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Journal of Clinical Microbiology, October 2003, p. 4542-4550, Vol. 41, No. 10
0095-1137/03/$08.00+0     DOI: 10.1128/JCM.41.10.4542-4550.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Molecular Detection and Identification of Influenza Viruses by Oligonucleotide Microarray Hybridization

Srikumar Sengupta,^1, Kenji Onodera,^1, Alexander Lai,² and Ulrich Melcher^1*

Department of Biochemistry and Molecular Biology,¹ Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078²

Received 31 January 2003/ Returned for modification 14 May 2003/ Accepted 28 July 2003

Microarrays of virus-specific oligonucleotides may provide a method of screening samples for the presence or absence of a large variety of viruses simultaneously. Influenza viruses are ideal for evaluating such microarrays because of their genetic and host diversity, and the availability of an extensive sequence database. A collection of 476 influenza virus-specific oligonucleotides was spotted onto glass slides as probes. Viral RNAs were reverse transcribed and amplified by PCR, and the products were labeled with cyanine dyes. The presence of viruses and their identities were determined by hybridization. The fluorescence intensities of oligonucleotide spots were highly reproducible within each slide and satisfactorily proportional between experiments. However, the intensities of probe spots completely complementary to target sequences varied from background to saturation. The variations did not correlate with base composition, nucleotide sequence, or internal secondary structures. Therefore, thresholds for determining whether hybridization to a spot should be judged as positive were assigned individually. Considering only positive spots from probes predicted to be monospecific for influenza virus species, subtype, host source, or gene segment, this method made correct identifications at the species, hemagglutinin subtype, and gene segment levels. Monospecific neuraminidase (NA) subtype probes were insufficiently diverse to allow confident NA subtype assignment. Incorporating positive spots from polyspecific probes into the identification scheme gave similar results. Overall, the results demonstrate the potential of microarray-based oligonucleotide hybridization for multiple virus detection.

Present address: Institute for Molecular Virology, University of Wisconsin, Madison, WI 53706.

Present address: Collaborative Research Center of Frontier Simulation Software for Industrial Science, Institute of Industrial Science, University of Tokyo, Meguro-ku, Tokyo 153-8505, Japan.

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