| Literature DB >> 32511352 |
Daniel J Butler1, Christopher Mozsary1, Cem Meydan1,2,3, David Danko1,4, Jonathan Foox1,2, Joel Rosiene5,6, Alon Shaiber5,6,7, Ebrahim Afshinnekoo1,2,3, Matthew MacKay1, Fritz J Sedlazeck8, Nikolay A Ivanov1,2,9, Maria Sierra1, Diana Pohle10, Michael Zietz11, Undina Gisladottir11, Vijendra Ramlall11,12, Craig D Westover1, Krista Ryon1, Benjamin Young1, Chandrima Bhattacharya1, Phyllis Ruggiero6, Bradley W Langhorst13, Nathan Tanner13, Justyna Gawrys6, Dmitry Meleshko1,4, Dong Xu14, Peter A D Steel15, Amos J Shemesh15, Jenny Xiang14,16, Jean Thierry-Mieg17, Danielle Thierry-Mieg17, Robert E Schwartz18, Angelika Iftner10, Daniela Bezdan10, John Sipley6, Lin Cong6, Arryn Craney6, Priya Velu6, Ari M Melnick18, Iman Hajirasouliha1,2,7, Stacy M Horner19,20, Thomas Iftner10, Mirella Salvatore16, Massimo Loda6, Lars F Westblade6,16, Melissa Cushing6, Shawn Levy21, Shixiu Wu22,23, Nicholas Tatonetti11, Marcin Imielinski5,6,7, Hanna Rennert6, Christopher E Mason1,2,3,24.
Abstract
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.Entities:
Keywords: 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)
Year: 2020 PMID： 32511352 PMCID： PMC7255793 DOI： 10.1101/2020.04.20.048066
Source DB: PubMed Journal: bioRxiv