ArticleCell2020
Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics.
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Article in Cell, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers.
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99citing papers in PubMed
1.8field-weighted citation impact, top 8% of its field
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Who cites it
99 citing papers in PubMed, 123 citations in OpenAlex.
- Genomics in containment: BSL-4-compatible workflows enable high-resolution genomic and transcriptomic analyses of Risk Group 4 viruses.iScience · 2026Article
- Ebola virus disease in the modern era: pathogenesis, therapeutic advances, vaccine strategies, and global health preparedness.Infection · 2026Review
- Implications of RNA virus persistence for post-acute sequelae and chronic inflammatory syndromes.Nature immunology · 2026Review
- A scalable, low-cost, sample hashing workflow for multiomic single-cell analysis using the Seq-Well SNature protocols · 2026Review
- Revisiting Ravn virus as the lesser known orthomarburgvirus.Npj viruses · 2026Review
- Platelet-like particles released from Ebola virus-infected megakaryocytic cells behave like virus-like particles.PLoS pathogens · 2026Article
- Agnostic viral detection at single-cell resolution reveals novel viruses.Nature biotechnology · 2026Article
- Molecular responses of human retinal pigment epithelial cells to ebolavirus VP24.Molecular vision · 2026Article
- Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes.Nature biotechnology · 2026Article
- Estimating time since influenza virus exposure using single-cell proteomic data.Frontiers in immunology · 2026Article
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- Single-cell RNA sequencing reveals T and B cell-related immune features in foot and mouth disease virus-infected mice.Virulence · 2025Article
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- Special Issue "Molecular Biology of Host and Pathogen Interactions: 2nd Edition".International journal of molecular sciences · 2025Article
- Filovirus infection disrupts epithelial barrier function and ion transport in human iPSC-derived gut organoids.PLoS pathogens · 2025Article
- Fluid-Squid: DIY Multiplexed Imaging of Cells and Tissues.bioRxiv : the preprint server for biology · 2025Article
- Spatial Transcriptomics to Study Virus-Host Interactions.Annual review of virology · 2025Review
- scIVNL-seq resolves in vivo single-cell RNA dynamics of immune cells during Salmonella infection.Nature communications · 2025Article
- Age-associated immune dysregulation and B cell dysfunction drive severe outcomes in SFTSV infection.PLoS pathogens · 2025Article
- Advances in Single-Cell Sequencing for Infectious Diseases: Progress and Perspectives.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
39 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
27 authors at 3 institutions in 3 countries.
Dylan KotliarDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address: dylan_kotliar@hms.harvard.edu.
Aaron E LinFAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: alin@broadinstitute.org.
James LogueIntegrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
Travis K HughesBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA.
Nadine M KhouryFAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Siddharth S RajuDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Marc H WadsworthBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA.
Han ChenDepartment of Pathology, Stanford University, Stanford, CA 94305, USA.
Jonathan R KurtzIntegrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
Bonnie Dighero-KempIntegrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
Zach B BjornsonDepartment of Pathology, Stanford University, Stanford, CA 94305, USA.
Nilanjan MukherjeeDepartment of Pathology, Stanford University, Stanford, CA 94305, USA.
Brian A SellersTrans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, MD 20814, USA.
Nancy TranBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA.
Matthew R BauerFAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Gordon C AdamsFAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Ricky AdamsIntegrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
John L RinnBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
Marta MeléBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia 08034, Spain.
Stephen F SchaffnerFAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA.
Garry P NolanDepartment of Pathology, Stanford University, Stanford, CA 94305, USA.
Kayla G BarnesBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK.
Lisa E HensleyIntegrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA. Electronic address: lisa.hensley@nih.gov.
David R McIlwainDepartment of Pathology, Stanford University, Stanford, CA 94305, USA. Electronic address: mcilwain@stanford.edu.
Alex K ShalekBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA.
Pardis C SabetiFAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
Richard S BennettIntegrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
Broad Institute · USNational Institutes of Health · USStanford University · US
Funding
Using a tonsil organoid system to probe conditions for the induction of protective antibody and T cell responses to influenza.U19AI057229 · NIAID · STANFORD UNIVERSITY · PI Mark Morris Davis · 2003 to 2026
$88.5MViral Genomics: evolution, spread, and host interactionsU19AI110818 · NIAID · BROAD INSTITUTE, INC. · PI CUOMO, CHRISTINA A · 2014 to 2024
$66.5MMedical Scientist Training ProgramT32GM007753 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI WALENSKY, LOREN DAVID · 1985 to 2021
$50.0MAn integrated multiplexed genomic assay for low input clinical samples1U24AI118672 · NIAID · BROAD INSTITUTE, INC. · PI SHALEK, ALEX K · 2015 to 2019
$2.0MIdentifying genetic determinants of Rotavirus Vaccine Failure in Malawian ChildrenK01TW010853 · FIC · HARVARD SCHOOL OF PUBLIC HEALTH · PI BARNES, KAYLA G · 2018 to 2022
$731kFIC NIH HHS K01 TW010853Howard Hughes Medical InstituteNIAID NIH HHS HHSN272200700016INIAID NIH HHS HHSN272201800013CNIAID NIH HHS U19 AI057229NIAID NIH HHS U19 AI110818NIAID NIH HHS U24 AI118672NIGMS NIH HHS T32 GM007753
Abstract
Ebola virus (EBOV) causes epidemics with high mortality yet remains understudied due to the challenge of experimentation in high-containment and outbreak settings. Here, we used single-cell transcriptomics and CyTOF-based single-cell protein quantification to characterize peripheral immune cells during EBOV infection in rhesus monkeys. We obtained 100,000 transcriptomes and 15,000,000 protein profiles, finding that immature, proliferative monocyte-lineage cells with reduced antigen-presentation capacity replace conventional monocyte subsets, while lymphocytes upregulate apoptosis genes and decline in abundance. By quantifying intracellular viral RNA, we identify molecular determinants of tropism among circulating immune cells and examine temporal dynamics in viral and host gene expression. Within infected cells, EBOV downregulates STAT1 mRNA and interferon signaling, and it upregulates putative pro-viral genes (e.g., DYNLL1 and HSPA5), nominating pathways the virus manipulates for its replication. This study sheds light on EBOV tropism, replication dynamics, and elicited immune response and provides a framework for characterizing host-virus interactions under maximum containment.
Indexed as
Single-Cell AnalysisAnimalsAntigens, CDBiomarkersBystander EffectCell DifferentiationCell ProliferationCytokinesEbolavirusEndoplasmic Reticulum Chaperone BiPGene Expression ProfilingGene Expression RegulationGene Expression Regulation, ViralHemorrhagic Fever, EbolaHistocompatibility Antigens Class IIHost-Pathogen InteractionsAntigens, CDBiomarkersCytokinesEndoplasmic Reticulum Chaperone BiPHistocompatibility Antigens Class IIHSPA5 protein, humanInterferonsRNA, Messengerbystander cellsCyTOFEbola virushost-virus interactionsinterferonmonocytesscRNA-SeqSeq-Wellsingle-cellviral tropism
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.