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...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Publishing Group
2021-03-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-021-21361-7 |
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| language |
English |
| format |
Article |
| sources |
DOAJ |
| 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 |
| spellingShingle |
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 Nature Communications |
| 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 Publishing Group |
| series |
Nature Communications |
| issn |
2041-1723 |
| publishDate |
2021-03-01 |
| 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. |
| url |
https://doi.org/10.1038/s41467-021-21361-7 |
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doaj-e049d27579f84e2b9f12b7b11bc7c4362021-03-14T12:06:54ZengNature Publishing GroupNature Communications2041-17232021-03-0112111710.1038/s41467-021-21361-7Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactionsDaniel Butler0Christopher Mozsary1Cem Meydan2Jonathan Foox3Joel Rosiene4Alon Shaiber5David Danko6Ebrahim Afshinnekoo7Matthew MacKay8Fritz J. Sedlazeck9Nikolay A. Ivanov10Maria Sierra11Diana Pohle12Michael Zietz13Undina Gisladottir14Vijendra Ramlall15Evan T. Sholle16Edward J. Schenck17Craig D. Westover18Ciaran Hassan19Krista Ryon20Benjamin Young21Chandrima Bhattacharya22Dianna L. Ng23Andrea C. Granados24Yale A. Santos25Venice Servellita26Scot Federman27Phyllis Ruggiero28Arkarachai Fungtammasan29Chen-Shan Chin30Nathaniel M. Pearson31Bradley W. Langhorst32Nathan A. Tanner33Youngmi Kim34Jason W. Reeves35Tyler D. Hether36Sarah E. Warren37Michael Bailey38Justyna Gawrys39Dmitry Meleshko40Dong Xu41Mara Couto-Rodriguez42Dorottya Nagy-Szakal43Joseph Barrows44Heather Wells45Niamh B. O’Hara46Jeffrey A. Rosenfeld47Ying Chen48Peter A. D. Steel49Amos J. Shemesh50Jenny Xiang51Jean Thierry-Mieg52Danielle Thierry-Mieg53Angelika Iftner54Daniela Bezdan55Elizabeth Sanchez56Thomas R. Campion57John Sipley58Lin Cong59Arryn Craney60Priya Velu61Ari M. Melnick62Sagi Shapira63Iman Hajirasouliha64Alain Borczuk65Thomas Iftner66Mirella Salvatore67Massimo Loda68Lars F. Westblade69Melissa Cushing70Shixiu Wu71Shawn Levy72Charles Chiu73Robert E. Schwartz74Nicholas Tatonetti75Hanna Rennert76Marcin Imielinski77Christopher E. Mason78Department of Physiology and Biophysics, Weill Cornell MedicineDepartment of Physiology and Biophysics, Weill Cornell MedicineDepartment of Physiology and Biophysics, Weill Cornell MedicineDepartment of Physiology and Biophysics, Weill Cornell MedicineNew York Genome CenterNew York Genome CenterDepartment of Physiology and Biophysics, Weill Cornell MedicineDepartment of Physiology and Biophysics, Weill Cornell MedicineDepartment of Physiology and Biophysics, Weill Cornell MedicineHuman Genome Sequencing Center, Baylor College of MedicineDepartment of Physiology and Biophysics, Weill Cornell MedicineDepartment of Physiology and Biophysics, Weill Cornell MedicineInstitute of Medical Virology and Epidemiology of Viral Diseases, University Hospital TuebingenDepartment of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia UniversityDepartment of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia UniversityDepartment of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia UniversityInformation Technologies & Services Department, Weill Cornell MedicineDepartment of Medicine, Weill Cornell MedicineDepartment of Physiology and Biophysics, Weill Cornell MedicineDepartment of Physiology and Biophysics, Weill Cornell MedicineDepartment of Physiology and Biophysics, Weill Cornell MedicineDepartment of Physiology and Biophysics, Weill Cornell MedicineDepartment of Physiology and Biophysics, Weill Cornell MedicineDepartment of Laboratory Medicine, University of CaliforniaDepartment of Laboratory Medicine, University of CaliforniaDepartment of Laboratory Medicine, University of CaliforniaDepartment of Laboratory Medicine, University of CaliforniaDepartment of Laboratory Medicine, University of CaliforniaDepartment of Pathology and Laboratory Medicine, Weill Cornell MedicineDNAnexus, Inc.DNAnexus, Inc.Root Deep InsightNew England BiolabsNew England BiolabsNanoString TechnologiesNanoString TechnologiesNanoString TechnologiesNanoString TechnologiesNanoString TechnologiesDepartment of Pathology and Laboratory Medicine, Weill Cornell MedicineDepartment of Physiology and Biophysics, Weill Cornell MedicineGenomics Resources Core Facility, Weill Cornell MedicineBiotia, Inc.Biotia, Inc.Biotia, Inc.Biotia, Inc.Biotia, Inc.Rutgers Cancer Institute of New JerseyRutgers Cancer Institute of New JerseyDepartment of Emergency Medicine, Weill Cornell MedicineDepartment of Emergency Medicine, Weill Cornell MedicineGenomics Resources Core Facility, Weill Cornell MedicineNational Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthNational Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthInstitute of Medical Virology and Epidemiology of Viral Diseases, University Hospital TuebingenInstitute of Medical Virology and Epidemiology of Viral Diseases, University Hospital TuebingenDepartment of Medicine, Weill Cornell MedicineInformation Technologies & Services Department, Weill Cornell MedicineDepartment of Pathology and Laboratory Medicine, Weill Cornell MedicineDepartment of Pathology and Laboratory Medicine, Weill Cornell MedicineDepartment of Pathology and Laboratory Medicine, Weill Cornell MedicineDepartment of Pathology and Laboratory Medicine, Weill Cornell MedicineDepartment of Medicine, Weill Cornell MedicineDepartment of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia UniversityDepartment of Physiology and Biophysics, Weill Cornell MedicineDepartment of Medicine, Weill Cornell MedicineInstitute of Medical Virology and Epidemiology of Viral Diseases, University Hospital TuebingenDepartment of Medicine, Weill Cornell MedicineDepartment of Pathology and Laboratory Medicine, Weill Cornell MedicineDepartment of Pathology and Laboratory Medicine, Weill Cornell MedicineDepartment of Pathology and Laboratory Medicine, Weill Cornell MedicineHangzhou Cancer Institute, Hangzhou Cancer HospitalHudsonAlpha Discovery InstituteDepartment of Laboratory Medicine, University of CaliforniaDepartment of Medicine, Weill Cornell MedicineDepartment of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia UniversityDepartment of Pathology and Laboratory Medicine, Weill Cornell MedicineNew York Genome CenterDepartment of Physiology and Biophysics, Weill Cornell MedicineHere, 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.https://doi.org/10.1038/s41467-021-21361-7 |