tetano
Editor, Senior Moderator
Sci Adv
. 2021 Feb 3;7(6):eabe5984.
doi: 10.1126/sciadv.abe5984. Print 2021 Feb.
A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood
Dianna L Ng[SUP] 1 2 [/SUP], Andrea C Granados[SUP] 2 3 [/SUP], Yale A Santos[SUP] 2 3 [/SUP], Venice Servellita[SUP] 2 3 [/SUP], Gregory M Goldgof[SUP] 2 [/SUP], Cem Meydan[SUP] 4 5 6 [/SUP], Alicia Sotomayor-Gonzalez[SUP] 2 3 [/SUP], Andrew G Levine[SUP] 2 [/SUP], Joanna Balcerek[SUP] 2 [/SUP], Lucy M Han[SUP] 1 [/SUP], Naomi Akagi[SUP] 1 [/SUP], Kent Truong[SUP] 1 [/SUP], Neil M Neumann[SUP] 1 [/SUP], David N Nguyen[SUP] 7 [/SUP], Sagar P Bapat[SUP] 2 7 8 [/SUP], Jing Cheng[SUP] 9 10 [/SUP], Claudia Sanchez-San Martin[SUP] 2 3 [/SUP], Scot Federman[SUP] 2 3 [/SUP], Jonathan Foox[SUP] 4 5 6 [/SUP], Allan Gopez[SUP] 2 3 [/SUP], Tony Li[SUP] 11 [/SUP], Ray Chan[SUP] 2 [/SUP], Cynthia S Chu[SUP] 2 [/SUP], Chiara A Wabl[SUP] 2 3 [/SUP], Amelia S Gliwa[SUP] 2 3 [/SUP], Kevin Reyes[SUP] 2 3 [/SUP], Chao-Yang Pan[SUP] 12 [/SUP], Hugo Guevara[SUP] 12 [/SUP], Debra Wadford[SUP] 12 [/SUP], Steve Miller[SUP] 2 3 [/SUP], Christopher E Mason[SUP] 4 5 13 14 [/SUP], Charles Y Chiu[SUP] 15 3 8 [/SUP]
Affiliations
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.
. 2021 Feb 3;7(6):eabe5984.
doi: 10.1126/sciadv.abe5984. Print 2021 Feb.
A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood
Dianna L Ng[SUP] 1 2 [/SUP], Andrea C Granados[SUP] 2 3 [/SUP], Yale A Santos[SUP] 2 3 [/SUP], Venice Servellita[SUP] 2 3 [/SUP], Gregory M Goldgof[SUP] 2 [/SUP], Cem Meydan[SUP] 4 5 6 [/SUP], Alicia Sotomayor-Gonzalez[SUP] 2 3 [/SUP], Andrew G Levine[SUP] 2 [/SUP], Joanna Balcerek[SUP] 2 [/SUP], Lucy M Han[SUP] 1 [/SUP], Naomi Akagi[SUP] 1 [/SUP], Kent Truong[SUP] 1 [/SUP], Neil M Neumann[SUP] 1 [/SUP], David N Nguyen[SUP] 7 [/SUP], Sagar P Bapat[SUP] 2 7 8 [/SUP], Jing Cheng[SUP] 9 10 [/SUP], Claudia Sanchez-San Martin[SUP] 2 3 [/SUP], Scot Federman[SUP] 2 3 [/SUP], Jonathan Foox[SUP] 4 5 6 [/SUP], Allan Gopez[SUP] 2 3 [/SUP], Tony Li[SUP] 11 [/SUP], Ray Chan[SUP] 2 [/SUP], Cynthia S Chu[SUP] 2 [/SUP], Chiara A Wabl[SUP] 2 3 [/SUP], Amelia S Gliwa[SUP] 2 3 [/SUP], Kevin Reyes[SUP] 2 3 [/SUP], Chao-Yang Pan[SUP] 12 [/SUP], Hugo Guevara[SUP] 12 [/SUP], Debra Wadford[SUP] 12 [/SUP], Steve Miller[SUP] 2 3 [/SUP], Christopher E Mason[SUP] 4 5 13 14 [/SUP], Charles Y Chiu[SUP] 15 3 8 [/SUP]
Affiliations
- PMID: 33536218
- DOI: 10.1126/sciadv.abe5984
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.