A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood. A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood

To elucidate key pathways in the host transcriptome of patients infected with SARS-CoV-2, we used RNA sequencing (RNA Seq) to analyze nasopharyngeal (NP) swab and whole blood (WB) samples from 333 COVID-19 patients and controls, including patients with other viral and bacterial infections. Analyses of differentially expressed genes (DEGs) and pathways was performed relative to other infections (e.g. influenza, other seasonal coronaviruses, bacterial sepsis) in both NP swabs and WB. Comparative COVID-19 host responses between NP swabs and WB were examined. Both hospitalized patients and outpatients exhibited upregulation of interferon-associated pathways, although heightened and more robust inflammatory and immune responses were observed in hospitalized patients with more clinically severe disease. A two-layer machine learning-based classifier, run on an independent test set of NP swab samples, was able to discriminate between COVID-19 and non-COVID-19 infectious or non-infectious acute respiratory illness using complete (>1,000 genes), medium (<100) and small (<20) gene biomarker panels with 85.1%-86.5% accuracy, respectively. These findings demonstrate that SARS-CoV-2 infection has a distinct biosignature that differs between NP swabs and WB and can be leveraged for differential diagnosis of COVID-19 disease. Overall design: Comparison of the gene expression profile of nasopharyngeal swabs from individuals with SARS-CoV-2 infection, other viral acute respiratory infections, non-viral acute respiratory illness, and donor controls as well as of whole blood from individuals with SARS-CoV-2 infection, influenza, bacterial sepsis, and donor controls. *** Raw sequence data are not provided because patient informed consent could not be obtained in this study. ***

为阐明新型冠状病毒（SARS-CoV-2）感染患者宿主转录组的关键通路，我们采用RNA测序（RNA sequencing, RNA Seq）技术，对333名COVID-19患者及对照人群的鼻咽拭子（nasopharyngeal swab, NP）和全血（whole blood, WB）样本开展分析，对照人群涵盖其他病毒与细菌感染患者。
针对鼻咽拭子与全血样本，我们分别以其他感染（如流感（influenza）、其他季节性冠状病毒（seasonal coronaviruses）感染、细菌性脓毒症（bacterial sepsis））为参照，进行差异表达基因（differentially expressed genes, DEGs）及通路分析，并对比了鼻咽拭子与全血样本的COVID-19宿主应答特征。
结果显示，住院患者与门诊患者均存在干扰素相关通路的上调；但临床病情更为严重的住院患者，其炎症与免疫应答更为亢进且强烈。
我们构建了基于双层机器学习的分类器，并在独立的鼻咽拭子样本测试集上进行验证。结果表明，采用完整（>1000个基因）、中等（<100个基因）与小型（<20个基因）基因标志物组合，该分类器可区分COVID-19与非COVID-19感染性或非感染性急性呼吸道疾病，准确率分别为85.1%~86.5%。
本研究结果证实，SARS-CoV-2感染具有独特的生物特征谱，且该特征在鼻咽拭子与全血样本中存在差异，可用于COVID-19的鉴别诊断。
整体实验设计：对比SARS-CoV-2感染患者、其他病毒性急性呼吸道感染患者、非病毒性急性呼吸道疾病患者及健康对照者的鼻咽拭子基因表达谱；同时对比SARS-CoV-2感染患者、流感（influenza）患者、细菌性脓毒症（bacterial sepsis）患者及健康对照者的全血基因表达谱。
*** 本研究未获取患者知情同意，故不提供原始测序数据。 ***