ArticleNature communications2021
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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In one paragraph
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 136 papers, 2 of them syntheses that pooled it.
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0cells of the map it votes in
136citing papers in PubMed, 2 pooled it
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
136 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Laboratory-based molecular test alternatives to RT-PCR for the diagnosis of SARS-CoV-2 infection.The Cochrane database of systematic reviews · 2024Pooled it
- Genome-scale metabolic modeling reveals SARS-CoV-2-induced metabolic changes and antiviral targets.Molecular systems biology · 2021Pooled it
- Long-term major histocompatibility complex class I suppression in astronauts and clinical implications.Communications biology · 2026Review
- Progress in the Application of Machine Learning in the Field of Single-Cell and Spatial Transcriptomics.Genes · 2026Review
- Identifying the optimal rapid antigen test for screening and determining the end of isolation: A modeling study.PLoS computational biology · 2026Article
- A method to enable clinical and translational research teams with custom real-world data from electronic health record systems.Journal of clinical and translational science · 2026Article
- Targeting G9a-miScience · 2025Article
- Deploying Metagenomics to Characterize Microbial Pathogens During Outbreak of Acute Febrile Illness Among Children in Tanzania.Pathogens (Basel, Switzerland) · 2025Article
- Structural insights into the assembly and regulation of 2'-O RNA methylation by SARS-CoV-2 nsp16/nsp10.Structure (London, England : 1993) · 2025Article
- SARS-CoV-2 biological clones are genetically heterogeneous and include clade-discordant residues.Journal of virology · 2025Article
- The Exon-Based Transcriptomic Analysis of Parkinson's Disease.Biomolecules · 2025Article
- Metatranscriptomic profiling reveals pathogen and host response signatures of pediatric acute sinusitis and upper respiratory infection.Genome medicine · 2025Article
- A general and biomedical perspective of viral quasispecies.RNA (New York, N.Y.) · 2025Review
- OPG and BAFF as predictive biomarkers of the severity of SARS-CoV-2 infection.Journal of cellular and molecular medicine · 2025Article
- lncRNA NORAD modulates STAT3/STAT1 balance and innate immune responses in human cells via interaction with STAT3.Nature communications · 2025Article
- Longitudinal host transcriptional responses to SARS-CoV-2 infection in adults with extremely high viral load.PloS one · 2025Article
- Lethal COVID-19 associates with RAAS-induced inflammation for multiple organ damage including mediastinal lymph nodes.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Differential Gene Expression in the Upper Respiratory Tract following Acute COVID-19 Infection in Ambulatory Patients That Develop Long COVID.Pathogens (Basel, Switzerland) · 2024Article
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Genomic surveillance of SARS-CoV-2 using long-range PCR primers.Frontiers in microbiology · 2024Article
76 more citing papers are in PubMed but not listed here.
Corrections and comments
- Update of
Authors and funding
79 authors.
Daniel Butler *Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.ORCID 0000-0002-3687-8419
Christopher Mozsary *Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Cem Meydan *Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.ORCID 0000-0002-0663-6216
Jonathan Foox *Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Joel Rosiene *New York Genome Center, New York, NY, USA.
Alon Shaiber *New York Genome Center, New York, NY, USA.
David Danko *Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Ebrahim AfshinnekooDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Matthew MacKayDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Fritz J SedlazeckHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.ORCID 0000-0001-6040-2691
Nikolay A IvanovDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.ORCID 0000-0003-4021-8875
Maria SierraDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Diana PohleInstitute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany.
Michael ZietzDepartment of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA.ORCID 0000-0003-0539-630X
Undina GisladottirDepartment of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA.ORCID 0000-0001-5892-0852
Vijendra RamlallDepartment of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA.
Evan T SholleInformation Technologies & Services Department, Weill Cornell Medicine, New York, NY, USA.ORCID 0000-0001-9518-4399
Edward J SchenckDepartment of Medicine, Weill Cornell Medicine, New York, NY, USA.
Craig D WestoverDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Ciaran HassanDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Krista RyonDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Benjamin YoungDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Chandrima BhattacharyaDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Dianna L NgDepartment of Laboratory Medicine, University of California, San Francisco, CA, USA.
Andrea C GranadosDepartment of Laboratory Medicine, University of California, San Francisco, CA, USA.
Yale A SantosDepartment of Laboratory Medicine, University of California, San Francisco, CA, USA.
Venice ServellitaDepartment of Laboratory Medicine, University of California, San Francisco, CA, USA.
Scot FedermanDepartment of Laboratory Medicine, University of California, San Francisco, CA, USA.ORCID 0000-0001-8712-3131
Phyllis RuggieroDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Arkarachai FungtammasanDNAnexus, Inc., Mountain View, CA, USA.
Chen-Shan ChinDNAnexus, Inc., Mountain View, CA, USA.
Nathaniel M PearsonRoot Deep Insight, Boston, MA, USA.
Bradley W LanghorstNew England Biolabs, Ipswich, MA, USA.ORCID 0000-0001-7390-1094
Nathan A TannerNew England Biolabs, Ipswich, MA, USA.
Youngmi KimNanoString Technologies, Seattle, WA, USA.
Jason W ReevesNanoString Technologies, Seattle, WA, USA.
Tyler D HetherNanoString Technologies, Seattle, WA, USA.
Sarah E WarrenNanoString Technologies, Seattle, WA, USA.
Michael BaileyNanoString Technologies, Seattle, WA, USA.
Justyna GawrysDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Dmitry MeleshkoDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Dong XuGenomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA.
Mara Couto-RodriguezBiotia, Inc., New York, NY, USA.ORCID 0000-0002-9799-0068
Dorottya Nagy-SzakalBiotia, Inc., New York, NY, USA.
Joseph BarrowsBiotia, Inc., New York, NY, USA.
Heather WellsBiotia, Inc., New York, NY, USA.
Niamh B O'HaraBiotia, Inc., New York, NY, USA.
Jeffrey A RosenfeldRutgers Cancer Institute of New Jersey, New York, NJ, USA.
Ying ChenRutgers Cancer Institute of New Jersey, New York, NJ, USA.ORCID 0000-0002-0072-1567
Peter A D SteelDepartment of Emergency Medicine, Weill Cornell Medicine, New York, NY, USA.
Amos J ShemeshDepartment of Emergency Medicine, Weill Cornell Medicine, New York, NY, USA.ORCID 0000-0002-1424-2196
Jenny XiangGenomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA.
Jean Thierry-MiegNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Danielle Thierry-MiegNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Angelika IftnerInstitute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany.
Daniela BezdanInstitute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany.ORCID 0000-0002-1203-8239
Elizabeth SanchezDepartment of Medicine, Weill Cornell Medicine, New York, NY, USA.
Thomas R CampionInformation Technologies & Services Department, Weill Cornell Medicine, New York, NY, USA.ORCID 0000-0001-7624-769X
John SipleyDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Lin CongDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Arryn CraneyDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Priya VeluDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Ari M MelnickDepartment of Medicine, Weill Cornell Medicine, New York, NY, USA.ORCID 0000-0002-8074-2287
Sagi ShapiraDepartment of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA.ORCID 0000-0002-5425-3682
Iman HajirasoulihaDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Alain BorczukDepartment of Medicine, Weill Cornell Medicine, New York, NY, USA.ORCID 0000-0001-6807-8064
Thomas IftnerInstitute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany.
Mirella SalvatoreDepartment of Medicine, Weill Cornell Medicine, New York, NY, USA.ORCID 0000-0002-8296-0376
Massimo LodaDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Lars F WestbladeDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Melissa CushingDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Shixiu WuHangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China.
Shawn LevyHudsonAlpha Discovery Institute, Huntsville, AL, USA.ORCID 0000-0002-1369-5740
Charles ChiuDepartment of Laboratory Medicine, University of California, San Francisco, CA, USA.ORCID 0000-0003-2915-2094
Robert E SchwartzDepartment of Medicine, Weill Cornell Medicine, New York, NY, USA. res2025@med.cornell.edu.ORCID 0000-0002-5417-5995
Nicholas TatonettiDepartment of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA. npt2105@cumc.columbia.edu.ORCID 0000-0002-2700-2597
Hanna RennertDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA. har2006@med.cornell.edu.ORCID 0000-0002-1759-2562
Marcin ImielinskiNew York Genome Center, New York, NY, USA. mai9037@med.cornell.edu.ORCID 0000-0002-2211-4741
Christopher E MasonDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu.ORCID 0000-0002-1850-1642
Funding
Disparities in COVID Disease Severity and Outcomes in New York CityUL1TR002384 · NCATS · WEILL MEDICAL COLL OF CORNELL UNIV · PI JULIANNE L IMPERATO-MCGINLEY · 2017 to 2026
$86.2MClinical and Translational Science CenterUL1TR000457 · NCATS · WEILL MEDICAL COLL OF CORNELL UNIV · PI IMPERATO-MCGINLEY, JULIANNE L · 2012 to 2016
$46.0MViral Diversity and Pathogenicity in Mucosal Respiratory and Gastrointestinal DiseaseU19AI144297 · NIAID · BAYLOR COLLEGE OF MEDICINE · PI MARESSO, ANTHONY W · 2019 to 2024
$30.1MTraining in Biomedical Informatics at Columbia UniversityT15LM007079 · NLM · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI NOEMIE ELHADAD, GEORGE M HRIPCSAK · 1992 to 2026
$28.9MJ. NRSA Training CoreTL1TR002386 · NCATS · WEILL MEDICAL COLL OF CORNELL UNIV · PI Genevieve Giny Fouda Amou ou · 2017 to 2026
$5.8MSupplement for MINI point-of-use deviceU01DA053941 · NIDA · UNIVERSITY OF MIAMI CORAL GABLES · PI MASON, CHRISTOPHER EDWARD, SCHURER, STEPHAN C · 2021 to 2022
$5.2MMetagenomic profiling of urinary cell-free DNA to monitor urinary tract infection after kidney transplantationR01AI151059 · NIAID · CORNELL UNIVERSITY · PI DADHANIA, DARSHANA, DE VLAMINCK, IWIJN · 2020 to 2024
$3.4MThe Spatiotemporal Landscape of the Human Brain EpitranscriptomeR01MH117406 · NIMH · WEILL MEDICAL COLL OF CORNELL UNIV · PI MASON, CHRISTOPHER EDWARD · 2018 to 2022
$3.3MPrecision Pharmacology and Pharmacovigilance: Leveraging AI to address drug safety knowledge gapsR35GM131905 · NIGMS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Nicholas P Tatonetti · 2019 to 2026
$3.3MOptimization of the engineered 3D hepatic microenvironment enhances pluripotent stem cell derived hepatocyteR01DK121072 · NIDDK · WEILL MEDICAL COLL OF CORNELL UNIV · PI SCHWARTZ, ROBERT E · 2020 to 2024
$2.6MImproving Metagenomic Analysis with Novel Algorithms and TechnologiesR35GM138152 · NIGMS · WEILL MEDICAL COLL OF CORNELL UNIV · PI Iman Hajirasouliha · 2020 to 2026
$2.5MCommunity Research Education and Engagement for Data Science (CREEDS)R25EB020393 · NIBIB · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI CLAUDIO, LUZ, KOVATCH, PATRICIA · 2015 to 2017
$578kNCATS NIH HHS TL1 TR002386NCATS NIH HHS UL1 TR000457NCATS NIH HHS UL1 TR002384NIAID NIH HHS R01 AI151059NIAID NIH HHS U19 AI144297NIBIB NIH HHS R25 EB020393NIDA NIH HHS U01 DA053941NIDDK NIH HHS R01 DK121072NIGMS NIH HHS R35 GM131905NIGMS NIH HHS R35 GM138152NIMH NIH HHS R01 MH117406NLM NIH HHS T15 LM007079
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.
Indexed as
AdultAgedAngiotensin-Converting Enzyme InhibitorsAngiotensin Receptor AntagonistsAntiviral AgentsCOVID-19COVID-19 Drug TreatmentCOVID-19 Nucleic Acid TestingDrug InteractionsFemaleGene Expression ProfilingGenome, ViralHLA AntigensHost Microbial InteractionsHumansMaleAngiotensin-Converting Enzyme InhibitorsAngiotensin Receptor AntagonistsAntiviral AgentsHLA Antigens
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