Detection and subtyping of influenza A virus based on a short oligonucleotide microarray

Diagnostic Microbiology and Infectious Disease

Volumn 65, Issue 3, 2009, Pages 261-270

  Li, Xihan ^a,b,c   Qi, Xian ^a,b,c,d   Miao, Lv ^a,e   Wang, Yu ^b,c   Liu, Fangzheng ^b,c   Gu, Hongwei ^a,b,c   Lu, Sangwei ^e   Yang, Yonghua ^a   Liu, Fenyong ^e  

^a NANJING UNIVERSITY   (China)

^b Taizhou Affynigen Biotechnologies Inc   (China)

^c Taizhou Institute of Virology   (China)

^d JIANGSU PROVINCIAL CENTER FOR DISEASE CONTROL AND PREVENTION   (China)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Influenza A virus; Microarray; Short oligonucleotide; Subtyping, Diagnostics

Indexed keywords

COMPLEMENTARY DNA; HEMAGGLUTININ; OLIGONUCLEOTIDE; VIRUS SIALIDASE;

ARTICLE; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA MICROARRAY; DNA MODIFICATION; FOWL; GENE AMPLIFICATION; HUMAN; INFLUENZA; INFLUENZA VIRUS A; INFLUENZA VIRUS A H1N1; INFLUENZA VIRUS A H1N2; INFLUENZA VIRUS A H3N2; INFLUENZA VIRUS A H5N1; INFLUENZA VIRUS A H9N2; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SPECIES DIFFERENCE; SWINE; VIRUS CULTURE; VIRUS DETECTION; VIRUS ISOLATION; VIRUS STRAIN;

FLUORESCENCE; HUMANS; INFLUENZA A VIRUS; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA A VIRUS, H1N2 SUBTYPE; INFLUENZA A VIRUS, H3N2 SUBTYPE; INFLUENZA A VIRUS, H5N1 SUBTYPE; INFLUENZA, HUMAN; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; SENSITIVITY AND SPECIFICITY;

EID: 71749113955     PISSN: 07328893     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.diagmicrobio.2009.07.016     Document Type: Article

References (35)

1. Amano Y., and Cheng Q. Detection of influenza virus: traditional approaches and development of biosensors. Anal. Bioanal. Chem. 381 (2005) 156-164
2. Cherkasova E., Laassri M., Chizhikov V., Korotkova E., Dragunsky E., Agol V.I., and Chumakov K. Microarray analysis of evolution of RNA viruses: evidence of circulation of virulent highly divergent vaccine-derived polioviruses. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 9398-9403
3. Chizhikov V., Wagner M., Ivshina A., Hoshino Y., Kapikian A.Z., and Chumakov K. Detection and genotyping of human group A rotaviruses by oligonucleotide microarray hybridization. J. Clin. Microbiol. 40 (2002) 2398-2407
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. DeRisi J., Penland L., Brown P.O., Bittner M.L., Meltzer P.S., Ray M., Chen Y., Su Y.A., and Trent J.M. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet. 14 (1996) 457-460
6. Eklund A.C., Turner L.R., Chen P., Jensen R.V., deFeo G., Kopf-Sill A.R., and Szallasi Z. Replacing cRNA targets with cDNA reduces microarray cross-hybridization. Nat. Biotechnol. 24 (2006) 1071-1073
7. Elnifro E.M., Ashshi A.M., Cooper R.J., and Klapper P.E. Multiplex PCR: optimization and application in diagnostic virology. Clin. Microbiol. Rev. 13 (2000) 559-570
8. 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 (2005) 2814-2822
9. Gall A., Hoffmann B., Harder T., Grund C., Hoper D., and Beer M. Design and validation of a microarray for detection, hemagglutinin subtyping, and pathotyping of avian influenza viruses. J. Clin. Microbiol. 47 (2009) 327-334
10. Hoffmann E., Stech J., Guan Y., Webster R.G., and Perez D.R. Universal primer set for the full-length amplification of all influenza A viruses. Arch. Virol. 146 (2001) 2275-2289
11. Huang Y., Tang H., Duffy S., Hong Y., Norman S., Ghosh M., He J., Bose M., Henrickson K.J., Fan J., Kraft A.J., Weisburg W.G., and Mather E.L. Multiplex assay for simultaneously typing and subtyping influenza viruses by use of an electronic microarray. J. Clin. Microbiol. 47 (2009) 390-396
12. Ivshina A.V., Vodeiko G.M., Kuznetsov V.A., Volokhov D., Taffs R., Chizhikov V.I., Levandowski R.A., and Chumakov K.M. Mapping of genomic segments of influenza B virus strains by an oligonucleotide microarray method. J. Clin. Microbiol. 42 (2004) 5793-5801
13. 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 (2004) 2173-2185
14. Laassri M., Chizhikov V., Mikheev M., Shchelkunov S., and Chumakov K. Detection and discrimination of orthopoxviruses using microarrays of immobilized oligonucleotides. J. Virol. Methods. 112 (2003) 67-78
15. 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 (2006) 1209-1218
16. Margalit O., Somech R., Amariglio N., and Rechavi G. Microarray-based gene expression profiling of hematologic malignancies: basic concepts and clinical applications. Blood. Rev. 19 (2005) 223-234
17. Markoulatos P., Siafakas N., and Moncany M. Multiplex polymerase chain reaction: a practical approach. J. Clin. Lab. Anal. 16 (2002) 47-51
18. Ng L.F., Barr I., Nguyen T., Noor S.M., Tan R.S., Agathe L.V., Gupta S., Khalil H., To T.L., Hassan S.S., and Ren E.C. Specific detection of H5N1 avian influenza A virus in field specimens by a one-step RT-PCR assay. BMC. Infect. Dis. 6 (2006) 40
19. Ong W.T., Omar A.R., Ideris A., and Hassan S.S. Development of a multiplex real-time PCR assay using SYBR Green 1 chemistry for simultaneous detection and subtyping of H9N2 influenza virus type A. J. Virol. Methods. 144 (2007) 57-64
20. Palese P., and Shaw M.L. Orthomyxoviridae: the viruses and their replications. In: Knipe D.M., and Howley P.M. (Eds). Field's Virology (2007), Lippincott Williams & Wilkins, Philadelphia 1647-1690
21. Reid A.H., Taubenberger J.K., and Fanning T.G. Evidence of an absence: the genetic origins of the 1918 pandemic influenza virus. Nat. Rev. Microbiol. 2 (2004) 909-914
22. Sengupta S., Onodera K., Lai A., and Melcher U. Molecular detection and identification of influenza viruses by oligonucleotide microarray hybridization. J. Clin. Microbiol. 41 (2003) 4542-4550
23. Shchepinov M.S., Case-Green S.C., and Southern E.M. Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic. Acids. Res. 25 (1997) 1155-1161
24. Southern E., Mir K., and Shchepinov M. Molecular interactions on microarrays. Nat. Genet. 21 (1999) 5-9
25. 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 (2002) 3256-3260
26. Storch G.A. Essentials of diagnostic virology (2000), Churchill Livingstone, New York
27. Suwannakarn K., Payungporn S., Chieochansin T., Samransamruajkit R., Amonsin A., Songserm T., Chaisingh A., Chamnanpood P., Chutinimitkul S., Theamboonlers A., and Poovorawan Y. Typing (A/B) and subtyping (H1/H3/H5) of influenza A viruses by multiplex real-time RT-PCR assays. J. Virol. Methods. 152 (2008) 25-31
28. Tomioka K., Peredelchuk M., Zhu X., Arena R., Volokhov D., Selvapandiyan A., Stabler K., Mellquist-Riemenschneider J., Chizhikov V., Kaplan G., Nakhasi H., and Duncan R. A multiplex polymerase chain reaction microarray assay to detect bioterror pathogens in blood. J. Mol. Diagn. 7 (2005) 486-494
29. 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 (2006) 2863-2871
30. Vora G.J., Meador C.E., Stenger D.A., and Andreadis J.D. Nucleic acid amplification strategies for DNA microarray-based pathogen detection. Appl. Environ. Microbiol. 70 (2004) 3047-3054
31. Wang D., Coscoy L., Zylberberg M., Avila P.C., Boushey H.A., Ganem D., and DeRisi J.L. Microarray-based detection and genotyping of viral pathogens. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 15687-15692
32. 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
33. Wright P.F., Neumann G., and Kawaoka Y. Orthomyxoviruses. In: Knipe D.M., and Howley P.M. (Eds). Field's Virology (2007), Lippincott Williams & Wilkins, Philadelphia 1691-1740
34. Wu C., Cheng X., He J., Lv X., Wang J., Deng R., Long Q., and Wang X. A multiplex real-time RT-PCR for detection and identification of influenza virus types A and B and subtypes H5 and N1. J. Virol. Methods. 148 (2008) 81-88
35. Zou S. A practical approach to genetic screening for influenza virus variants. J. Clin. Microbiol. 35 (1997) 2623-2627