Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions.
RNA-seq
coronavirus disease 2019 (COVID-19)
global health
loop-mediated isothermal amplification (LAMP)
next-generation sequencing (NGS)
quantitative reverse transcription polymerase chain reaction (qRT-PCR)
severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Journal
bioRxiv : the preprint server for biology
Titre abrégé: bioRxiv
Pays: United States
ID NLM: 101680187
Informations de publication
Date de publication:
01 May 2020
01 May 2020
Historique:
entrez:
9
6
2020
pubmed:
9
6
2020
medline:
9
6
2020
Statut:
epublish
Résumé
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets.
Identifiants
pubmed: 32511352
doi: 10.1101/2020.04.20.048066
pmc: PMC7255793
pii:
doi:
Types de publication
Preprint
Langues
eng
Subventions
Organisme : NCATS NIH HHS
ID : TL1 TR002386
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR002384
Pays : United States
Commentaires et corrections
Type : UpdateIn
Déclaration de conflit d'intérêts
Conflicts of Interest Nathan Tanner and Bradley W. Langhorst are employees at New England Biolabs.
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