 Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactionsDaniel Butler,
Christopher Mozsary,
Cem Meydan,
Jonathan Foox,
Joel Rosiene,
Alon Shaiber,
David Danko,
Ebrahim Afshinnekoo,
Matthew MacKay,
Fritz J. Sedlazeck,
Nikolay A. Ivanov,
Maria Sierra,
Diana Pohle,
Michael Zietz,
Undina Gisladottir,
Vijendra Ramlall,
Evan T. Sholle,
Edward J. Schenck,
Craig D. Westover,
Ciaran Hassan,
Krista Ryon,
Benjamin Young,
Chandrima Bhattacharya,
Dianna L. Ng,
Andrea C. Granados,
Yale A. Santos,
Venice Servellita,
Scot Federman,
Phyllis Ruggiero,
Arkarachai Fungtammasan,
Chen-Shan Chin,
Nathaniel M. Pearson,
Bradley W. Langhorst,
Nathan A. Tanner,
Youngmi Kim,
Jason W. Reeves,
Tyler D. Hether,
Sarah E. Warren,
Michael Bailey,
Justyna Gawrys,
Dmitry Meleshko,
Dong Xu,
Mara Couto-Rodriguez,
Dorottya Nagy-Szakal,
Joseph Barrows,
Heather Wells,
Niamh B. O’Hara,
Jeffrey A. Rosenfeld,
Ying Chen,
Peter A. D. Steel,
Amos J. Shemesh,
Jenny Xiang,
Jean Thierry-Mieg,
Danielle Thierry-Mieg,
Angelika Iftner,
Daniela Bezdan,
Elizabeth Sanchez,
Thomas R. Campion,
John Sipley,
Lin Cong,
Arryn Craney,
Priya Velu,
Ari M. Melnick,
Sagi Shapira,
Iman Hajirasouliha,
Alain Borczuk,
Thomas Iftner,
Mirella Salvatore,
Massimo Loda,
Lars F. Westblade,
Melissa Cushing,
Shixiu Wu,
Shawn Levy,
Charles Chiu,
Robert E. Schwartz (),
Nicholas Tatonetti (),
Hanna Rennert (),
Marcin Imielinski () and
Christopher E. Mason ()
Nature Communications, 2021, vol. 12, issue 1, 1-17 Abstract: Abstract In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin–angiotensin–aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies. Date: 2021 Downloads: (external link) Related works: Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21361-7 Ordering information: This journal article can be ordered from DOI: 10.1038/s41467-021-21361-7 Access Statistics for this article Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie More articles in Nature Communications from Nature |
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