Emergence and multiple reassortments of French 2015–2016 highly pathogenic H5 avian influenza viruses

Infection, Genetics and Evolution

Volumn 61, Issue , 2018, Pages 208-214

  Briand, F X ^a   Niqueux, E ^a   Schmitz, A ^a   Hirchaud, E ^a   Quenault, H ^a   Allee C ^a   Le Prioux, A ^a   Guillou Cloarec, C ^a   Ogor, K ^a   Le Bras, M O ^a   Gares, H ^b   Daniel, P ^c   Fediaevsky, A ^d   Martenot, C ^a   Massin, P ^a   Le Bouquin, S ^a   Blanchard, Y ^a   Eterradossi, N ^a  

^a FRENCH AGENCY FOR FOOD   (France)

^b Laboratoire Départemental d'Analyses et de Recherche   (France)

^c Laboratoire des Pyrénées et des Landes   (France)

^d l'Environnement et des Ressources Hy   (France)

Author keywords

Avian influenza; Emerging; Hemagglutinin; Reassortment; Viruses

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE SEQUENCE; GENETIC REASSORTMENT; GENOTYPE; H5 GENE; HIGHLY PATHOGENIC AVIAN INFLUENZA VIRUS; HIGHLY PATHOGENIC AVIAN INFLUENZA VIRUS (H5N1); HIGHLY PATHOGENIC AVIAN INFLUENZA VIRUS (H5N2); HIGHLY PATHOGENIC AVIAN INFLUENZA VIRUS (H5N9); MOLECULAR CLOCK; N1 GENE; N2 GENE; N9 GENE; NEXT GENERATION SEQUENCING; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; VIRUS GENE; VIRUS ISOLATION; ZYGOTE; ANIMAL; AVIAN INFLUENZA; BIRD DISEASE; FRANCE; GENETICS; INFLUENZA A VIRUS (H5N1); INFLUENZA A VIRUS (H5N2); PATHOGENICITY; POULTRY; VIROLOGY;

HEMAGGLUTININ, AVIAN INFLUENZA A VIRUS; INFLUENZA VIRUS HEMAGGLUTININ; SIALIDASE; VIRAL PROTEIN;

ANIMALS; FRANCE; HEMAGGLUTININ GLYCOPROTEINS, INFLUENZA VIRUS; INFLUENZA A VIRUS, H5N1 SUBTYPE; INFLUENZA A VIRUS, H5N2 SUBTYPE; INFLUENZA IN BIRDS; NEURAMINIDASE; PHYLOGENY; POULTRY; POULTRY DISEASES; REASSORTANT VIRUSES; VIRAL PROTEINS;

EID: 85045472441     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2018.04.007     Document Type: Article

References (35)

1. Arafa, A., El-Masry, I., Kholosy, S., Hassan, M.K., Dauphin, G., Lubroth, J., Makonnen, Y.J., Phylodynamics of avian influenza clade 2.2.1 H5N1 viruses in Egypt. Virol. J., 13, 2016, 49.
2. Barton, H.D., Rohani, P., Stallknecht, D.E., Brown, J., Drake, J.M., Subtype diversity and reassortment potential for co-circulating avian influenza viruses at a diversity hot spot. J. Anim. Ecol. 83 (2014), 566–575.
3. Briand, F.X., Le Gall-Recule, G., Guillou-Cloarec, C., Ogor, K., Jestin, V., Phylogeny and genotyping of recent avian low-pathogenic H5 subtype influenza viruses from French ducks. J. Gen. Virol. 91 (2010), 960–970.
4. Briand, F.X., Niqueux, E., Brochet, A.L., Hars, J., Jestin, V., Unusual H5N2 avian influenza virus escapes current detection. J. Clin. Microbiol. 49 (2011), 2376–2377.
5. Briand, F.X., Guillou-Cloarec, C., Schmitz, A., Niqueux, E., Scoizec, A., Le Bouquin-Leneveu, S., Banses, X., Corrand, L., Pinsard, J., Faurez, F., Eterradossi, N., 2017a. Détection a posteriori de virus H5 hautement pathogènes dans des élevages de canards avant le premier cas déclaré de l'épizootie de l'hiver 2015–2016, XIXes Journées Francophones de Virologie. Virologie, Paris, (P62, 107).
6. Briand, F.X., Schmitz, A., Ogor, K., Le Prioux, A., Guillou-Cloarec, C., Guillemoto, C., Allee, C., Le Bras, M.O., Hirchaud, E., Quenault, H., Touzain, F., Cherbonnel-Pansart, M., Lemaitre, E., Courtillon, C., Gares, H., Daniel, P., Fediaevsky, A., Massin, P., Blanchard, Y., Eterradossi, N., van der Werf, S., Jestin, V., Niqueux, E., Emerging highly pathogenic H5 avian influenza viruses in France during winter 2015/16: phylogenetic analyses and markers for zoonotic potential. Euro Surveill, 22, 2017.
7. Capua, I., Marangon, S., The avian influenza epidemic in Italy, 1999–2000: a review. Avian Pathol. 29 (2000), 289–294.
8. Capua, I., Marangon, S., Selli, L., Alexander, D.J., Swayne, D.E., Pozza, M.D., Parenti, E., Cancellotti, F.M., Outbreaks of highly pathogenic avian influenza (H5N2) in Italy during October 1997 to January 1998. Avian Pathol. 28 (1999), 455–460.
9. Chen, H., H5N1 avian influenza in China. Sci. China C Life Sci. 52 (2009), 419–427.
10. Commission, E, COUNCIL DIRECTIVE 2005/94/EC COUNCIL DIRECTIVE 2005/94/EC on community measures for the control of avian influenza and repealing Directive 92/40/EEC. Official Journal of the European Union, 2005, 10–65 https://www.agriculture.gov.ie/media/migration/animalhealthwelfare/diseasecontrols/avianinfluenzabirdflu/legislation/2005_94directive.pdf.
11. Drummond, A.J., Suchard, M.A., Xie, D., Rambaut, A., Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29 (2012), 1969–1973.
12. Elbers, A.R., Kamps, B., Koch, G., Performance of gross lesions at postmortem for the detection of outbreaks during the avian influenza A virus (H7N7) epidemic in the Netherlands in 2003. Avian Pathol. 33 (2004), 418–422.
13. Fu, Y., Zhang, Z., Sheehan, J., Avnir, Y., Ridenour, C., Sachnik, T., Sun, J., Hossain, M.J., Chen, L.M., Zhu, Q., Donis, R.O., Marasco, W.A., A broadly neutralizing anti-influenza antibody reveals ongoing capacity of haemagglutinin-specific memory B cells to evolve. Nat. Commun., 7, 2016, 12780.
14. Guan, Y., Peiris, J.S., Lipatov, A.S., Ellis, T.M., Dyrting, K.C., Krauss, S., Zhang, L.J., Webster, R.G., Shortridge, K.F., Emergence of multiple genotypes of H5N1 avian influenza viruses in Hong Kong SAR. Proc. Natl. Acad. Sci. U. S. A. 99 (2002), 8950–8955.
15. ICTV, Virus Taxonomy: 2017 Release. https://talk.ictvonline.org/taxonomy/, 2017.
16. Kawaoka, Y., Krauss, S., Webster, R.G., Avian-to-human transmission of the PB1 gene of influenza a viruses in the 1957 and 1968 pandemics. J. Virol. 63 (1989), 4603–4608.
17. Kumar, S., Tamura, K., Nei, M., MEGA: molecular evolutionary genetics analysis software for microcomputers. Comput. Appl. Biosci. 10 (1994), 189–191.
18. Lee, C.C., Zhu, H., Huang, P.Y., Peng, L., Chang, Y.C., Yip, C.H., Li, Y.T., Cheung, C.L., Compans, R., Yang, C., Smith, D.K., Lam, T.T., King, C.C., Guan, Y., Emergence and evolution of avian H5N2 influenza viruses in chickens in Taiwan. J. Virol. 88 (2014), 5677–5686.
19. Lee, D.H., Bertran, K., Kwon, J.H., Swayne, D.E., Evolution, global spread, and pathogenicity of highly pathogenic avian influenza H5Nx clade 2.3.4.4. J. Vet. Sci. 18 (2017), 269–280.
20. Lu, L., Lycett, S.J., Leigh Brown, A.J., Reassortment patterns of avian influenza virus internal segments among different subtypes. BMC Evol. Biol., 14, 2014, 16.
21. Marinova-Petkova, A., Georgiev, G., Petkov, T., Darnell, D., Franks, J., Kayali, G., Walker, D., Seiler, P., Danner, A., Graham, A., McKenzie, P., Krauss, S., Webby, R.J., Webster, R.G., Influenza surveillance on ‘foie gras’ duck farms in Bulgaria, 2008-2012. Influenza Other Respir. Viruses 10 (2016), 98–108.
22. Monne, I., Fusaro, A., Nelson, M.I., Bonfanti, L., Mulatti, P., Hughes, J., Murcia, P.R., Schivo, A., Valastro, V., Moreno, A., Holmes, E.C., Cattoli, G., Emergence of a highly pathogenic avian influenza virus from a low-pathogenic progenitor. J. Virol. 88 (2014), 4375–4388.
23. Nagarajan, N., Kingsford, C., GiRaF: robust, computational identification of influenza reassortments via graph mining. Nucleic Acids Res., 39, 2011, e34.
24. Niqueux, E., H5 HPAI Outbreaks in Poultry in France: Update on the Current Situation. https://ec.europa.eu/food/sites/food/files/animals/docs/ad_cm_20160419_22nd-annual-meetings-pres4.pdf, 2016.
25. Olsen, B., Munster, V.J., Wallensten, A., Waldenstrom, J., Osterhaus, A.D., Fouchier, R.A., Global patterns of influenza a virus in wild birds. Science 312 (2006), 384–388.
26. Pabbaraju, K., Tellier, R., Wong, S., Li, Y., Bastien, N., Tang, J.W., Drews, S.J., Jang, Y., Davis, C.T., Fonseca, K., Tipples, G.A., Full-genome analysis of avian influenza a(H5N1) virus from a human, North America, 2013. Emerg. Infect. Dis. 20 (2014), 887–891.
27. Pantin-Jackwood, M.J., Swayne, D.E., Pathogenesis and pathobiology of avian influenza virus infection in birds. Rev. Sci. Tech. 28 (2009), 113–136.
28. Pulit-Penaloza, J.A., Sun, X., Creager, H.M., Zeng, H., Belser, J.A., Maines, T.R., Tumpey, T.M., Pathogenesis and transmission of novel highly pathogenic avian influenza H5N2 and H5N8 viruses in ferrets and mice. J. Virol. 89 (2015), 10286–10293.
29. Qi, W., Jia, W., Liu, D., Li, J., Bi, Y., Xie, S., Li, B., Hu, T., Du, Y., Xing, L., Zhang, J., Zhang, F., Wei, X., Eden, J.S., Li, H., Tian, H., Li, W., Su, G., Lao, G., Xu, C., Xu, B., Liu, W., Zhang, G., Ren, T., Holmes, E.C., Cui, J., Shi, W., Gao, G.F., Liao, M., Emergence and adaptation of a novel highly pathogenic H7N9 influenza virus in birds and humans from a 2013-human-infecting low pathogenic ancestor. J. Virol., 92, 2018 (e000921-17).
30. Ramey, A.M., Pearce, J.M., Ely, C.R., Guy, L.M., Irons, D.B., Derksen, D.V., Ip, H.S., Transmission and reassortment of avian influenza viruses at the Asian-North American interface. Virology 406 (2010), 352–359.
31. Scoizec, A., Huneau, A., Schmitz, A., Briand, F.X., Hamon, M., Bronner, A., Niqueux, E., Le Bouquin, S., Caractérisations des foyers français d'Influenza aviaire hautement pathogènes de l'hiver 2015–2016 : analyse des données issues des enquêtes épidémiologiques. E-book JRA-JRPFG, 2017.
32. Shapiro, B., Rambaut, A., Drummond, A.J., Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol. Biol. Evol. 23 (2006), 7–9.
33. Siddique, N., Naeem, K., Abbas, M.A., Ahmed, Z., Malik, S.A., Sequence and phylogenetic analysis of highly pathogenic avian influenza H5N1 viruses isolated during 2006-2008 outbreaks in Pakistan reveals genetic diversity. Virol. J., 9, 2012, 300.
34. Thompson, J.D., Higgins, D.G., Gibson, T.J., CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994), 4673–4680.
35. Webster, R.G., Bean, W.J., Gorman, O.T., Chambers, T.M., Kawaoka, Y., Evolution and ecology of influenza a viruses. Microbiol. Rev. 56 (1992), 152–179.