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A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood.
Ng, Dianna L; Granados, Andrea C; Santos, Yale A; Servellita, Venice; Goldgof, Gregory M; Meydan, Cem; Sotomayor-Gonzalez, Alicia; Levine, Andrew G; Balcerek, Joanna; Han, Lucy M; Akagi, Naomi; Truong, Kent; Neumann, Neil M; Nguyen, David N; Bapat, Sagar P; Cheng, Jing; Martin, Claudia Sanchez-San; Federman, Scot; Foox, Jonathan; Gopez, Allan; Li, Tony; Chan, Ray; Chu, Cynthia S; Wabl, Chiara A; Gliwa, Amelia S; Reyes, Kevin; Pan, Chao-Yang; Guevara, Hugo; Wadford, Debra; Miller, Steve; Mason, Christopher E; Chiu, Charles Y.
  • Ng DL; Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.
  • Granados AC; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
  • Santos YA; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
  • Servellita V; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
  • Goldgof GM; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
  • Meydan C; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
  • Sotomayor-Gonzalez A; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
  • Levine AG; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
  • Balcerek J; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
  • Han LM; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
  • Akagi N; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
  • Truong K; WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
  • Neumann NM; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
  • Nguyen DN; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
  • Bapat SP; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
  • Cheng J; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
  • Martin CS; Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.
  • Federman S; Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.
  • Foox J; Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.
  • Gopez A; Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.
  • Li T; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
  • Chan R; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
  • Chu CS; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
  • Wabl CA; Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA.
  • Gliwa AS; Department of Preventive and Restorative Dental Sciences, University of California, San Francisco, San Francisco, CA, USA.
  • Reyes K; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
  • Pan CY; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
  • Guevara H; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
  • Wadford D; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
  • Miller S; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
  • Mason CE; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
  • Chiu CY; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
Sci Adv ; 7(6)2021 02.
Article in English | MEDLINE | ID: covidwho-1066793
ABSTRACT
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: RNA, Viral / Nasopharynx / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Prognostic study Limits: Humans Language: English Year: 2021 Document Type: Article Affiliation country: Sciadv.abe5984

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Full text: Available Collection: International databases Database: MEDLINE Main subject: RNA, Viral / Nasopharynx / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Prognostic study Limits: Humans Language: English Year: 2021 Document Type: Article Affiliation country: Sciadv.abe5984