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Journal of Clinical Microbiology, October 2006, p. 3752-3759, Vol. 44, No. 10
0095-1137/06/$08.00+0     doi:10.1128/JCM.00998-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Genotyping of Measles Virus in Clinical Specimens on the Basis of Oligonucleotide Microarray Hybridization Patterns

Center for Biologics Evaluation and Research, Food and Drug Administration, Rockville,¹ W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland,² Measles, Mumps, Rubella, and Herpesvirus Branch, Centers for Disease Control and Prevention/WHO Global Measles Reference Laboratory, Atlanta, Georgia,³ Victorian Infectious Diseases Reference Laboratory/WHO Western Pacific Region Measles Reference Laboratory, Melbourne, Victoria, Australia,⁴ Vaccine-Preventable Virus Infections Unit, National Institute for Communicable Diseases, Johannesburg, Republic of South Africa,⁵ Institute of Molecular Biology, State Research Center of Virology and Biotechnology "Vector," Koltsovo, Novosibirsk Region, Russian Federation⁶

Received 12 May 2006/ Returned for modification 6 June 2006/ Accepted 20 July 2006

An oligonucleotide microarray hybridization method for identification of most known measles virus (MV) genotypes was developed. Like the conventional genotyping method, the microarray relied on detecting sequence differences in the 450-nucleotide region coding for the COOH-terminal 150 amino acids of the nucleoprotein (N). This region was amplified using PCR primers binding to all known MV genotypes. The microarray included 71 pairs of oligonucleotide probes (oligoprobes) immobilized on glass slides. Each pair consisted of a genotype-specific oligoprobe, which matched the sequence of only one target genotype, and a control oligoprobe, which contained mismatches at the nucleotide positions unique to this genotype. A pattern recognition algorithm based on cluster analysis of the ratios of hybridization signals from specific and control oligoprobes was used to identify the specific MV genotype. Following the initial validation, the method was used for rapid genotyping of two panels of coded samples. The results of this study showed good sensitivity (90.7%), specificity (100%), and genotype agreement (91.8%) for the new method compared to the results of genotyping conducted using phylogenetic analysis of viral sequences of the C terminus of the N gene. In addition, the microarray demonstrated the ability to identify potential new genotypes of MV based on the similarity of their hybridization patterns with those of known MV genotypes.

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