Rapid haemagglutinin subtyping and pathotyping of avian influenza viruses by a DNA microarray

Journal of Virological Methods

Volumn 160, Issue 1-2, 2009, Pages 200-205

  Gall, Astrid ^a   Hoffmann, Bernd ^a   Harder, Timm ^a   Grund, Christian ^a   Ehricht, Ralf ^b   Beer, Martin ^a  

^a FEDERAL RESEARCH INSTITUTE FOR ANIMAL HEALTH   (Germany)

^b CLONDIAG GmbH   (Germany)

Author keywords

Avian influenza virus; HA0 cleavage site; Haemagglutinin subtype; Microarray; Pathotype

Indexed keywords

ARTICLE; AVIAN INFLUENZA; BIRD; CLOACA; CONTROLLED STUDY; DNA MICROARRAY; FEASIBILITY STUDY; INFLUENZA VIRUS A; INFLUENZA VIRUS A H5N1; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; VIRUS DETECTION; VIRUS DIAGNOSIS; VIRUS HEMAGGLUTINATION; VIRUS ISOLATION; VIRUS STRAIN; VIRUS TYPING;

ANIMALS; BIRDS; HEMAGGLUTININS, VIRAL; INFLUENZA A VIRUS; INFLUENZA A VIRUS, H5N1 SUBTYPE; INFLUENZA IN BIRDS; MICROARRAY ANALYSIS; SENSITIVITY AND SPECIFICITY;

AVES; AVIAN INFLUENZA VIRUS; INFLUENZA A VIRUS;

EID: 67649252920     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2009.05.004     Document Type: Article

References (29)

1. Anon., 2005. Manual of Diagnostic Tests and Vaccines for Terrestrial Animal OIE. Chapter 2.7.12. Avian influenza. http://www.oie.int/eng/normes/mmanual/A_00037.htm.
2. Anon., 2006. Commission decision of 4 August 2006 approving a Diagnostic Manual for Avian Influenza as provided for in Council Directive 2005/94/EC (notified under document number C(2006) 3477) (2006/437/EC). http://eur-lex.europa.eu/LexUriServ/site/en/oj/2006/l_237/l_23720060831e n00010027.pdf.
3. Anon., 2007. Terrestrial Animal Health Code OIE. Chapter 2.7.12. Avian influenza. http://www.oie.int/eng/normes/mcode/en_chapitre_2.7.12.htm.
4. Dawson E.D., Moore C.L., Smagala J.A., Dankbar D.M., Mehlmann M., Townsend M.B., Smith C.B., Cox N.J., Kuchta R.D., and Rowlen K.L. MChip: a tool for influenza surveillance. Anal. Chem. 78 (2006) 7610-7615
5. Fereidouni S.R., Harder T.C., and Starick E. Rapid pathotyping of recent H5N1 highly pathogenic avian influenza viruses and of H5 viruses with low pathogenicity by RT-PCR and restriction enzyme cleavage pattern (RECP). J. Virol. Methods 154 (2008) 14-19
6. Fereidouni S.R., Starick E., Grund C., Globig A., Mettenleiter T.C., Beer M., and Harder T. Rapid molecular subtyping by reverse transcription polymerase chain reaction of the neuraminidase gene of avian influenza A viruses. Vet. Microbiol. 135 (2009) 253-260
7. Fouchier R.A., Munster V., Wallensten A., Bestebroer T.M., Herfst S., Smith D., Rimmelzwaan G.F., Olsen B., and Osterhaus A.D. Characterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black-headed gulls. J. Virol. 79 5 (2005) 2814-2822
8. 0 cleavage sites of all influenza A viruses. J. Clin. Microbiol. 46 8 (2008) 2561-2567
9. Gall A., Hoffmann B., Harder T., Grund C., Höper D., and Beer M. Design and validation of a microarray for detection, hemagglutinin subtyping, and pathotyping of avian influenza viruses. J. Clin. Microbiol. 47 2 (2008) 327-334
10. Globig A., Staubach C., Beer M., Koeppen U., Fiedler W., Nieburg M., Wilking H., Starick E., Teifke J.P., Werner O., Unger F., Grund C., Wolf C., Roost H., Feldhusen F., Conraths F.J., Mettenleiter T.C., and Harder T.C. Epidemiological and ornithological aspects of outbreaks of highly pathogenic avian influenza virus H5N1 of Asian lineage in wild birds in Germany, 2006 and 2007. Transboundary Emerg. Dis. 56 (2009) 57-72
11. Han X., Lin X., Liu B., Hou Y., Huang J., Wu S., Liu J., Mei L., Jia G., and Zhu Q. Simultaneously subtyping of all influenza A viruses using DNA microarrays. J. Virol. Methods 152 (2008) 117-121
12. Höper D., Hoffmann B., and Beer M. Simple, sensitive, and swift sequencing of complete avian influenza H5N1 genomes. J. Clin. Microbiol. 47 3 (2009) 674-679
13. Hoffmann B., Depner K., Schirrmeier H., and Beer M. A universal heterologous internal control system for duplex real-time RT-PCR assays used in a detection system for pestiviruses. J. Virol. Methods 136 (2006) 200-209
14. Hoffmann B., Harder T., Starick E., Depner K., Werner O., and Beer M. Rapid and highly sensitive pathotyping of avian influenza A H5N1 virus by using real-time reverse transcription-PCR. J. Clin. Microbiol. 45 (2007) 600-603
15. Kessler N., Ferraris O., Palmer K., Marsh W., and Steel A. Use of the DNA flow-thru chip, a three-dimensional biochip, for typing and subtyping of influenza viruses. J. Clin. Microbiol. 42 5 (2004) 2173-2185
16. Li H., McCormac M.A., Estes R.W., Sefers S.E., Dare R.K., Chappell J.D., Erdman D.D., Wright P.F., and Tang Y.-W. Simultaneous detection and high-throughput identification of a panel of RNA viruses causing respiratory tract infections. J. Clin. Microbiol. 45 7 (2007) 2105-2109
17. Lin B., Blaney K.M., Malanoski A.P., Ligler A.G., Schnur J.M., Metzgar D., Russell K.L., and Stenger D.A. Using a resequencing microarray as a multiple respiratory pathogen detection assay. J. Clin. Microbiol. 45 2 (2007) 443-452
18. Liu R.H., Lodes M.J., Nguyen T., Siuda T., Slota M., Fuji H.S., and McShea A. Validation of a fully integrated microfluidic array device for influenza A subtype identification and sequencing. Anal. Chem. 78 (2006) 4184-4193
19. Lodes M.J., Suciu D., Elliott M., Stover A.G., Ross M., Caraballo M., Dix K., Crye J., Webby R.J., Lyon W.J., Danley D.L., and McShea A. Use of semiconductor-based oligonucleotide microarrays for influenza A virus subtype identification and sequencing. J. Clin. Microbiol. 44 4 (2006) 1209-1218
20. Monecke S., and Ehricht B. Rapid genotyping of methicillin-resistant Staphylococcus aureus (MRSA) isolates using miniaturised oligonuclotide arrays. Clin. Microbiol. Infect. 11 (2005) 825-833
21. Phipps L.P., Essen S.C., and Brown I.H. Genetic subtyping of influenza A viruses using RT-PCR with a single set of primers based on conserved sequences within the HA2 coding region. J. Virol. Methods 122 (2004) 119-122
22. Quan P.-L., Palacios G., Jabado O.J., Conlan S., Hirschberg D.L., Pozo F., Jack P.J.M., Cisterna D., Renwick N., Hui J., Drysdale A., Amos-Ritchie R., Baumeister E., Savy V., Lager K.M., Richt J.A., Boyle D.B., Garcia-Sastre A., Casas I., Perez-Brena P., Briese T., and Lipkin W.I. Detection of respiratory viruses and subtype identification of influenza A viruses by GreeneChipResp oligonucleotide microarray. J. Clin. Microbiol. 45 8 (2007) 2359-2364
23. Sengupta S., Onodera K., Lai A., and Melcher U. Molecular detection and identification of influenza viruses by oligonucleotide microarray hybridization. J. Clin. Microbiol. 41 10 (2003) 4542-4550
24. Spackman E., Senne D.A., Myers T.J., Bulaga L.L., Garber L.P., Perdue M.L., Lohman K., Daum L.T., and Suarez D.L. Development of a real-time reverse transcriptase PCR assay for type A influenza virus and the avian H5 and H7 hemagglutinin subtypes. J. Clin. Microbiol. 40 9 (2002) 3256-3260
25. Starick E., Beer M., Hoffmann B., Staubach C., Werner O., Globig A., Strebelow G., Grund C., Durban M., Conraths F.J., Mettenleiter T., and Harder T. Phylogenetic analyses of highly pathogenic avian influenza virus isolates from Germany in 2006 and 2007 suggest at least three separate introductions of H5N1 virus. Vet. Microbiol. 128 (2008) 243-252
26. Townsend M.B., Dawson E.D., Mehlmann M., Smagala J.A., Dankbar D.M., Moore C.L., Smith C.B., Cox N.J., Kuchta R.D., and Rowlen K.L. Experimental evaluation of the FluChip diagnostic microarray for influenza virus surveillance. J. Clin. Microbiol. 44 8 (2006) 2863-2871
27. Vijaykrishna D., Bahl J., Riley S., Duan L., Zhang J.X., Chen H., Peiris M., Smith G., and Guan Y. Evolutionary dynamics and emergence of panzootic H5N1 influenza viruses. PlosPathog g4 9 (2008) e1000161 10.1371/journal.ppat.1000161
28. Wang L.-C., Pan C.-H., Severinghaus L.L., Liu L.-Y., Chen C.-T., Pu C.-E., Huang D., Lir J.-T., Chin S.-C., Cheng M.-C., Lee S.-H., and Wang C.-H. Simultaneous detection and differentiation of Newcastle disease and avian influenza viruses using oligonucleotide microarrays. Vet. Microbiol. 127 (2008) 217-226
29. Wood G.W., McCauley J.W., Bashruddin J.B., and Alexander D.J. Deduced amino acid sequences at the haemagglutinin cleavage site of avian influenza A viruses of H5 and H7 subtypes. Arch. Virol. 130 (1993) 209-217