo, G.B., Kang, Y.M., Cho, H.K., Kang, H.M., Cheon, S.H., Lee, M., Park, B.K., Kim, Y.J., Lee, Y.J., 2018. Characterization of a novel reassortant H5N6 highly pathogenic avian influenza virus clade 2.3.4.4 in Korea, 2017. Emerg Microbes Infect 7, 103.
114 Lee, Y.N., Cheon, S.H., Kye, S.J., Lee, E.K., Sagong, M., Heo, G.B., Kang, Y.M., Cho, H.K., Kim, Y.J., Kang, H.M., Lee, M.H., Lee, Y.J., 2018. Novel reassortants of clade 2.3.4.4 H5N6 highly pathogenic avian influenza viruses possessing genetic heterogeneity in South Korea in late 2017. J Vet Sci 19, 850- 854.
115 Kim, Y.I., Si, Y.J., Kwon, H.I., Kim, E.H., Park, S.J., Robles, N.J., Nguyen, H.D., Yu, M.A., Yu, K.M., Lee, Y.J., Lee, M.H., Choi, Y.K., 2018. Pathogenicity and genetic characterisation of a novel reassortant, highly pathogenic avian influenza (HPAI) H5N6 virus isolated in Korea, 2017. Euro Surveill 23, 18- 00045
116 Huson, D.H., Scornavacca, C., 2012. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 61, 1061-1067.
117 Alerstam, T., Backman, J., Gudmundsson, G.A., Hedenstrom, A., Henningsson, S.S., Karlsson, H., Rosen, M., Strandberg, R., 2007. A polar system of intercontinental bird migration. Proc Biol Sci 274, 2523-2530.
118 Boere, G.C., Stroud, D.A., 2006. The flyway concept: what it is and what it isn't. Waterbirds around the World 40-47.
119 Sivay, M.V., Sayfutdinova, S.G., Sharshov, K.A., Alekseev, A.Y., Yurlov, A.K., Runstadler, J., Shestopalov, A.M., 2012. Surveillance of influenza A virus in wild birds in the Asian portion of Russia in 2008. Avian Dis 56, 456-463.
120 Sharshov, K., Sivay, M., Liu, D., Pantin-Jackwood, M., Marchenko, V., Durymanov, A., Alekseev, A., Damdindorj, T., Gao, G.F., Swayne, D.E., Shestopalov, A., 2014. Molecular characterization and phylogenetics of a reassortant H13N8 influenza virus isolated from gulls in Mongolia. Virus Genes 49, 237-249.
121 Lee, D.H., Kwon, J.H., Noh, J.Y., Park, J.K., Yuk, S.S., Erdene-Ochir, T.O., Lee, J.B., Park, S.Y., Choi, I.S., Lee, S.W., Song, C.S., 2016. Pathogenicity of the Korean H5N8 highly pathogenic avian influenza virus in commercial domestic poultry species. Avian Pathol 45, 208-211.
122 Lee, D.H., Bertran, K., Kwon, J.H., Swayne, D.E., 2017. Evolution, global spread, and pathogenicity of highly pathogenic avian influenza H5Nx clade 2.3.4.4. J Vet Sci 18, 269-280.
123 Sun, H., Pu, J., Hu, J., Liu, L., Xu, G., Gao, G.F., Liu, X., Liu, J., 2016. Characterization of clade 2.3.4.4 highly pathogenic H5 avian influenza viruses in ducks and chickens. Vet Microbiol 182, 116-122.
124 Kanehira, K., Uchida, Y., Takemae, N., Hikono, H., Tsunekuni, R., Saito, T., 2015. Characterization of an H5N8 influenza A virus isolated from chickens during an outbreak of severe avian influenza in Japan in April 2014. Arch Virol 160, 1629-1643.
125 Bertran, K., Swayne, D.E., Pantin-Jackwood, M.J., Kapczynski, D.R., Spackman, E., Suarez, D.L., 2016. Lack of chicken adaptation of newly emergent Eurasian H5N8 and reassortant H5N2 high pathogenicity avian influenza viruses in the U.S. is consistent with restricted poultry outbreaks in the Pacific flyway during 2014-2015. Virology 494, 190-197.
126 DeJesus, E., Costa-Hurtado, M., Smith, D., Lee, D.H., Spackman, E., Kapczynski, D.R., Torchetti, M.K., Killian, M.L., Suarez, D.L., Swayne, D.E., Pantin-Jackwood, M.J., 2016. Changes in adaptation of H5N2 highly pathogenic avian influenza H5 clade 2.3.4.4 viruses in chickens and mallards. Virology 499, 52-64.
127 Webster, R.G., Bean, W.J., Gorman, O.T., Chambers, T.M., Kawaoka, Y., 1992. Evolution and ecology of influenza A viruses. Microbiol Rev 56, 152-179.
128 van Gils, J.A., Munster, V.J., Radersma, R., Liefhebber, D., Fouchier, R.A., Klaassen, M., 2007. Hampered foraging and migratory performance in swans infected with low-pathogenic avian influenza A virus. PLoS One 2, e184.
129 Latorre-Margalef, N., Gunnarsson, G., Munster, V.J., Fouchier, R.A., Osterhaus, A.D., Elmberg, J., Olsen, B., Wallensten, A., Haemig, P.D., Fransson, T., Brudin, L., Waldenstrom, J., 2009. Effects of influenza A virus infection on migrating mallard ducks. Proc Biol Sci 276, 1029-1036.
130 Dugan, V.G., Chen, R., Spiro, D.J., Sengamalay, N., Zaborsky, J., Ghedin, E., Nolting, J., Swayne, D.E., Runstadler, J.A., Happ, G.M., Senne, D.A., Wang, R., Slemons, R.D., Holmes, E.C., Taubenberger, J.K., 2008. The evolutionary genetics and emergence of avian influenza viruses in wild birds. PLoS Pathog 4, e1000076.
131 Koehler, A.V., Pearce, J.M., Flint, P.L., Franson, J.C., Ip, H.S., 2008. Genetic evidence of intercontinental movement of avian influenza in a migratory bird: the northern pintail (Anas acuta). Mol Ecol 17, 4754-4762.
132 Wille, M., Robertson, G.J., Whitney, H., Bishop, M.A., Runstadler, J.A., Lang, A.S., 2011. Extensive geographic mosaicism in avian influenza viruses from gulls in the northern hemisphere. PLoS One 6, e20664.
133 Wille, M., Robertson, G.J., Whitney, H., Ojkic, D., Lang, A.S., 2011. Reassortment of American and Eurasian genes in an influenza A virus isolated from a great black-backed gull (Larus marinus), a species demonstrated to move between these regions. Arch Virol 156, 107-115.
134 Hall, J.S., Teslaa, J.L., Nashold, S.W., Halpin, R.A., Stockwell, T., Wentworth, D.E., Dugan, V., Ip, H.S., 2013. Evolution of a reassortant North American gull influenza virus lineage: drift, shift and stability. Virol J 10, 179.
135 Dusek, R.J., Hallgrimsson, G.T., Ip, H.S., Jonsson, J.E., Sreevatsan, S., Nashold, S.W., TeSlaa, J.L., Enomoto, S., Halpin, R.A., Lin, X., Fedorova, N., Stockwell, T.B., Dugan, V.G., Wentworth, D.E., Hall, J.S., 2014. North Atlantic migratory bird flyways provide routes for intercontinental movement of avian influenza viruses. PLoS One 9, e92075.
136 Becker, W.B., 1966. The isolation and classification of Tern virus: influenza A- Tern South Africa--1961. J Hyg 64, 309-320.
137 Morgan, I.R., Kelly, A.P., 1990. Epidemiology of an avian influenza outbreak in Victoria in 1985. Aust Vet J 67, 125-128.
138 Ellis, T.M., Bousfield, R.B., Bissett, L.A., Dyrting, K.C., Luk, G.S., Tsim, S.T., Sturm-Ramirez, K., Webster, R.G., Guan, Y., Malik Peiris, J.S., 2004. Investigation of outbreaks of highly pathogenic H5N1 avian influenza in waterfowl and wild birds in Hong Kong in late 2002. Avian Pathol 33, 492-505.
139 Chen, H., Smith, G.J., Zhang, S.Y., Qin, K., Wang, J., Li, K.S., Webster, R.G., Peiris, J.S., Guan, Y., 2005. Avian flu: H5N1 virus outbreak in migratory waterfowl. Nature 436, 191-192.
140 Lipatov, A.S., Evseenko, V.A., Yen, H.L., Zaykovskaya, A.V., Durimanov, A.G., Zolotykh, S.I., Netesov, S.V., Drozdov, I.G., Onishchenko, G.G., Webster, R.G., Shestopalov, A.M., 2007. Influenza (H5N1) viruses in poultry, Russian Federation, 2005-2006. Emerg Infect Dis 13, 539-546.
141 Kilpatrick, A.M., Chmura, A.A., Gibbons, D.W., Fleischer, R.C., Marra, P.P., Daszak, P., 2006. Predicting the global spread of H5N1 avian influenza. Proc Natl Acad Sci U S A 103, 19368-19373.
142 Ducatez, M.F., Olinger, C.M., Owoade, A.A., Tarnagda, Z., Tahita, M.C., Sow, A., De Landtsheer, S., Ammerlaan, W., Ouedraogo, J.B., Osterhaus, A.D., Fouchier, R.A., Muller, C.P., 2007. Molecular and antigenic evolution and geographical spread of H5N1 highly pathogenic avian influenza viruses in western Africa. J Gen Virol 88, 2297-2306.
143 Zhou, S., Tian, H., Wu, X., Xu, B., Yang, J., Chan, K.K., Huang, S., Dong, L., Brownstein, J., Xu, B., 2016. Genetic evidence for avian influenza H5N1 viral transmission along the Black Sea-Mediterranean Flyway. J Gen Virol 97, 2129- 2134.
144 Li, S., Meng, W., Liu, D., Yang, Q., Chen, L., Dai, Q., Ma, T., Gao, R., Ru, W., Li, Y., Yu, P., Lu, J., Zhang, G., Tian, H., Chai, H., Li, Y., 2018. Migratory whooper swans Cygnus cygnus transmit H5N1 virus between China and Mongolia: combination evidence from satellite tracking and phylogenetics analysis. Sci Rep 8, 7049.
145 Global Consortium for, H.N., Related Influenza, V., 2016. Role for migratory wild birds in the global spread of avian influenza H5N8. Science 354, 213-217.
146 Pasick, J., Berhane, Y., Joseph, T., Bowes, V., Hisanaga, T., Handel, K., Alexandersen, S., 2015. Reassortant highly pathogenic influenza A H5N2 virus containing gene segments related to Eurasian H5N8 in British Columbia, Canada, 2014. Sci Rep 5, 9484.
147 Bevins, S.N., Dusek, R.J., White, C.L., Gidlewski, T., Bodenstein, B., Mansfield, K.G., DeBruyn, P., Kraege, D., Rowan, E., Gillin, C., Thomas, B., Chandler, S., Baroch, J., Schmit, B., Grady, M.J., Miller, R.S., Drew, M.L., Stopak, S., Zscheile, B., Bennett, J., Sengl, J., Brady, C., Ip, H.S., Spackman, E., Killian, M.L., Torchetti, M.K., Sleeman, J.M., Deliberto, T.J., 2016. Widespread detection of highly pathogenic H5 influenza viruses in wild birds from the Pacific flyway of the United States. Sci Rep 6, 28980.
148 Perkins, L.E., Swayne, D.E., 2003. Comparative susceptibility of selected avian and mammalian species to a Hong Kong-origin H5N1 high-pathogenicity avian influenza virus. Avian diseases 47, 956-967.
149 Bodewes, R., Kuiken, T., 2018. Changing role of wild birds in the epidemiology of avian influenza A viruses. Adv Virus Res 100, 279-307.
150 Shibata, A., Hiono, T., Fukuhara, H., Sumiyoshi, R., Ohkawara, A., Matsuno, K., Okamatsu, M., Osaka, H., Sakoda, Y., 2018. Isolation and characterization of avian influenza viruses from raw poultry products illegally imported to Japan by international flight passengers. Transbound Emerg Dis 65, 465-475.
151 Bielejec, F., Baele, G., Vrancken, B., Suchard, M.A., Rambaut, A., Lemey, P., 2016. SpreaD3: interactive visualization of spatiotemporal history and trait evolutionary processes. Mol Biol Evol 33, 2167-2169.
152 Parker, J., Rambaut, A., Pybus, O.G., 2008. Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. Infect Genet Evol 8, 239- 246.
153 World health organization/World organization for animal health/Food and agriculture organization H5N1 Evolution Working Group, 2008. Toward a unified nomenclature system for highly pathogenic avian influenza virus (H5N1). Emerg Infect Dis 14, e1.
154 Olsen, B., Munster, V.J., Wallensten, A., Waldenstrom, J., Osterhaus, A.D., Fouchier, R.A., 2006. Global patterns of influenza a virus in wild birds. Science 312, 384-388.
155 Verhagen, J.H., van der Jeugd, H.P., Nolet, B.A., Slaterus, R., Kharitonov, S.P., de Vries, P.P., Vuong, O., Majoor, F., Kuiken, T., Fouchier, R.A., 2015. Wild bird surveillance around outbreaks of highly pathogenic avian influenza A(H5N8) virus in the Netherlands, 2014, within the context of global flyways. Euro Surveill 20, 21069
156 Lewis, N.S., Verhagen, J.H., Javakhishvili, Z., Russell, C.A., Lexmond, P., Westgeest, K.B., Bestebroer, T.M., Halpin, R.A., Lin, X., Ransier, A., Fedorova, N.B., Stockwell, T.B., Latorre-Margalef, N., Olsen, B., Smith, G., Bahl, J., Wentworth, D.E., Waldenstrom, J., Fouchier, R.A., de Graaf, M., 2015. Influenza A virus evolution and spatio-temporal dynamics in Eurasian wild birds: a phylogenetic and phylogeographical study of whole-genome sequence data. J Gen Virol 96, 2050-2060.
157 Yang, L., Zhu, W., Li, X., Bo, H., Zhang, Y., Zou, S., Gao, R., Dong, J., Zhao, X., Chen, W., Dong, L., Zou, X., Xing, Y., Wang, D., Shu, Y., 2017. Genesis and dissemination of highly pathogenic H5N6 avian influenza viruses. J Virol 91: e02199-16
158 Ip, H.S., Flint, P.L., Franson, J.C., Dusek, R.J., Derksen, D.V., Gill, R.E., Jr., Ely, C.R., Pearce, J.M., Lanctot, R.B., Matsuoka, S.M., Irons, D.B., Fischer, J.B., Oates, R.M., Petersen, M.R., Fondell, T.F., Rocque, D.A., Pedersen, J.C., Rothe, T.C., 2008. Prevalence of influenza A viruses in wild migratory birds in Alaska: patterns of variation in detection at a crossroads of intercontinental flyways. Virol J 5, 71.
159 Shmueli, M., Izhaki, I., Zinder, O., Arad, Z., 2000. The physiological state of captive and migrating Great White Pelicans (Pelecanus onocrotalus) revealed by their blood chemistry. Comp Biochem Physiol A Mol Integr Physiol 125, 25-32.
160 Shittu, I., Meseko, C.A., Gado, D.A., Olawuyi, A.K., Chinyere, C.N., Anefu, E., Solomon, P., Okewole, P.A., Shamaki, D., Joannis, T.M., 2017. Highly pathogenic avian influenza (H5N1) in Nigeria in 2015: evidence of widespread circulation of WA2 clade 2.3.2.1c. Arch Virol 162, 841-847.
161 Selim, A.A., Erfan, A.M., Hagag, N., Zanaty, A., Samir, A.H., Samy, M., Abdelhalim, A., Arafa, A.A., Soliman, M.A., Shaheen, M., Ibraheem, E.M., Mahrous, I., Hassan, M.K., Naguib, M.M., 2017. Highly pathogenic avian influenza virus (H5N8) clade 2.3.4.4 infection in migratory birds, Egypt. Emerg Infect Dis 23, 1048-1051.
162 Twabela, A.T., Tshilenge, G.M., Sakoda, Y., Okamatsu, M., Bushu, E., Kone, P., Wiersma, L., Zamperin, G., Drago, A., Zecchin, B., Monne, I., 2018. Highly pathogenic avian influenza A(H5N8) virus, Democratic Republic of the Congo, 2017. Emerg Infect Dis 24, 1371-1374.
163 Wade, A., Jumbo, S.D., Zecchin, B., Fusaro, A., Taiga, T., Bianco, A., Rodrigue, P.N., Salomoni, A., Kameni, J.M.F., Zamperin, G., Nenkam, R., Foupouapouognigni, Y., Abdoulkadiri, S., Aboubakar, Y., Wiersma, L., Cattoli, G., Monne, I., 2018. Highly pathogenic avian influenza A(H5N8) virus, Cameroon, 2017. Emerg Infect Dis 24, 1367-1370.
164 Mediterranean/ Black Sea Flyway - BirdLife Data Zone (http://datazone.birdlife.org/userfiles/file/sowb/flyways/5_Mediterranean_Black_Sea_Factsheet.pdf) Accessed 5 December 2018.
165 Venkatesh, D., Poen, M.J., Bestebroer, T.M., Scheuer, R.D., Vuong, O., Chkhaidze, M., Machablishvili, A., Mamuchadze, J., Ninua, L., Fedorova, N.B., Halpin, R.A., Lin, X., Ransier, A., Stockwell, T.B., Wentworth, D.E., Kriti, D., Dutta, J., van Bakel, H., Puranik, A., Slomka, M.J., Essen, S., Brown, I.H., Fouchier, R.A.M., Lewis, N.S., 2018. Avian influenza viruses in wild birds: virus evolution in a multihost ecosystem. J Virol 92, e00433-18
166 Tonnessen, R., Hauge, A.G., Hansen, E.F., Rimstad, E., Jonassen, C.M., 2013. Host restrictions of avian influenza viruses: in silico analysis of H13 and H16 specific signatures in the internal proteins. PLoS One 8, e63270.
167 Kawaoka, Y., Gorman, O.T., Ito, T., Wells, K., Donis, R.O., Castrucci, M.R., Donatelli, I., Webster, R.G., 1998. Influence of host species on the evolution of the nonstructural (NS) gene of influenza A viruses. Virus Res 55, 143-156.