Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

Here, using clinical samples and autopsy tissues, the authors combine fast-colorimetric test (LAMP) for SARS-CoV-2 infection and large-scale shotgun metatranscriptomics for host, viral, and microbial profiling and provide a map of the viral genetic features of the New York City outbreak and associat...

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Autores principales:	Daniel 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, Christopher E. Mason
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Science Q
Acceso en línea:	https://doaj.org/article/e049d27579f84e2b9f12b7b11bc7c436
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spelling	oai:doaj.org-article:e049d27579f84e2b9f12b7b11bc7c4362021-12-02T11:36:20ZShotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions10.1038/s41467-021-21361-72041-1723https://doaj.org/article/e049d27579f84e2b9f12b7b11bc7c4362021-03-01T00:00:00Zhttps://doi.org/10.1038/s41467-021-21361-7https://doaj.org/toc/2041-1723Here, using clinical samples and autopsy tissues, the authors combine fast-colorimetric test (LAMP) for SARS-CoV-2 infection and large-scale shotgun metatranscriptomics for host, viral, and microbial profiling and provide a map of the viral genetic features of the New York City outbreak and associate specific host responses and gene expression perturbations with SARS-CoV-2 infection.Daniel ButlerChristopher MozsaryCem MeydanJonathan FooxJoel RosieneAlon ShaiberDavid DankoEbrahim AfshinnekooMatthew MacKayFritz J. SedlazeckNikolay A. IvanovMaria SierraDiana PohleMichael ZietzUndina GisladottirVijendra RamlallEvan T. SholleEdward J. SchenckCraig D. WestoverCiaran HassanKrista RyonBenjamin YoungChandrima BhattacharyaDianna L. NgAndrea C. GranadosYale A. SantosVenice ServellitaScot FedermanPhyllis RuggieroArkarachai FungtammasanChen-Shan ChinNathaniel M. PearsonBradley W. LanghorstNathan A. TannerYoungmi KimJason W. ReevesTyler D. HetherSarah E. WarrenMichael BaileyJustyna GawrysDmitry MeleshkoDong XuMara Couto-RodriguezDorottya Nagy-SzakalJoseph BarrowsHeather WellsNiamh B. O’HaraJeffrey A. RosenfeldYing ChenPeter A. D. SteelAmos J. ShemeshJenny XiangJean Thierry-MiegDanielle Thierry-MiegAngelika IftnerDaniela BezdanElizabeth SanchezThomas R. CampionJohn SipleyLin CongArryn CraneyPriya VeluAri M. MelnickSagi ShapiraIman HajirasoulihaAlain BorczukThomas IftnerMirella SalvatoreMassimo LodaLars F. WestbladeMelissa CushingShixiu WuShawn LevyCharles ChiuRobert E. SchwartzNicholas TatonettiHanna RennertMarcin ImielinskiChristopher E. MasonNature PortfolioarticleScienceQENNature Communications, Vol 12, Iss 1, Pp 1-17 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Science Q
spellingShingle	Science Q Daniel 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 Christopher E. Mason Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions
description	Here, using clinical samples and autopsy tissues, the authors combine fast-colorimetric test (LAMP) for SARS-CoV-2 infection and large-scale shotgun metatranscriptomics for host, viral, and microbial profiling and provide a map of the viral genetic features of the New York City outbreak and associate specific host responses and gene expression perturbations with SARS-CoV-2 infection.
format	article
author	Daniel 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 Christopher E. Mason
author_facet	Daniel 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 Christopher E. Mason
author_sort	Daniel Butler
title	Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions
title_short	Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions
title_full	Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions
title_fullStr	Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions
title_full_unstemmed	Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions
title_sort	shotgun transcriptome, spatial omics, and isothermal profiling of sars-cov-2 infection reveals unique host responses, viral diversification, and drug interactions
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/e049d27579f84e2b9f12b7b11bc7c436
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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

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