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Normandin E, Triana S, Raju SS, Lan TCT, Lagerborg K, Rudy M, Adams GC, DeRuff KC, Logue J, Liu D, Strebinger D, Rao A, Messer KS, Sacks M, Adams RD, Janosko K, Kotliar D, Shah R, Crozier I, Rinn JL, Melé M, Honko AN, Zhang F, Babadi M, Luban J, Bennett RS, Shalek AK, Barkas N, Lin AE, Hensley LE, Sabeti PC, Siddle KJ. Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses. CELL GENOMICS 2023; 3:100440. [PMID: 38169842 PMCID: PMC10759212 DOI: 10.1016/j.xgen.2023.100440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/27/2023] [Accepted: 10/15/2023] [Indexed: 01/05/2024]
Abstract
Ebola virus (EBOV) causes Ebola virus disease (EVD), marked by severe hemorrhagic fever; however, the mechanisms underlying the disease remain unclear. To assess the molecular basis of EVD across time, we performed RNA sequencing on 17 tissues from a natural history study of 21 rhesus monkeys, developing new methods to characterize host-pathogen dynamics. We identified alterations in host gene expression with previously unknown tissue-specific changes, including downregulation of genes related to tissue connectivity. EBOV was widely disseminated throughout the body; using a new, broadly applicable deconvolution method, we found that viral load correlated with increased monocyte presence. Patterns of viral variation between tissues differentiated primary infections from compartmentalized infections, and several variants impacted viral fitness in a EBOV/Kikwit minigenome system, suggesting that functionally significant variants can emerge during early infection. This comprehensive portrait of host-pathogen dynamics in EVD illuminates new features of pathogenesis and establishes resources to study other emerging pathogens.
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Affiliation(s)
- Erica Normandin
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sergio Triana
- Broad Institute of Harvard and MIT, 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.
| | - Siddharth S Raju
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Tammy C T Lan
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Molecular and Cellular Biology, Harvard University, Boston, MA, USA
| | - Kim Lagerborg
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Melissa Rudy
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Gordon C Adams
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - James Logue
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - David Liu
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Daniel Strebinger
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arya Rao
- Columbia University, New York, NY, USA; Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA 02115, USA
| | | | - Molly Sacks
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ricky D Adams
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Krisztina Janosko
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Dylan Kotliar
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rickey Shah
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, 08034 Barcelona, Catalonia, Spain
| | - Anna N Honko
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Feng Zhang
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mehrtash Babadi
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jeremy Luban
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA; Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Richard S Bennett
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Alex K Shalek
- Broad Institute of Harvard and MIT, 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
| | - Nikolaos Barkas
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Aaron E Lin
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Lisa E Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
| | - Katherine J Siddle
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA.
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3
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Singh VA, Kumar CS, Khare B, Kuhn RJ, Banerjee M, Tomar S. Surface decorated reporter-tagged chikungunya virus-like particles for clinical diagnostics and identification of virus entry inhibitors. Virology 2023; 578:92-102. [PMID: 36473281 DOI: 10.1016/j.virol.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
The ever-evolving and versatile VLP technology is becoming an increasingly popular area of science. This study presents surface decorated reporter-tagged VLPs of CHIKV, an enveloped RNA virus of the genus alphavirus and its applications. Western blot, IFA and live-cell imaging confirm the expression of reporter-tagged CHIK-VLPs from transfected HEK293Ts. CryoEM micrographs reveal particle diameter as ∼67nm and 56-70 nm, respectively, for NLuc CHIK-VLPs and mCherry CHIK-VLPs. Our study demonstrates that by exploiting NLuc CHIK-VLPs as a detector probe, robust ratiometric luminescence signal in CHIKV-positive sera compared to healthy controls can be achieved swiftly. Moreover, the potential activity of the Suramin drug as a CHIKV entry inhibitor has been validated through the reporter-tagged CHIK-VLPs. The results reported in this study open new avenues in the eVLPs domain and offer potential for large-scale screening of clinical samples and antiviral agents targeting entry of CHIKV and other alphaviruses.
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Affiliation(s)
- Vedita Anand Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India; Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Chandra Shekhar Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology - Delhi, Hauz Khas, New Delhi, 110016, India
| | - Baldeep Khare
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Manidipa Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology - Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India.
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5
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Obermeyer F, Jankowiak M, Barkas N, Schaffner SF, Pyle JD, Yurkovetskiy L, Bosso M, Park DJ, Babadi M, MacInnis BL, Luban J, Sabeti PC, Lemieux JE. Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2021.09.07.21263228. [PMID: 35194619 PMCID: PMC8863165 DOI: 10.1101/2021.09.07.21263228] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Repeated emergence of SARS-CoV-2 variants with increased fitness necessitates rapid detection and characterization of new lineages. To address this need, we developed PyR 0 , a hierarchical Bayesian multinomial logistic regression model that infers relative prevalence of all viral lineages across geographic regions, detects lineages increasing in prevalence, and identifies mutations relevant to fitness. Applying PyR 0 to all publicly available SARS-CoV-2 genomes, we identify numerous substitutions that increase fitness, including previously identified spike mutations and many non-spike mutations within the nucleocapsid and nonstructural proteins. PyR 0 forecasts growth of new lineages from their mutational profile, identifies viral lineages of concern as they emerge, and prioritizes mutations of biological and public health concern for functional characterization. ONE SENTENCE SUMMARY A Bayesian hierarchical model of all SARS-CoV-2 viral genomes predicts lineage fitness and identifies associated mutations.
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Affiliation(s)
- Fritz Obermeyer
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
- Pyro Committee, Linux AI & Data Foundation; 548 Market St San Francisco, California 94104
| | - Martin Jankowiak
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
- Pyro Committee, Linux AI & Data Foundation; 548 Market St San Francisco, California 94104
| | - Nikolaos Barkas
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
| | - Stephen F. Schaffner
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University; Boston, MA, USA
| | - Jesse D. Pyle
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
| | - Lonya Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Medical School; Worcester, MA 01605, USA
| | - Matteo Bosso
- Program in Molecular Medicine, University of Massachusetts Medical School; Worcester, MA 01605, USA
| | - Daniel J. Park
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
| | - Mehrtash Babadi
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
| | - Bronwyn L. MacInnis
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University; Boston, MA, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
| | - Jeremy Luban
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
- Program in Molecular Medicine, University of Massachusetts Medical School; Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
- Ragon Institute of MGH, MIT, and Harvard; 400 Technology Square, Cambridge, MA 02139, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University; Boston, MA, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
- Howard Hughes Medical Institute; 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
| | - Jacob E. Lemieux
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
- Division of Infectious Diseases, Massachusetts General Hospital; Boston, MA, USA
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