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10.1038/s41467-021-21361-7

http://scihub22266oqcxt.onion/10.1038/s41467-021-21361-7
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33712587!7954844!33712587
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suck abstract from ncbi


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pmid33712587      Nat+Commun 2021 ; 12 (1): 1660
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  • Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions #MMPMID33712587
  • Butler D; Mozsary C; Meydan C; Foox J; Rosiene J; Shaiber A; Danko D; Afshinnekoo E; MacKay M; Sedlazeck FJ; Ivanov NA; Sierra M; Pohle D; Zietz M; Gisladottir U; Ramlall V; Sholle ET; Schenck EJ; Westover CD; Hassan C; Ryon K; Young B; Bhattacharya C; Ng DL; Granados AC; Santos YA; Servellita V; Federman S; Ruggiero P; Fungtammasan A; Chin CS; Pearson NM; Langhorst BW; Tanner NA; Kim Y; Reeves JW; Hether TD; Warren SE; Bailey M; Gawrys J; Meleshko D; Xu D; Couto-Rodriguez M; Nagy-Szakal D; Barrows J; Wells H; O'Hara NB; Rosenfeld JA; Chen Y; Steel PAD; Shemesh AJ; Xiang J; Thierry-Mieg J; Thierry-Mieg D; Iftner A; Bezdan D; Sanchez E; Campion TR Jr; Sipley J; Cong L; Craney A; Velu P; Melnick AM; Shapira S; Hajirasouliha I; Borczuk A; Iftner T; Salvatore M; Loda M; Westblade LF; Cushing M; Wu S; Levy S; Chiu C; Schwartz RE; Tatonetti N; Rennert H; Imielinski M; Mason CE
  • Nat Commun 2021[Mar]; 12 (1): 1660 PMID33712587show ga
  • 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.
  • |Adult[MESH]
  • |Aged[MESH]
  • |Angiotensin Receptor Antagonists/pharmacology[MESH]
  • |Angiotensin-Converting Enzyme Inhibitors/pharmacology[MESH]
  • |Antiviral Agents/pharmacology[MESH]
  • |COVID-19 Drug Treatment[MESH]
  • |COVID-19 Nucleic Acid Testing[MESH]
  • |COVID-19/epidemiology/*genetics/*virology[MESH]
  • |Drug Interactions[MESH]
  • |Female[MESH]
  • |Gene Expression Profiling[MESH]
  • |Genome, Viral[MESH]
  • |HLA Antigens/genetics[MESH]
  • |Host Microbial Interactions/drug effects/genetics[MESH]
  • |Humans[MESH]
  • |Male[MESH]
  • |Middle Aged[MESH]
  • |Molecular Diagnostic Techniques[MESH]
  • |New York City/epidemiology[MESH]
  • |Nucleic Acid Amplification Techniques[MESH]
  • |Pandemics[MESH]
  • |RNA-Seq[MESH]


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