SARS-CoV-2 infection elicits a distinct host response in nasal swabs and blood that can be used to diagnose COVID-19. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease-19 (COVID-19), has emerged as the cause of a global pandemic. We used RNA sequencing to analyze 286 nasopharyngeal (NP) swab and 53 whole-blood (WB) samples from 333 patients with COVID-19 and controls. Overall, a muted immune response was observed in COVID-19 relative to other infections (influenza, other seasonal coronaviruses, and bacterial sepsis), with paradoxical down-regulation of several key differentially expressed genes. Hospitalized patients and outpatients exhibited up-regulation of interferon-associated pathways, although heightened and more robust inflammatory responses were observed in hospitalized patients with more clinically severe illness. Two-layer machine learning–based host classifiers consisting of complete (>1000 genes), medium (<100), and small (<20) gene biomarker panels identified COVID-19 disease with 85.1–86.5% accuracy when benchmarked using an independent test set. SARS-CoV-2 infection has a distinct biosignature that differs between NP swabs and WB and can be leveraged for COVID-19 diagnosis.
【초록키워드】 COVID-19, SARS-CoV-2, coronavirus, immune response, Biomarker, Influenza, SARS-COV-2 infection, Infection, host response, COVID-19 disease, global pandemic, Coronavirus disease-19, Accuracy, nasopharyngeal, RNA sequencing, Patient, COVID-19 diagnosis, Swab, nasal swab, NP swab, seasonal coronaviruses, Differentially expressed genes, Bacterial sepsis, Blood, diagnose, Outpatient, Inflammatory response, Pathways, acute respiratory syndrome, Classifier, medium, down-regulation, Host, Genes, Complete, controls, independent, robust, clinically, exhibited, can be used, hospitalized patient, elicit, cause, paradoxical, patients with COVID-19, 【제목키워드】 COVID-19, diagnostic, host response, RNA, nasal swab, Blood,