In Vivo Cluster AI Prediction (CLAIRE) of COVID-19 Disease Progression

COVID-19 疾病进展的体内集群 AI 预测 (CLAIRE)

• 批准号: 10256828
• 负责人: Patricia Buendia
• 金额: $ 24.87万
• 依托单位: LIFETIME OMICS, INC.
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2022-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10256828
• 关键词: 2019-nCoV; Affect; Algorithms; Antibiotics; Area; Artificial Intelligence; Bacteria; Biological Markers; COVID-19; COVID-19 outbreak; COVID-19 pandemic; COVID-19 patient; Cessation of life; China; Cities; Clinical; Communities; Contact Tracing; Coronavirus; Country; County; Data; Data Set; Detection; Deterioration; Diagnosis; Diagnostic; Diagnostic Sensitivity; Disease; Disease Outbreaks; Disease Progression; Evolution; Fatal Outcome; Gene Frequency; Genetic; Geography; Goals; HIV; Health system; Hospitals; Immune; Infection; Infection Control; Influenza; International; Lifting; Lung diseases; Measures; Medical; Metagenomics; Microbe; Minor; Modeling; Molecular; Molecular Epidemiology; Mutation; Outcome; Pathogenicity; Patient Care; Patient risk; Patients; Performance; Phylogenetic Analysis; Physicians; Population; Predictive Value; Primary Infection; Process; Prognosis; Quarantine; RNA Sequences; ROC Curve; Records; Reporting; Resources; Risk Factors; SARS-CoV-2 positive; Saliva; Sampling; Seasons; Sensitivity and Specificity; Services; Severities; Ships; Testing; Time; Training; Travel; Universities; Validation; Viral; Virus; Virus Diseases; anti-viral efficacy; base; co-infection; computerized tools; data modeling; health care service utilization; improved outcome; in vivo; infection rate; influenzavirus; markov model; metagenome; metagenomic sequencing; microbiome; microbiota; negative affect; pathogen; pathogenic bacteria; patient subsets; phase 1 study; predictive modeling; predictive tools; pressure; reproductive; saliva analysis; saliva sample; seasonal influenza; supervised learning; tool; vaccine efficacy; viral RNA

ABSTRACT The coronavirus COVID-19 pandemic, which early this year forced entire countries into lockdown, has reached a global death toll of 890,000+ by early September 2020. Based on the high number of COVID-19 cases that are asymptomatic but infectious, an estimated reproductive rate of infection of about 2 and a high mutation rate, it is expected that the virus will remain in the population as the influenza virus does. For hospitals serving areas whose economy relies on international travel, tourism, and cruise ship tourism, such as Miami-Dade county, new COVID-19 cases related to travel will require treatment during infection outbreaks which will strain health systems, especially during the infectious respiratory disease season in the winter. Patient risk factors during the current COVID-19 outbreak as well as during other viral outbreaks, such as seasonal influenza, are poorly characterized, consequently negatively affecting patient care. The saliva microbiome, which includes viruses and bacteria, is not currently used as in diagnostic tools. However, it may reveal risk factors associated with severe disease and/or a fatal outcome, and it allows for the detection and study of the viral RNA sequence for potential contact tracing and molecular epidemiology, all of which affect both vaccine and antiviral efficacy. In this proposed study, Lifetime Omics will develop CLAIRE, a proof-of-concept in vivo cluster AI platform for predicting disease progression of viral infectious respiratory diseases such as COVID-19 through the analysis of the saliva metagenome. The University of Miami Medical Group Infection Control (UMMGIC) division will collaborate in this effort by collecting saliva samples from COVID-19 patients with de-identified clinical information. The samples will undergo metagenomic sequencing and Lifetime Omics will repurpose algorithms used for prediction of in vivo HIV evolution to perform genetic/phylogenetic analysis on SARS-CoV-2 RNA sequences, estimating mutation rate and immune selection pressures and identifying both the in vivo quasispecies clusters and the geographic cluster to which the patient belongs. The CLAIRE models will be trained with public datasets and tested on the metagenomic sequences generated from saliva samples of UMMGIC patients with the goal of assisting physicians in predicting disease progression in COVID-19.

抽象的 冠状病毒covid-19-19，今年年初迫使整个国家进入 锁定到2020年9月初，全球死亡人数已达到890,000多。 无症状但传染性的大量共vid案例，估计 生殖感染率约为2和高突变率，预计该病毒将会 像流感病毒一样留在人群中。对于服务地区的医院 经济依赖国际旅行，旅游和游轮旅游业，例如迈阿密戴德 县，新的Covid-19案件与旅行有关的案件将需要在感染暴发期间进行治疗 这将使卫生系统扭曲，尤其是在感染性呼吸道疾病季节 冬天。当前共同爆发期间以及其他期间的患者危险因素 病毒爆发，例如季节性流感，其特征很差，因此是负面的 影响患者护理。包括病毒和细菌在内的唾液微生物组不是 目前用作诊断工具。但是，它可能揭示了与严重相关的风险因素 疾病和/或致命的结果，它可以检测和研究病毒RNA 潜在接触追踪和分子流行病学的序列，所有这些都影响 疫苗和抗病毒功效。 在这项拟议的研究中，Lifetime Omics将发展Claire，这是体内群集AI的概念验证 预测病毒感染呼吸道疾病的疾病进展的平台，例如 COVID-19通过分析唾液元基因组。迈阿密大学医学 小组感染控制（UMMGIC）部门将通过收集唾液来合作 来自COVID-19患者的样品具有去识别的临床信息。样品会 进行宏基因组测序和寿命元素将重新使用用于 体内HIV进化的预测对SARS-COV-2进行遗传/系统发育分析 RNA序列，估计突变率和免疫选择压力以及识别 体内准蛋白酶簇和患者所属的地理集群。这 Claire模型将接受公共数据集培训，并对元基因组序列进行测试 由UMMGIC患者的唾液样本产生，目的是协助医生 预测COVID-19的疾病进展。