Metagenomic analysis of the human virome

人类病毒组的宏基因组分析

基本信息

批准号：
7393194
负责人：
ERIC L DELWART
金额：
$ 40.06万
依托单位：
VITALANT
依托单位国家：
美国
项目类别：
财政年份：
2007
资助国家：
美国
起止时间：
2007-04-01 至 2011-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7393194
关键词：
Acquired Immunodeficiency Syndrome Acute African Algorithms Animal Viruses Appendix Base Sequence Bioinformatics Biological Blast Cell Blood Donations Blood donor California Capsid Centers for Disease Control and Prevention (U.S.)Classification Clinical Critical Illness Cultured Cells DNA Depth Detection Diagnostic Dinucleoside Phosphates Disease Outbreaks Distant Egypt Emulsions Encephalitis Etiology Feces Fractionation Frequencies Future Genome HIV HIV Infections Health Services Hepatitis Hepatitis B Virus Hepatology Human Human Virus In Vitro Infection Injecting drug user Institutes Laboratories Libraries Liquid substance Metagenomics Methodology Methods Nucleic Acid Amplification Tests Nucleic Acid Hybridization Nucleic Acids Nucleic acid sequencing Nucleotides Numbers Open Reading Frames Organism Parvovirus Patients Persons Pharmacologic Substance Phylogenetic Analysis Plasma Plasmids Pneumonia Polymerase Chain Reaction Population Prevalence Prevalence Study Proteins Publishing RNA Viruses RNA amplification Range Reading Recruitment Activity Relative (related person)Research Research Personnel Risk Safety Sampling Seawater Serological Shotgun Sequencing Shotguns Source Standards of Weights and Measures Surveys Symptoms Technology Testing Time Urban Health Vascular blood supply Viral Viral Genome Virus Virus Diseases analytical tool base cohort cross reactivity genome sequencing health economics high risk behavior human virome improved interest markov model nonhuman primate novel novel strategies particle pathogen programs sample collection success tool viral DNA virus genetics

项目摘要

DESCRIPTION (provided by applicant): Viral discovery is made difficult by the frequent inability to replicate these agents in vitro and the limitations of traditional methods requiring antigenic/serological cross-reactivity or nucleic acid hybridization. We postulate, based on our recent study of viral capsid-protected nucleic acids in symptomatic humans, that new viruses, both commensal and pathogenic, can be readily identified using a metagenomic approach. Our successes finding both new as well as a diverse mix of previously known human viruses in unprocessed biological samples using a minimal amount of sequencing indicate that a rich yield of previously unknown viruses is present in human samples. We have assembled for this nucleic acid survey a collection of samples from extensively characterized patients showing a range of symptoms including hepatitis, encephalitis and pneumonia of unexplained etiology. Samples from heavily virus-exposed (IDUs, MSM) and susceptible subjects (AIDS patients) and from humans frequently exposed to non-human primates will be similarly analyzed. Using an unbiased viral DNA and RNA amplification method, together with both traditional shotgun library sequencing and high throughput pyrosequencing, we will conduct a metagenomic survey of the human virome. Virus-specific bioinformatics methods will be developed to facilitate the detection of phylogenetically close as well as distant relatives of known viral species. Initial viral sequence similarity matches will be followed by full viral genome sequencing and phylogenetic analysis. The prevalence of newly identified viruses will then be determined using real-time PCR on different populations including healthy blood donors, IDUs and patients with identical symptoms or exposure risks. This metagenomic survey of non-human nucleic acids in humans will therefore begin the task of determining the full range of viral diversity in humans.

描述（由申请人提供）：由于经常无法在体外复制这些药物以及需要抗原/血清学交叉反应性或核酸杂交的传统方法的局限性，因此很难发现病毒发现。我们假设，根据我们最近对有症状性人类病毒capsid保护的核酸的研究，可以使用元基因组方法可以轻松地鉴定出共生和致病性的新病毒。我们在未经处理的生物样品中使用最少的测序在未经处理的生物样品中发现了新的和多样的人类病毒的成功，也表明人类样品中存在丰富的先前未知病毒的产量。我们为此核酸调查组装了来自广泛特征的患者的样本的集合，这些症状包括肝炎，脑炎和无法解释的病因的肺炎。类似地分析了来自病毒暴露（IDU，MSM）和易感受试者（AIDS患者）以及经常暴露于非人类灵长类动物的人类的样本。使用公正的病毒DNA和RNA扩增方法，再加上传统的shot弹枪库测序和高吞吐量的焦磷酸测序，我们将对人类病毒组进行元基因组学调查。将开发病毒特异性的生物信息学方法，以促进检测已知病毒物种的系统发育近距离和遥远的亲属。最初的病毒序列相似性匹配将进行全病毒基因组测序和系统发育分析。然后，将使用针对不同人群的实时PCR（包括健康的献血者，IDU和具有相同症状或暴露风险的患者）确定新确定的病毒的患病率。因此，这种对人类非人类核酸的宏基因组学调查将开始确定人类病毒多样性的全部任务。