Nature Communications (Mar 2021)
Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions
- 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
Affiliations
- Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Joel Rosiene
- New York Genome Center
- Alon Shaiber
- New York Genome Center
- David Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine
- Nikolay A. Ivanov
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Maria Sierra
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Diana Pohle
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen
- Michael Zietz
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University
- Undina Gisladottir
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University
- Vijendra Ramlall
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University
- Evan T. Sholle
- Information Technologies & Services Department, Weill Cornell Medicine
- Edward J. Schenck
- Department of Medicine, Weill Cornell Medicine
- Craig D. Westover
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Ciaran Hassan
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Krista Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Benjamin Young
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Chandrima Bhattacharya
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Dianna L. Ng
- Department of Laboratory Medicine, University of California
- Andrea C. Granados
- Department of Laboratory Medicine, University of California
- Yale A. Santos
- Department of Laboratory Medicine, University of California
- Venice Servellita
- Department of Laboratory Medicine, University of California
- Scot Federman
- Department of Laboratory Medicine, University of California
- Phyllis Ruggiero
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
- Arkarachai Fungtammasan
- DNAnexus, Inc.
- Chen-Shan Chin
- DNAnexus, Inc.
- Nathaniel M. Pearson
- Root Deep Insight
- Bradley W. Langhorst
- New England Biolabs
- Nathan A. Tanner
- New England Biolabs
- Youngmi Kim
- NanoString Technologies
- Jason W. Reeves
- NanoString Technologies
- Tyler D. Hether
- NanoString Technologies
- Sarah E. Warren
- NanoString Technologies
- Michael Bailey
- NanoString Technologies
- Justyna Gawrys
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
- Dmitry Meleshko
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Dong Xu
- Genomics Resources Core Facility, Weill Cornell Medicine
- Mara Couto-Rodriguez
- Biotia, Inc.
- Dorottya Nagy-Szakal
- Biotia, Inc.
- Joseph Barrows
- Biotia, Inc.
- Heather Wells
- Biotia, Inc.
- Niamh B. O’Hara
- Biotia, Inc.
- Jeffrey A. Rosenfeld
- Rutgers Cancer Institute of New Jersey
- Ying Chen
- Rutgers Cancer Institute of New Jersey
- Peter A. D. Steel
- Department of Emergency Medicine, Weill Cornell Medicine
- Amos J. Shemesh
- Department of Emergency Medicine, Weill Cornell Medicine
- Jenny Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine
- Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
- Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
- Angelika Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen
- Daniela Bezdan
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen
- Elizabeth Sanchez
- Department of Medicine, Weill Cornell Medicine
- Thomas R. Campion
- Information Technologies & Services Department, Weill Cornell Medicine
- John Sipley
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
- Lin Cong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
- Arryn Craney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
- Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
- Ari M. Melnick
- Department of Medicine, Weill Cornell Medicine
- Sagi Shapira
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University
- Iman Hajirasouliha
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Alain Borczuk
- Department of Medicine, Weill Cornell Medicine
- Thomas Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen
- Mirella Salvatore
- Department of Medicine, Weill Cornell Medicine
- Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
- Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
- Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
- Shixiu Wu
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital
- Shawn Levy
- HudsonAlpha Discovery Institute
- Charles Chiu
- Department of Laboratory Medicine, University of California
- Robert E. Schwartz
- Department of Medicine, Weill Cornell Medicine
- Nicholas Tatonetti
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University
- Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
- Marcin Imielinski
- New York Genome Center
- Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine
- DOI
- https://doi.org/10.1038/s41467-021-21361-7
- Journal volume & issue
-
Vol. 12,
no. 1
pp. 1 – 17
Abstract
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.
