Digital genotyping of avian influenza viruses of H7 subtype detected in central Europe in 2007-2011

Virus Research

Volumn 165, Issue 2, 2012, Pages 126-133

  Nagy, Alexander ^a   Černíková, Lenka ^a   Křivda, Vlastimil ^a   Horníčková, Jitka ^a  

^a Statni veterinarni ustav Praha   (Czech Republic)

Author keywords

Digital genotyping; Genotyping; H7N7; H7N9; Influenza; LPAI

Indexed keywords

ARTICLE; AVIAN INFLUENZA VIRUS; CZECH REPUBLIC; DIGITAL IMAGING; EUROPE; GENETIC ANALYSIS; GENOTYPE; HUNGARY; INFLUENZA VIRUS A; INFLUENZA VIRUS A H7N7; INFLUENZA VIRUS A H7N9; NONHUMAN; PHYLOGENY; POLAND; PRIORITY JOURNAL; SLOVENIA; SPAIN; VIRUS DETECTION; VIRUS GENOME;

ANIMALS; BIRDS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; EUROPE; GENOTYPE; INFLUENZA A VIRUS; INFLUENZA IN BIRDS; MOLECULAR EPIDEMIOLOGY; MOLECULAR SEQUENCE DATA; MOLECULAR TYPING; PHYLOGENY; SEQUENCE ANALYSIS, DNA; VIROLOGY;

AVIAN INFLUENZA VIRUS; INFLUENZA A VIRUS;

EID: 84859442052     PISSN: 01681702     EISSN: 18727492     Source Type: Journal    
DOI: 10.1016/j.virusres.2012.02.005     Document Type: Article

References (37)

1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
2. 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. 2010, 91:960-970.
3. Busquets N., Alba A., Napp S., Sanchez A., Serrano E., Rivas R., Nunez J.I., Majo N. Influenza A virus subtypes in wild birds in North-Eastern Spain (Catalonia). Virus Res. 2010, 149:10-18.
4. Campitelli L., Di Martino A., Spagnolo D., Smith G.J.D., Di Trani L., Facchini M., De Marco M.A., Foni E., Chiapponi Martin A.M., Chen H., Guan Y., Delogu M., Donatelli I. Molecular analysis of avian H7 influenza viruses circulating in Eurasia in 1999-2005: detection of multiple reassortant virus genotypes. J. Gen. Virol. 2008, 89:48-59.
5. Capua I., Alexander D.J. Avian influenza: recent developments. Avian Pathol. 2004, 33:393-404.
6. Cecchinato M., Ceolin C., Busani L., Dalla Poza M., Terregino C., Moreno A., Bonfanti L., Marangon S. Low pathogenicity avian influenza in Italy during 2007 and 2008: epidemiology and control. Avian Dis. 2010, 54:323-328.
7. Community Reference Laboratory for Avian Influenza Annual Report on Surveillance for Avian Influenza in Wild Birds in the EU in 2008 2008, Veterinary Laboratory Agency, Weybridge, UK.
8. Community Reference Laboratory for Avian Influenza Annual Report on Surveillance for Avian Influenza in Wild Birds in the EU in 2008 2009, Veterinary Laboratory Agency, Weybridge, UK.
9. Diagnostic Manual for Avian Influenza, 2006. Accessible through: with methods accessible through: http://www.defra.gov.uk/vla/science/sci_ai_reflab_prot.htm.
10. Dugan V.G., Chen R., Spiro D.J., Sengamalay N., Zaborsky J., Ghedin E., Nolting J., Runstadler Swayne D.E., Happ J.A., Senne G.M., Wang D.A., Slemons R.R.D., Holmes E.C., Taubenberger J.K. The evolutionary genetics and emergence of avian influenza viruses in wild birds. PLoS Pathog. 2008, 4:1-9.
11. Felsenstein J. PHYLIP (Phylogeny Inference Package) Version 3.6. Distributed by the Author 2004, Department of Genome Sciences, University of Washington, Seattle, Accessible through: http://evolution.genetics.washington.edu/phylip.html.
12. Fereidouni S.R., Starick E., Grund C., Globig A., Mettenleiter T.C., Beer M., Harder T. Rapid molecular subtyping by reverse transcription polymerase chain reaction of the neuraminidase gene of avian influenza A viruses. Vet. Microbiol. 2009, 135:253-260.
13. GISAID, Global Initiative of Sharing Avian Influenza Data, 2011. Accessible through: http://platform.gisaid.org/dante-cms/struktur.jdante?aid=1131.
14. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, vol. 41 1999, 95-98. Available through: http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html.
15. Halvorson D.A. Prevention and management of avian influenza outbreaks: experiences from the United States of America. Rev. Sci. Tech. Off. Int. Epiz. 2009, 28:359-369.
16. Hatchette T.F., Walker D., Johnson Ch Baker A., Pryor P.S., Webster R.G. Influenza A viruses in feral Canadian ducks: extensive reassortment in nature. J. Gen. Virol. 2004, 85:2327-2337.
17. Hoffmann E., Stech J., Guan Y., Webster R.G., Perez D.R. Universal primer set for the full-length amplification of all influenza A viruses. Arch. Virol. 2001, 146:2275-2289.
18. Bao Y., Bolotov P., Dernovoy D., Kiryutin B., Zaslavsky L., Tatusova T., Ostell J., Lipman D. The influenza virus resource at the National Center for Biotechnology Information. J. Virol. 2008, 82:596-601. IVSD, Influenza virus sequence database, Accessible through: http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html.
19. Katoh K., Misawa K., Kuma K., Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acid Res. 2002, 30:3059-3066. Accessible through: http://align.bmr.kyushu-u.ac.jp/mafft/online/server/.
20. Li K.S., Guan Y., Wang J., Smith G.J.D., Xu K.M., Duan L., Rahardjo A.P., Puthavathana P., Buranathai C., Nguyen T.D., Estoepangestie A.T.S., Chaisingh A., Auewarakul P., Long H.T., Hanh N.T.H., Webby R.J., Poon L.L.M., Chen H., Shortridge K.F., Yuen K.Y., webster R.G., Pieris J.S.M. Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia. Nature 2004, 430:209-213.
21. Li O.T.W., Barr I., Leung C.Y.H., Chen H., Guan Y., Peiris J.S.M., Poon L.L.M. Reliable universal RT-PCR assays for studying influenza polymerase subunit gene sequences from all 16 haemagglutinin subtypes. J. Virol. Methods 2007, 142:218-222.
22. Macken K., Webby R.J., Bruno W.J. Genotype turnover by reassortment of replication complex genes from avian influenza A virus. J. Gen. Virol. 2006, 87:2803-2815.
23. Munster V.J., Baas Ch Lexmond P., Waldemstrom J., Wallensten A., Fransson T., Rimmelzwaan G.F., Beyer W.E.P., Schutten M., Olsen B., Osterhaus A.D.M.E., Fouchier R.A.M. Spatial, temporal, and species variation in prevalence of influenza A viruses in wild migratory birds. PLOS Pathog. 2007, 3:630-638.
24. Munster V.J., Wallensten A., Baas Ch Rimmelzwaan G.F., Schutten M., Olsen B., Osterhaus A.D.M.E., Fouchier R.A.M. Mallards and highly pathogenic avian influenza ancestral viruses, Northern Europe. Emerg. Infect. Dis. 2005, 11:1545-1551.
25. Nagy A., Vostinakova V., Pirchanova Z., Cernikova L., Dirbakova Z., Mojzis M., Jirincova H., Havlickova M., Dan A., Ursu K., Vilcek S., Hornickova J. Development and evaluation of one step real-time RT-PCR assay for universal detection of influenza A viruses from avian and mammal species. Arch. Virol. 2010, 155:665-673.
26. Olsen B., Munster V.J., Wallensten A., Waldenström J., Osterhaus A.D.M.E., Fouchier R.A.M. Global patterns of influenza A virus in wild birds. Science 2006, 312:384-388.
27. Perez-Ramirez E., Gerrikagoitia X., Barral M., Hofle U. Detection of low pathogenic avian influenza viruses in wild birds in Castilla-La Mancha (south central Spain). Vet. Microbiol. 2010, 146:200-208.
28. Smietanka K., Pikuła A., Minta Z., Meissner W. Evidence of persistence and multiple genetic modifications of H7N7 low-pathogenic avian influenza virus in wild mallards in Poland provided by phylogenetic studies. Avian Pathol. 2011, 40:131-138.
29. Swayne D.E. Epidemiology of avian influenza in agricultural and other man-made systems. Avian Influenza 2008, 65. Blackwell Publishing Ltd., Oxford, UK. D.E. Swayne (Ed.).
30. Szeleczky Z., Bálint A., Gyarmati P., Metreveli G., Dán A., Ursu K., Belák S., Lomniczi B., Kiss I. Characterization of two low pathogenic avian influenza viruses isolated in Hungary in 2007. Vet. Microbiol. 2010, 28:142-147.
31. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
32. Terregino C., De Nardi R., Guberti V., Scremin V., Raffini E., Martin A.M., Cattoli G., Bonfanti L., Capua I. Active surveillance for avian influenza viruses in wild birds and backyard flaks in Northern Italy during 2004 to 2006. Avian Pathol. 2007, 36:337-344.
33. WAHID, World Animal Health Information Database Low Pathogenic Avian Influenza (Poultry), United States of America 2007, Accessible through: http://www.oie.int/wahis/public.php?page=event_summary&reportid=5776.
34. WAHID, World Animal Health Information Database Low Pathogenic Avian Influenza (Poultry), United States of America 2009, Accessible through: http://www.oie.int/wahis/public.php?page=event_summary&reportid=8346.
35. Wallensten A., Munster V.J., Latorre-Margalef N., Brytting M., Elmberg J., Fouchier R.A.M., Fransson T., Haemig P.D., Karlsson M., Lundkvist A., Osterhaus A.D.M.E., Stervander M., Waldenstrom J., Olsen B. Surveillance of influenza A virus in migratory waterfowl in Northern Europe. Emerg. Infect. Dis. 2007, 13:404-411.
36. Webster R.G., Bean W.J., Gorman O.T., Chambers T.M., Kawaoka Y. Evolution and ecology of influenza A viruses. Microbiol. Rev. 1992, 56:152-179.
37. Xu K.M., Smith G.J.D., Bahl J., Duan L., Tai H., Vijaykrishna D., Wang J., Zhang J.X., Li K.S., Fan X.H., Webster R.G., Chen H., Pieris J.S.M., Guan Y. The genesis and evolution of H9N2 influenza viruses in poultry from Southern China, 2000 to 2005. J. Virol. 2007, 81:10389-10401.