Microarray-based detection and typing of rhinoviruses

基于微阵列的鼻病毒检测和分型

• 批准号: 6703885
• 负责人: Homer A Boushey
• 金额: $ 22.47万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-05-01 至 2006-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6703885
• 关键词: bioinformatics; clinical research; genome; genotype; human subject; microarray technology; microorganism classification; nucleic acid hybridization; oligonucleotides; polymerase chain reaction; respiratory disorder epidemiology; respiratory virus; rhinovirus; serotyping; technology /technique development

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.

描述（由研究者提供）：本申请的目的是进一步开发一种新的DNA微阵列，用于检测气道分泌物中的鼻病毒（RV）、血清型和基因型，并进行一项研究，检查引起下呼吸道症状的RV毒株是否与仅引起上呼吸道症状的RV毒株在遗传上不同。这些目标将通过三个方面来实现。目标1：通过培养每种血清型的原型并在微阵列上确定其杂交模式，确定所有102种RV血清型的特异性杂交模式。微阵列现在有204个RV的检测寡核苷酸，从仅有的5个完全测序的血清型（RV 1B，RV 2，RV 14，RV 16，RV 89）的基因组设计。在应用微阵列确定所有102种血清型的杂交模式之前，我们将对尚未测序的所有其他97种血清型进行完全测序，以设计新的检测寡核苷酸并扩展微阵列。目的2：开发生物信息学软件分析芯片结果，确定血清型匹配。我们将使用来自3个来源的数据开发该软件：（a）每种RV血清型的杂交数据（来自目标1）;（B）从田间样本中分离的单个血清型的最多10个菌株的杂交数据（以评估单个血清型的杂交变异性）;和（c）基于RV基因组和寡核苷酸序列的杂交模式的计算机模型预测。目标三：验证微阵列和生物信息学软件在急性呼吸道感染受试者的现场样本中的有效性和良好的临床表现。此外，将引起下呼吸道疾病（例如支气管炎、哮喘和COPD的恶化）的RV的杂交模式与仅引起上呼吸道症状的RV的模式进行比较，以确定微阵列基因分型是否可以鉴定毒性变体。这些研究将与PPG-1 PO 1-AIS 0496的目标相结合：检查鼻病毒株之间的差异是否决定了感染引起哮喘急性发作的可能性。我们已经从患有呼吸道感染的受试者收集了>75个样本。PPG的病毒学核心（加州国家病毒学实验室，VRDL）进行RV血清分型，并具有大多数RV原型和特定血清型的多种分离株。一旦验证，微阵列将允许在一个步骤中检测、血清分型和基因分型所有RV，其不仅引起普通感冒，而且引起具有显著发病率的疾病，例如哮喘和COPD的恶化。