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

Abstract

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.

Genotyping human papillomaviruses: Development and evaluation of a comprehensive DNA microarray

“…This may be explained by the expense of the reagents, microarrays, and processing costs of the specimens. In comparison to other studies using oligonucleotide microarrays for virus genotyping from measles to potato viruses, our results affirm the utility of this technology for potential clinical use [22,23]. In fact, commercially available kits are already available for identification of respiratory viruses using different microarray platforms [24].…”

Detection and Identification of Common Food-Borne Viruses with a Tiling Microarray

“…For these reasons, there is an urgent need for the development of viral genome based rapid detection and identification methods for food-borne viruses with discriminatory power at the level of species and strain/genotype (or genogroup). Based on our previous results using a lower density array [15] as well as the work of others on non-food-borne viral pathogens [16][17][18], microarray based methods offer one such methodological approach. Initial attempts at virus detection and typing by microarray hybridization were limited to detection of known mutations in the viral genome based on hybridization to a "handful" of oligonucleotide probes immobilized on a solid support.…”

Development of DNA-Biochip for Identification of Influenza A Virus Subtypes

“…В мире разработаны биочипы для идентификации и типирования энтеровирусов [12], субтипирования вируса гриппа [2,7,6], генотипирования вируса кори [9], дифференциальной диагностики микозов [8] и другие.…”