Microarray-based detection and typing of rhinoviruses

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DESCRIPTION (provided by investigator): The goals of this application are to further develop a novel DNA microarray to detect, serotype, and genotype rhinoviruses (RV) in airway secretions, and to conduct a study examining whether RV strains causing lower respiratory symptoms differ genetically from those causing only upper respiratory symptoms. These goals will be achieved through 3 aims. Aim 1: To define specific hybridization patterns for all 102 RV serotypes by growing a prototype of each and determining its hybridization pattern on the microarray. The microarray now has 204 detection oligonucleotides for RV's, designed from the genomes of the only 5 fully sequenced serotypes (RV1B, RV2, RV14, RV16, RV89). Before applying the microarray to determine the hybridization pattern for all 102 serotypes, we will fully sequence all additional 97 serotypes not yet sequenced to design new detection oligonucleotides and expand the microarray. Aim 2: To develop bioinformatics software to analyze microarray results and determine a serotype match. We will develop this software using data from 3 sources: (a) hybridization data for each RV serotype (from Aim 1); (b) hybridization data from up to 10 strains of a single serotype isolated from field samples (to assess the hybridization variability for a single serotype); and (c) from computer model prediction of hybridization patterns based on the sequences of RV genomes and of oligonucleotides. Aim 3: To validate the microarray and bioinformatics software in field samples from subjects with acute respiratory infections and well-characterized clinical presentations. In addition, hybridization patterns of RV's that cause lower airway disease (e.g. bronchitis, exacerbations of asthma and COPD) will be compared with the patterns of RV's that cause only upper airway symptoms to determine whether microarray genotyping can identify virulent variants. These studies will interface with a goal of PPG-1PO1-AIS0496: To examine whether differences among strains of rhinovirus determine the likelihood of infection provoking asthma exacerbations. We have collected >75 samples from subjects with respiratory infections. The PPG's Virology Core (California State Virology Laboratory, VRDL) performs RV serotyping, and has most RV prototypes and multiple isolates for specific serotypes. Once validated, the microarray will allow, in a single step, detection, serotyping and genotyping of all RV's, which cause not only common colds, but also illnesses with significant morbidity such as exacerbations of asthma and COPD.