Multiplexed, rapid detection of H5N1 using a PCR-free nanoparticle-based genomic microarray assay

BMC Biotechnology

Volumn 10, Issue , 2010, Pages

  Zhao, Jiangqin ^a   Tang, Shixing ^a   Storhoff, James ^b   Marla, Sudhakar ^b   Bao, Y Paul ^b   Wang, Xue ^a   Wong, Eric Y ^a   Ragupathy, Viswanath ^a   Ye, Zhiping ^a   Hewlett, Indira K ^a  

^a CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

^b Nanosphere Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AVIAN INFLUENZA; CONSENSUS SEQUENCE; DIAGNOSTIC APPLICATIONS; ENZYMATIC REACTION; GOLD NANOPARTICLES; INFLUENZA A VIRUS; LOWER LIMIT OF DETECTIONS; MATRIX; NEURAMINIDASE; OLIGONUCLEOTIDE HYBRIDIZATION; PCR-FREE; RAPID DETECTION; SILVER STAINING; SIMULTANEOUS DETECTION; SUBTYPINGS; VIRAL RNA;

GENES; NANOPARTICLES; OLIGONUCLEOTIDES; REACTION INTERMEDIATES; RNA; VIRUSES;

COMPUTER VIRUSES;

GOLD NANOPARTICLE; HEMAGGLUTININ; OLIGONUCLEOTIDE; SIALIDASE; VIRUS RNA; NANOPARTICLE;

ARTICLE; DNA MICROARRAY; INFLUENZA VIRUS A H1N1; INFLUENZA VIRUS A H3N2; INFLUENZA VIRUS A H5N1; NONHUMAN; NUCLEOTIDE SEQUENCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; VIRUS DETECTION; VIRUS GENE; VIRUS TYPING; CLASSIFICATION; ISOLATION AND PURIFICATION; METHODOLOGY; OLIGONUCLEOTIDE PROBE;

AVIAN INFLUENZA VIRUS; INFLUENZA A VIRUS;

INFLUENZA A VIRUS, H5N1 SUBTYPE; NANOPARTICLES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; SENSITIVITY AND SPECIFICITY;

EID: 77957745711     PISSN: None     EISSN: 14726750     Source Type: Journal    
DOI: 10.1186/1472-6750-10-74     Document Type: Article

References (40)

1. Ng EK, Cheng PK, Ng AY, Hoang TL, Lim WW. Influenza A H5N1 detection. Emerg Infect Dis 2005, 11(8):1303-1305.
2. Sengupta S, Onodera K, Lai A, Melcher U. Molecular detection and identification of influenza viruses by oligonucleotide microarray hybridization. J Clin Microbiol 2003, 41(10):4542-4550. 10.1128/JCM.41.10.4542-4550.2003, 254299, 14532180.
3. Fouchier RA, Munster V, Wallensten A, Bestebroer TM, Herfst S, Smith D, Rimmelzwaan GF, Olsen B, Osterhaus AD. Characterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black-headed gulls. J Virol 2005, 79(5):2814-2822. 10.1128/JVI.79.5.2814-2822.2005, 548452, 15709000.
4. Krauss S, Walker D, Pryor SP, Niles L, Chenghong L, Hinshaw VS, Webster RG. Influenza A viruses of migrating wild aquatic birds in North America. Vector Borne Zoonotic Dis 2004, 4(3):177-189. 10.1089/vbz.2004.4.177, 15631061.
5. Webster RG, Bean WJ, Gorman OT, Chambers TM, Kawaoka Y. Evolution and ecology of influenza A viruses. Microbiol Rev 1992, 56(1):152-179. 372859, 1579108.
6. Kerr JR. Swine influenza. J Clin Pathol 2009, 62(7):577-578. 10.1136/jcp.2009.067710, 19433408.
7. Scholtissek C, Burger H, Kistner O, Shortridge KF. The nucleoprotein as a possible major factor in determining host specificity of influenza H3N2 viruses. Virology 1985, 147(2):287-294. 10.1016/0042-6822(85)90131-X, 2416114.
8. Stevens J, Blixt O, Paulson JC, Wilson IA. Glycan microarray technologies: tools to survey host specificity of influenza viruses. Nat Rev Microbiol 2006, 4(11):857-864. 10.1038/nrmicro1530, 17013397.
9. Herrmann B, Larsson C, Zweygberg BW. Simultaneous detection and typing of influenza viruses A and B by a nested reverse transcription-PCR: comparison to virus isolation and antigen detection by immunofluorescence and optical immunoassay (FLU OIA). J Clin Microbiol 2001, 39(1):134-138. 10.1128/JCM.39.1.134-138.2001, 87692, 11136761.
10. Leonardi GP, Leib H, Birkhead GS, Smith C, Costello P, Conron W. Comparison of rapid detection methods for influenza A virus and their value in health-care management of institutionalized geriatric patients. J Clin Microbiol 1994, 32(1):70-74. 262972, 8126207.
11. Liolios L, Jenney A, Spelman D, Kotsimbos T, Catton M, Wesselingh S. Comparison of a multiplex reverse transcription-PCR-enzyme hybridization assay with conventional viral culture and immunofluorescence techniques for the detection of seven viral respiratory pathogens. J Clin Microbiol 2001, 39(8):2779-2783. 10.1128/JCM.39.8.2779-2783.2001, 88238, 11473991.
12. Jindal N, Chander Y, de Abin M, Sreevatsan S, Stallknecht D, Halvorson DA, Goyal SM. Amplification of four genes of influenza A viruses using a degenerate primer set in a one step RT-PCR method. J Virol Methods 2009, 160(1-2):163-166. 10.1016/j.jviromet.2009.05.003, 19447141.
13. Fouchier RA, Bestebroer TM, Herfst S, Van Der Kemp L, Rimmelzwaan GF, Osterhaus AD. Detection of influenza A viruses from different species by PCR amplification of conserved sequences in the matrix gene. J Clin Microbiol 2000, 38(11):4096-4101. 87547, 11060074.
14. Spackman E, Senne DA, Myers TJ, Bulaga LL, Garber LP, Perdue ML, Lohman K, Daum LT, Suarez DL. 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 2002, 40(9):3256-3260. 10.1128/JCM.40.9.3256-3260.2002, 130722, 12202562.
15. Poddar SK. Influenza virus types and subtypes detection by single step single tube multiplex reverse transcription-polymerase chain reaction (RT-PCR) and agarose gel electrophoresis. J Virol Methods 2002, 99(1-2):63-70. 10.1016/S0166-0934(01)00380-9, 11684304.
16. Imai M, Ninomiya A, Minekawa H, Notomi T, Ishizaki T, Tashiro M, Odagiri T. Development of H5-RT-LAMP (loop-mediated isothermal amplification) system for rapid diagnosis of H5 avian influenza virus infection. Vaccine 2006, 24(44-46):6679-6682. 10.1016/j.vaccine.2006.05.046, 16797110.
17. Collins RA, Ko LS, So KL, Ellis T, Lau LT, Yu AC. Detection of highly pathogenic and low pathogenic avian influenza subtype H5 (Eurasian lineage) using NASBA. J Virol Methods 2002, 103(2):213-225. 10.1016/S0166-0934(02)00034-4, 12008015.
18. Payungporn S, Chutinimitkul S, Chaisingh A, Damrongwantanapokin S, Buranathai C, Amonsin A, Theamboonlers A, Poovorawan Y. Single step multiplex real-time RT-PCR for H5N1 influenza A virus detection. J Virol Methods 2006, 131(2):143-147. 10.1016/j.jviromet.2005.08.004, 16183140.
19. Ellis JS, Smith JW, Braham S, Lock M, Barlow K, Zambon MC. Design and validation of an H5 TaqMan real-time one-step reverse transcription-PCR and confirmatory assays for diagnosis and verification of influenza A virus H5 infections in humans. J Clin Microbiol 2007, 45(5):1535-1543. 10.1128/JCM.02007-06, 1865909, 17473050.
20. Marschall J, Schulz B, Harder Priv-Doz TC, Vahlenkamp Priv-Doz TW, Huebner J, Huisinga E, Hartmann K. Prevalence of influenza A H5N1 virus in cats from areas with occurrence of highly pathogenic avian influenza in birds. J Feline Med Surg 2008, 10(4):355-358. 10.1016/j.jfms.2008.03.007, 18640861.
21. Hoffmann B, Harder T, Starick E, Depner K, Werner O, Beer M. Rapid and highly sensitive pathotyping of avian influenza A H5N1 virus by using real-time reverse transcription-PCR. J Clin Microbiol 2007, 45(2):600-603. 10.1128/JCM.01681-06, 1829000, 17182758.
22. Townsend MB, Dawson ED, Mehlmann M, Smagala JA, Dankbar DM, Moore CL, Smith CB, Cox NJ, Kuchta RD, Rowlen KL. Experimental evaluation of the FluChip diagnostic microarray for influenza virus surveillance. J Clin Microbiol 2006, 44(8):2863-2871. 10.1128/JCM.00134-06, 1594652, 16891504.
23. Dawson ED, Moore CL, Smagala JA, Dankbar DM, Mehlmann M, Townsend MB, Smith CB, Cox NJ, Kuchta RD, Rowlen KL. MChip: a tool for influenza surveillance. Anal Chem 2006, 78(22):7610-7615. 10.1021/ac061739f, 17105150.
24. Kessler N, Ferraris O, Palmer K, Marsh W, Steel A. Use of the DNA flow-thru chip, a three-dimensional biochip, for typing and subtyping of influenza viruses. J Clin Microbiol 2004, 42(5):2173-2185. 10.1128/JCM.42.5.2173-2185.2004, 404638, 15131186.
25. Li J, Chen S, Evans DH. Typing and subtyping influenza virus using DNA microarrays and multiplex reverse transcriptase PCR. J Clin Microbiol 2001, 39(2):696-704. 10.1128/JCM.39.2.696-704.2001, 87799, 11158130.
26. Mehlmann M, Dawson ED, Townsend MB, Smagala JA, Moore CL, Smith CB, Cox NJ, Kuchta RD, Rowlen KL. Robust sequence selection method used to develop the FluChip diagnostic microarray for influenza virus. J Clin Microbiol 2006, 44(8):2857-2862. 10.1128/JCM.00135-06, 1594657, 16891503.
27. Dawson ED, Moore CL, Dankbar DM, Mehlmann M, Townsend MB, Smagala JA, Smith CB, Cox NJ, Kuchta RD, Rowlen KL. Identification of A/H5N1 influenza viruses using a single gene diagnostic microarray. Anal Chem 2007, 79(1):378-384. 10.1021/ac061920o, 17194164.
28. Lodes MJ, Suciu D, Elliott M, Stover AG, Ross M, Caraballo M, Dix K, Crye J, Webby RJ, Lyon WJ, et al. Use of semiconductor-based oligonucleotide microarrays for influenza a virus subtype identification and sequencing. J Clin Microbiol 2006, 44(4):1209-1218. 10.1128/JCM.44.4.1209-1218.2006, 1448669, 16597840.
29. Gall A, Hoffmann B, Harder T, Grund C, Hoper D, Beer M. Design and validation of a microarray for detection, hemagglutinin subtyping, and pathotyping of avian influenza viruses. J Clin Microbiol 2009, 47(2):327-334. 10.1128/JCM.01330-08, 2643657, 19052173.
30. Takahashi H, Norman SA, Mather EL, Patterson BK. Evaluation of the NanoChip 400 system for detection of influenza A and B, respiratory syncytial, and parainfluenza viruses. J Clin Microbiol 2008, 46(5):1724-1727. 10.1128/JCM.01947-07, 2395092, 18322066.
31. Tang S, Zhao J, Storhoff JJ, Norris PJ, Little RF, Yarchoan R, Stramer SL, Patno T, Domanus M, Dhar A, et al. Nanoparticle-Based biobarcode amplification assay (BCA) for sensitive and early detection of human immunodeficiency type 1 capsid (p24) antigen. J Acquir Immune Defic Syndr 2007, 46(2):231-237. 10.1097/QAI.0b013e31814a554b, 17693896.
32. Taton TA, Mirkin CA, Letsinger RL. Scanometric DNA array detection with nanoparticle probes. Science 2000, 289(5485):1757-1760. 10.1126/science.289.5485.1757, 10976070.
33. Bao YP, Huber M, Wei TF, Marla SS, Storhoff JJ, Muller UR. SNP identification in unamplified human genomic DNA with gold nanoparticle probes. Nucleic Acids Res 2005, 33(2):e15. 10.1093/nar/gni017, 548375, 15659576.
34. FDA_influenza_tests Cautions in Using Rapid Tests for Detecting Influenza A Viruses. 2009, FDA_influenza_tests., http://www.fda.gov/MedicalDevices/Safety/AlertsandNotices/TipsandArticlesonDeviceSafety/ucm109385.htm
35. Gallaher WR. Towards a sane and rational approach to management of Influenza H1N1 2009. Virol J 2009, 6(1):51. 10.1186/1743-422X-6-51, 2691743, 19422701.
36. Zou S. A practical approach to genetic screening for influenza virus variants. J Clin Microbiol 1997, 35(10):2623-2627. 230022, 9316919.
37. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007, 24(8):1596-1599. 10.1093/molbev/msm092, 17488738.
38. Winter G, Fields S. Cloning of influenza cDNA ino M13: the sequence of the RNA segment encoding the A/PR/8/34 matrix protein. Nucleic Acids Res 1980, 8(9):1965-1974. 10.1093/nar/8.9.1965, 324050, 6927841.
39. Lamb RA, Lai CJ, Choppin PW. Sequences of mRNAs derived from genome RNA segment 7 of influenza virus: colinear and interrupted mRNAs code for overlapping proteins. Proc Natl Acad Sci USA 1981, 78(7):4170-4174. 10.1073/pnas.78.7.4170, 319750, 6945577.
40. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31(13):3406-3415. 10.1093/nar/gkg595, 169194, 12824337.