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（由研究人员提供）：该应用的目标是进一步开发一种新型的DNA微阵列，以检测气道分泌物中的血清型和基因型鼻病毒（RV），并进行一项研究，研究导致遗传性抑郁症状的RV菌株是否与仅引起上呼吸道症状的人有不同。这些目标将通过3个目标实现。目标1：通过生长每个102 RV血清型的特定杂交模式，并确定其在微阵列上的杂交模式。现在，微阵列具有204个用于RV的检测寡核苷酸，它是根据仅有5个完全测序的血清型（RV1B，RV2，RV14，RV14，RV16，RV89）设计的。在应用微阵列以确定所有102种血清型的杂交模式之前，我们将对所有其他97种血清型尚未测序尚未测序以设计新的检测寡核苷酸并扩展微阵列。目标2：开发生物信息学软件以分析微阵列结果并确定血清型匹配。我们将使用来自3个来源的数据开发此软件：（a）每种RV血清型的杂交数据（来自AIM 1）； （b）从现场样品中分离出的单个血清型的杂交数据（以评估单个血清型的杂交变异性）； （c）根据RV基因组和寡核苷酸的序列对杂交模式的计算机模型预测。 AIM 3：验证来自具有急性呼吸道感染和表征良好的临床表现的受试者的现场样本中的微阵列和生物信息学软件。此外，将将降低气道疾病（例如支气管炎，哮喘和COPD加剧）的RV的杂交模式与仅引起高气道症状的RV模式进行比较，以确定微阵列基因分型是否可以识别恶毒变体。这些研究将与PPG-1PO1-AIS0496的目标接触：检查鼻病毒菌株之间的差异是否确定感染引起哮喘加重的可能性。我们从患有呼吸道感染的受试者中收集了> 75个样本。 PPG的病毒学核心（加利福尼亚州病毒学实验室，VRDL）执行RV血清分型，并且具有大多数RV原型和多个分离株用于特定的血清型。一旦得到验证，微阵列将允许对所有RV进行检测，血清分型和基因分型，这不仅引起普通感冒，而且会引起明显的发病率，例如哮喘和COPD加剧的疾病。