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Schäfer A, Marzi A, Furuyama W, Catanzaro NJ, Nguyen C, Haddock E, Feldmann F, Meade-White K, Thomas T, Hubbard ML, Gully KL, Leist SR, Hock P, Bell TA, De la Cruz GE, Midkiff BR, Martinez DR, Shaw GD, Miller DR, Vernon MJ, Graham RL, Cowley DO, Montgomery SA, Schughart K, de Villena FPM, Wilkerson GK, Ferris MT, Feldmann H, Baric RS. Mapping of susceptibility loci for Ebola virus pathogenesis in mice. Cell Rep 2024; 43:114127. [PMID: 38652660 DOI: 10.1016/j.celrep.2024.114127] [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: 04/11/2023] [Revised: 03/11/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Ebola virus (EBOV), a major global health concern, causes severe, often fatal EBOV disease (EVD) in humans. Host genetic variation plays a critical role, yet the identity of host susceptibility loci in mammals remains unknown. Using genetic reference populations, we generate an F2 mapping cohort to identify host susceptibility loci that regulate EVD. While disease-resistant mice display minimal pathogenesis, susceptible mice display severe liver pathology consistent with EVD-like disease and transcriptional signatures associated with inflammatory and liver metabolic processes. A significant quantitative trait locus (QTL) for virus RNA load in blood is identified in chromosome (chr)8, and a severe clinical disease and mortality QTL is mapped to chr7, which includes the Trim5 locus. Using knockout mice, we validate the Trim5 locus as one potential driver of liver failure and mortality after infection. The identification of susceptibility loci provides insight into molecular genetic mechanisms regulating EVD progression and severity, potentially informing therapeutics and vaccination strategies.
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Affiliation(s)
- Alexandra Schäfer
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA.
| | - Wakako Furuyama
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Cameron Nguyen
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Elaine Haddock
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Kimberly Meade-White
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Tina Thomas
- Rocky Mountain Veterinary Branch, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Miranda L Hubbard
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kendra L Gully
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Timothy A Bell
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Gabriela E De la Cruz
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Bentley R Midkiff
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Darla R Miller
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael J Vernon
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rachel L Graham
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dale O Cowley
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Animal Models Core Facility, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Stephanie A Montgomery
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Klaus Schughart
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Institute of Virology, University of Muenster, 48149 Muenster, Germany
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Gregory K Wilkerson
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA.
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Mensah-Bonsu M, Doss C, Gloster C, Muganda P. Identification and Potential Roles of Human MicroRNAs in Ebola Virus Infection and Disease Pathogenesis. Genes (Basel) 2024; 15:403. [PMID: 38674337 PMCID: PMC11049046 DOI: 10.3390/genes15040403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Ebola virus (EBOV) is a highly pathogenic virus that causes a severe illness called Ebola virus disease (EVD). EVD has a high mortality rate and remains a significant threat to public health. Research on EVD pathogenesis has traditionally focused on host transcriptional responses. Limited recent studies, however, have revealed some information on the significance of cellular microRNAs (miRNAs) in EBOV infection and pathogenic mechanisms, but further studies are needed. Thus, this study aimed to identify and validate additional known and novel human miRNAs in EBOV-infected adult retinal pigment epithelial (ARPE) cells and predict their potential roles in EBOV infection and pathogenic mechanisms. We analyzed previously available small RNA-Seq data obtained from ARPE cells and identified 23 upregulated and seven downregulated miRNAs in the EBOV-infected cells; these included two novel miRNAs and 17 additional known miRNAs not previously identified in ARPE cells. In addition to pathways previously identified by others, these miRNAs are associated with pathways and biological processes that include WNT, FoxO, and phosphatidylinositol signaling; these pathways were not identified in the original study. This study thus confirms and expands on the previous study using the same datasets and demonstrates further the importance of human miRNAs in the host response and EVD pathogenesis during infection.
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Affiliation(s)
- Melvin Mensah-Bonsu
- Applied Science and Technology Ph.D. Program, North Carolina A&T State University, Greensboro, NC 27411, USA;
| | - Christopher Doss
- Department of Electrical and Computer Engineering, North Carolina A&T State University, Greensboro, NC 27411, USA;
| | - Clay Gloster
- Department of Computer Systems Technology, North Carolina A&T State University, Greensboro, NC 27411, USA;
| | - Perpetua Muganda
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
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3
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Garcia A, Grundmann O. The Utilization and Development of Viral Vectors in Vaccines as a Prophylactic Treatment Against Ebola Virus as an Emerging and Zoonotic Infectious Disease. Mini Rev Med Chem 2024; 24:289-299. [PMID: 37489781 DOI: 10.2174/1389557523666230725115324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/26/2023] [Accepted: 03/15/2023] [Indexed: 07/26/2023]
Abstract
Alongside the prescription of commonly used antivirals, such as acyclovir, remdesivir, oseltamivir, and ciprofloxacin, the most efficient way to prevent or treat communicable diseases is by vaccination. Vaccines have been the most efficient way to prevent or treat highly transmissible infectious agents, such as Ebola, Anthrax, and Dengue Fever. Most epidemics of these highly transmissible infectious agents occur in places, such as South America, Central America, Tropical Asia, and Africa, where the availability of resources and access to adequate healthcare are limited. However, recent events in history have proven that even with access to resources and proper healthcare, those in firstworld countries are not invincible when it comes to infectious diseases and epidemics. The Ebola virus outbreak in West Africa highlighted the gaps in therapeutic advancement and readiness and led to the rapid development of novel vaccine approaches. Viral vectors, in the case of the Ebola vaccine the Vesicular Stomatitis Virus (VSV), can be safely used to activate or initiate the innate adaptive immune response to protect against viral infection. When developed properly and with extensive study, novel vaccine approaches allow physicians and health experts to control the rate at which viruses spread or prevent transmission. This review will discuss the advantages of viral vector vaccines, their chemistry and development, and the pathophysiology of the Ebola virus to develop advantageous and efficacious treatments.
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Affiliation(s)
- Anthony Garcia
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1345 Center Drive, Room P3-20, Gainesville, FL 32611, USA
| | - Oliver Grundmann
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1345 Center Drive, Room P3-20, Gainesville, FL 32611, USA
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4
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Clancy CS, Smart G, Rhoderick JF, O’Donnell KL, Rosenke R, Schäfer A, Marzi A. Establishing a Mouse Model for Sexual Transmission and Male Reproductive Tract Persistence of Ebola Virus. J Infect Dis 2023; 228:S554-S558. [PMID: 37102262 PMCID: PMC10651199 DOI: 10.1093/infdis/jiad118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/21/2023] [Indexed: 04/28/2023] Open
Abstract
Ebola virus disease (EVD) has resulted in the death of over 15 000 people since its discovery in 1976. At least 1 incident of re-emergence of EVD has been associated with persistent male reproductive tract infection in a patient surviving EVD greater than 500 days prior. To date, animal models of Ebola virus (EBOV) infection have failed to fully characterize the pathogenesis of reproductive tract infection. Furthermore, no animal model of sexual transmission of EBOV exists. In this study, we describe a roadmap to modeling sexual transmission of EBOV using a mouse-adapted EBOV isolate in immunocompetent male mice and female Ifnar-/- mice.
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Affiliation(s)
- Chad S Clancy
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, USA
| | - Gabrielle Smart
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, USA
| | - J Fred Rhoderick
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, USA
| | - Kyle L O’Donnell
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, USA
| | - Rebecca Rosenke
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, USA
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5
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Layton R, Layton D, Beggs D, Fisher A, Mansell P, Stanger KJ. The impact of stress and anesthesia on animal models of infectious disease. Front Vet Sci 2023; 10:1086003. [PMID: 36816193 PMCID: PMC9933909 DOI: 10.3389/fvets.2023.1086003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/09/2023] [Indexed: 02/05/2023] Open
Abstract
Stress and general anesthesia have an impact on the functional response of the organism due to the detrimental effects on cardiovascular, immunological, and metabolic function, which could limit the organism's response to an infectious event. Animal studies have formed an essential step in understanding and mitigating infectious diseases, as the complexities of physiology and immunity cannot yet be replicated in vivo. Using animals in research continues to come under increasing societal scrutiny, and it is therefore crucial that the welfare of animals used in disease research is optimized to meet both societal expectations and improve scientific outcomes. Everyday management and procedures in animal studies are known to cause stress, which can not only cause poorer welfare outcomes, but also introduces variables in disease studies. Whilst general anesthesia is necessary at times to reduce stress and enhance animal welfare in disease research, evidence of physiological and immunological disruption caused by general anesthesia is increasing. To better understand and quantify the effects of stress and anesthesia on disease study and welfare outcomes, utilizing the most appropriate animal monitoring strategies is imperative. This article aims to analyze recent scientific evidence about the impact of stress and anesthesia as uncontrolled variables, as well as reviewing monitoring strategies and technologies in animal models during infectious diseases.
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Affiliation(s)
- Rachel Layton
- Australian Centre for Disease Preparedness, CSIRO, Geelong, VIC, Australia,*Correspondence: Rachel Layton ✉
| | - Daniel Layton
- Australian Centre for Disease Preparedness, CSIRO, Geelong, VIC, Australia
| | - David Beggs
- Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, University of Melbourne, Melbourne, VIC, Australia
| | - Andrew Fisher
- Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, University of Melbourne, Melbourne, VIC, Australia
| | - Peter Mansell
- Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, University of Melbourne, Melbourne, VIC, Australia
| | - Kelly J. Stanger
- Australian Centre for Disease Preparedness, CSIRO, Geelong, VIC, Australia
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6
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History and impact of the mouse-adapted Ebola virus model. Antiviral Res 2023; 210:105493. [PMID: 36567023 DOI: 10.1016/j.antiviral.2022.105493] [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: 11/15/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Ebola virus (EBOV) is a member of the filoviridae family, which are comprised of negative sense, enveloped RNA hemorrhagic fever viruses that can cause severe disease and high lethality rates. These viruses require BSL-4 containment laboratories for study. Early studies of EBOV pathogenesis relied heavily on the use of nonhuman primates, which are expensive and cumbersome to handle in large numbers. Guinea pig models were also developed, but even to this day limited reagents are available in this model. In 1998, Mike Bray and colleagues developed a mouse-adapted EBOV (maEBOV) that caused lethality in adult immunocompetent mice. This model had significant advantages, including being inexpensive, allowing for higher animal numbers for statistical analysis, availability of reagents for studying pathogenesis, and availability of a vast array of genetically modified strains. The model has been used to test vaccines, therapeutic drugs, EBOV mutants, and pathogenesis, and its importance is demonstrated by the hundreds of citations referencing the original publication. This review will cover the history of the maEBOV model and its use in filovirus research.
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Kuhn JH, Schmaljohn CS. Of mice and Mike-An underappreciated Ebola virus disease model may have paved the road for future filovirology. Antiviral Res 2023; 210:105522. [PMID: 36592667 PMCID: PMC9852096 DOI: 10.1016/j.antiviral.2022.105522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
In 1998, Mike Bray and colleagues published the first immunocompetent laboratory mouse model of Ebola virus disease. Often labeled by peer reviewers as inferior to large nonhuman primate efforts, this model initially laid the foundation for the recent establishment of panel-derived cross-bred and humanized mouse models and a golden hamster model. Nonhuman primate research has always been associated with ethical concerns and is sometimes deemed scientifically questionable due to the necessarily low animal numbers in individual studies. Independent of these concerns, the now-global severe shortage of commercially available large nonhuman primates may pragmatically push research toward increased and improved rodent modeling that may altogether replace nonhuman primate studies in the short term as well as in an optimal future.
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Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA.
| | - Connie S Schmaljohn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA.
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8
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Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection. Cell Syst 2022; 13:1002-1015.e9. [PMID: 36516834 DOI: 10.1016/j.cels.2022.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/30/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022]
Abstract
When challenged with an invading pathogen, the host-defense response is engaged to eliminate the pathogen (resistance) and to maintain health in the presence of the pathogen (disease tolerance). However, the identification of distinct molecular programs underpinning disease tolerance and resistance remained obscure. We exploited transcriptional and physiological monitoring across 33 mouse strains, during in vivo influenza virus infection, to identify two host-defense gene programs-one is associated with hallmarks of disease tolerance and the other with hallmarks of resistance. Both programs constitute generic responses in multiple mouse and human cell types. Our study describes the organizational principles of these programs and validates Arhgdia as a regulator of disease-tolerance states in epithelial cells. We further reveal that the baseline disease-tolerance state in peritoneal macrophages is associated with the pathophysiological response to injury and infection. Our framework provides a paradigm for the understanding of disease tolerance and resistance at the molecular level.
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Artificial Intelligence Models for Zoonotic Pathogens: A Survey. Microorganisms 2022; 10:microorganisms10101911. [PMID: 36296187 PMCID: PMC9607465 DOI: 10.3390/microorganisms10101911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 11/22/2022] Open
Abstract
Zoonotic diseases or zoonoses are infections due to the natural transmission of pathogens between species (animals and humans). More than 70% of emerging infectious diseases are attributed to animal origin. Artificial Intelligence (AI) models have been used for studying zoonotic pathogens and the factors that contribute to their spread. The aim of this literature survey is to synthesize and analyze machine learning, and deep learning approaches applied to study zoonotic diseases to understand predictive models to help researchers identify the risk factors, and develop mitigation strategies. Based on our survey findings, machine learning and deep learning are commonly used for the prediction of both foodborne and zoonotic pathogens as well as the factors associated with the presence of the pathogens.
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Sperry MM, Novak R, Keshari V, Dinis ALM, Cartwright MJ, Camacho DM, Paré J, Super M, Levin M, Ingber DE. Enhancers of Host Immune Tolerance to Bacterial Infection Discovered Using Linked Computational and Experimental Approaches. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200222. [PMID: 35706367 PMCID: PMC9475558 DOI: 10.1002/advs.202200222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/10/2022] [Indexed: 05/31/2023]
Abstract
Current therapeutic strategies against bacterial infections focus on reduction of pathogen load using antibiotics; however, stimulation of host tolerance to infection in the presence of pathogens might offer an alternative approach. Computational transcriptomics and Xenopus laevis embryos are used to discover infection response pathways, identify potential tolerance inducer drugs, and validate their ability to induce broad tolerance. Xenopus exhibits natural tolerance to Acinetobacter baumanii, Klebsiella pneumoniae, Staphylococcus aureus, and Streptococcus pneumoniae bacteria, whereas Aeromonas hydrophila and Pseudomonas aeruginosa produce lethal infections. Transcriptional profiling leads to definition of a 20-gene signature that discriminates between tolerant and susceptible states, as well as identification of a more active tolerance response to gram negative compared to gram positive bacteria. Gene pathways associated with active tolerance in Xenopus, including some involved in metal ion binding and hypoxia, are found to be conserved across species, including mammals, and administration of a metal chelator (deferoxamine) or a HIF-1α agonist (1,4-DPCA) in embryos infected with lethal A. hydrophila increased survival despite high pathogen load. These data demonstrate the value of combining the Xenopus embryo infection model with computational multiomics analyses for mechanistic discovery and drug repurposing to induce host tolerance to bacterial infections.
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Affiliation(s)
- Megan M. Sperry
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
- Department of BiologyTufts UniversityMedfordMA02155USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
- Present address:
Unravel Biosciences, Inc.BostonMA02125USA
| | - Vishal Keshari
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
| | - Alexandre L. M. Dinis
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
- Present address:
University of Massachusetts Medical SchoolWorcesterMA01655USA
| | - Mark J. Cartwright
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
| | - Diogo M. Camacho
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
- Present address:
Rheos MedicinesCambridgeMA02142USA
| | - Jean‐François Paré
- Department of BiologyTufts UniversityMedfordMA02155USA
- Present address:
Queen's UniversityKingstonON K7L 3N6Canada
| | - Michael Super
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
| | - Michael Levin
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
- Department of BiologyTufts UniversityMedfordMA02155USA
- Allen Discovery Center at Tufts UniversityMedfordMA02155USA
| | - Donald E. Ingber
- Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMA02115USA
- Vascular Biology Program and Department of SurgeryBoston Children's Hospital and Harvard Medical SchoolBostonMA02115USA
- Harvard John A. Paulson School of Engineering and Applied SciencesCambridgeMA02138USA
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Hackett J, Gibson H, Frelinger J, Buntzman A. Using the Collaborative Cross and Diversity Outbred Mice in Immunology. Curr Protoc 2022; 2:e547. [PMID: 36066328 PMCID: PMC9612550 DOI: 10.1002/cpz1.547] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The Collaborative Cross (CC) and the Diversity Outbred (DO) stock mouse panels are the most powerful murine genetics tools available to the genetics community. Together, they combine the strength of inbred animal models with the diversity of outbred populations. Using the 63 CC strains or a panel of DO mice, each derived from the same 8 parental mouse strains, researchers can map genetic contributions to exceptionally complex immunological and infectious disease traits that would require far greater powering if performed by genome-wide association studies (GWAS) in human populations. These tools allow genes to be studied in heterozygous and homozygous states and provide a platform to study epistasis between interacting loci. Most importantly, once a quantitative phenotype is investigated and quantitative trait loci are identified, confirmatory genetic studies can be performed, which is often problematic using the GWAS approach. In addition, novel stable mouse models for immune phenotypes are often derived from studies utilizing the DO and CC mice that can serve as stronger model systems than existing ones in the field. The CC/DO systems have contributed to the fields of cancer immunology, autoimmunity, vaccinology, infectious disease, allergy, tissue rejection, and tolerance but have thus far been greatly underutilized. In this article, we present a recent review of the field and point out key areas of immunology that are ripe for further investigation and awaiting new CC/DO research projects. We also highlight some of the strong computational tools that have been developed for analyzing CC/DO genetic and phenotypic data. Additionally, we have formed a centralized community on the CyVerse infrastructure where immunogeneticists can utilize those software tools, collaborate with groups across the world, and expand the use of the CC and DO systems for investigating immunogenetic phenomena. © 2022 Wiley Periodicals LLC.
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Affiliation(s)
- Justin Hackett
- Barbara Ann Karmanos Cancer Institute, Hudson-Webber Cancer Research Center, Detroit, Michigan
| | - Heather Gibson
- Barbara Ann Karmanos Cancer Institute, Hudson-Webber Cancer Research Center, Detroit, Michigan
| | - Jeffrey Frelinger
- University of Arizona, Valley Fever Center for Excellence, Tucson, Arizona
- Department of Microbiology and Immunology, University of North Carolina System, Chapel Hill, North Carolina
| | - Adam Buntzman
- University of Arizona, BIO5 Institute, Valley Fever Center for Excellence, Tucson, Arizona
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12
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Elucidating Mechanisms of Tolerance to Salmonella Typhimurium across Long-Term Infections Using the Collaborative Cross. mBio 2022; 13:e0112022. [PMID: 35880881 PMCID: PMC9426527 DOI: 10.1128/mbio.01120-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Understanding the molecular mechanisms underlying resistance and tolerance to pathogen infection may present the opportunity to develop novel interventions. Resistance is the absence of clinical disease with a low pathogen burden, while tolerance is minimal clinical disease with a high pathogen burden. Salmonella is a worldwide health concern. We studied 18 strains of collaborative cross mice that survive acute Salmonella Typhimurium (STm) infections. We infected these strains orally and monitored them for 3 weeks. Five strains cleared STm (resistant), six strains maintained a bacterial load and survived (tolerant), while seven strains survived >7 days but succumbed to infection within the study period and were called “delayed susceptible.” Tolerant strains were colonized in the Peyer’s patches, mesenteric lymph node, spleen, and liver, while resistant strains had significantly reduced bacterial colonization. Tolerant strains had lower preinfection core body temperatures and had disrupted circadian patterns of body temperature postinfection sooner than other strains. Tolerant strains had higher circulating total white blood cells than resistant strains, driven by increased numbers of neutrophils. Tolerant strains had more severe tissue damage and higher circulating levels of monocyte chemoattractant protein 1 (MCP-1) and interferon gamma (IFN-γ), but lower levels of epithelial neutrophil-activating protein 78 (ENA-78) than resistant strains. Quantitative trait locus (QTL) analysis revealed one significant association and six suggestive associations. Gene expression analysis identified 22 genes that are differentially regulated in tolerant versus resistant animals that overlapped these QTLs. Fibrinogen genes (Fga, Fgb, and Fgg) were found across the QTL, RNA, and top canonical pathways, making them the best candidate genes for differentiating tolerance and resistance.
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13
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Howard FHN, Kwan A, Winder N, Mughal A, Collado-Rojas C, Muthana M. Understanding Immune Responses to Viruses-Do Underlying Th1/Th2 Cell Biases Predict Outcome? Viruses 2022; 14:1493. [PMID: 35891472 PMCID: PMC9324514 DOI: 10.3390/v14071493] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 12/15/2022] Open
Abstract
Emerging and re-emerging viral diseases have increased in number and geographical extent during the last decades. Examples include the current COVID-19 pandemic and the recent epidemics of the Chikungunya, Ebola, and Zika viruses. Immune responses to viruses have been well-characterised within the innate and adaptive immunity pathways with the outcome following viral infection predominantly attributed to properties of the virus and circumstances of the infection. Perhaps the belief that the immune system is often considered as a reactive component of host defence, springing into action when a threat is detected, has contributed to a poorer understanding of the inherent differences in an individual's immune system in the absence of any pathology. In this review, we focus on how these host factors (age, ethnicity, underlying pathologies) may skew the T helper cell response, thereby influencing the outcome following viral infection but also whether we can use these inherent biases to predict patients at risk of a deviant response and apply strategies to avoid or overcome them.
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Affiliation(s)
- Faith H. N. Howard
- Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK; (A.K.); (N.W.); (A.M.); (C.C.-R.); (M.M.)
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14
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Lee AJ, Feng E, Chew MV, Balint E, Poznanski SM, Giles E, Zhang A, Marzok A, Revill SD, Vahedi F, Dubey A, Ayaub E, Jimenez-Saiz R, McGrath JJC, Ritchie TM, Jordana M, Jonigk DD, Ackermann M, Ask K, Miller M, Richards CD, Ashkar AA. Type I interferon regulates proteolysis by macrophages to prevent immunopathology following viral infection. PLoS Pathog 2022; 18:e1010471. [PMID: 35512020 PMCID: PMC9113601 DOI: 10.1371/journal.ppat.1010471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 05/17/2022] [Accepted: 03/24/2022] [Indexed: 11/18/2022] Open
Abstract
The ability to treat severe viral infections is limited by our understanding of the mechanisms behind virus-induced immunopathology. While the role of type I interferons (IFNs) in early control of viral replication is clear, less is known about how IFNs can regulate the development of immunopathology and affect disease outcomes. Here, we report that absence of type I IFN receptor (IFNAR) is associated with extensive immunopathology following mucosal viral infection. This pathology occurred independent of viral load or type II immunity but required the presence of macrophages and IL-6. The depletion of macrophages and inhibition of IL-6 signaling significantly abrogated immunopathology. Tissue destruction was mediated by macrophage-derived matrix metalloproteinases (MMPs), as MMP inhibition by doxycycline and Ro 28–2653 reduced the severity of tissue pathology. Analysis of post-mortem COVID-19 patient lungs also displayed significant upregulation of the expression of MMPs and accumulation of macrophages. Overall, we demonstrate that IFNs inhibit macrophage-mediated MMP production to prevent virus-induced immunopathology and uncover MMPs as a therapeutic target towards viral infections.
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Affiliation(s)
- Amanda J. Lee
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Emily Feng
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Marianne V. Chew
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Elizabeth Balint
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Sophie M. Poznanski
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Elizabeth Giles
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Ali Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Art Marzok
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Spencer D. Revill
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, Firestone Institute of Respiratory Health, McMaster University, Hamilton, Ontario, Canada
| | - Fatemeh Vahedi
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Anisha Dubey
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, Firestone Institute of Respiratory Health, McMaster University, Hamilton, Ontario, Canada
| | - Ehab Ayaub
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, Firestone Institute of Respiratory Health, McMaster University, Hamilton, Ontario, Canada
| | - Rodrigo Jimenez-Saiz
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Joshua J. C. McGrath
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Tyrah M. Ritchie
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Manel Jordana
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Danny D. Jonigk
- Institute of Pathology, Hannover Medical School, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
| | - Maximilian Ackermann
- Institute of Pathology and Molecular Pathology, Helios University Clinic Wuppertal, University of Witten/Herdecke, Wuppertal, Germany
- Institute of Functional and Clinical Anatomy, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Kjetil Ask
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, Firestone Institute of Respiratory Health, McMaster University, Hamilton, Ontario, Canada
| | - Matthew Miller
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Carl D. Richards
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Ali A. Ashkar
- Department of Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
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15
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Genetic background influences survival of infections with Salmonella enterica serovar Typhimurium in the Collaborative Cross. PLoS Genet 2022; 18:e1010075. [PMID: 35417454 PMCID: PMC9067680 DOI: 10.1371/journal.pgen.1010075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/04/2022] [Accepted: 03/25/2022] [Indexed: 12/18/2022] Open
Abstract
Salmonella infections typically cause self-limiting gastroenteritis, but in some individuals these bacteria can spread systemically and cause disseminated disease. Salmonella Typhimurium (STm), which causes severe systemic disease in most inbred mice, has been used as a model for disseminated disease. To screen for new infection phenotypes across a range of host genetics, we orally infected 32 Collaborative Cross (CC) mouse strains with STm and monitored their disease progression for seven days by telemetry. Our data revealed a broad range of phenotypes across CC strains in many parameters including survival, bacterial colonization, tissue damage, complete blood counts (CBC), and serum cytokines. Eighteen CC strains survived to day 7, while fourteen susceptible strains succumbed to infection before day 7. Several CC strains had sex differences in survival and colonization. Surviving strains had lower pre-infection baseline temperatures and were less active during their daily active period. Core body temperature disruptions were detected earlier after STm infection than activity disruptions, making temperature a better detector of illness. All CC strains had STm in spleen and liver, but susceptible strains were more highly colonized. Tissue damage was weakly negatively correlated to survival. We identified loci associated with survival on Chromosomes (Chr) 1, 2, 4, 7. Polymorphisms in Ncf2 and Slc11a1, known to reduce survival in mice after STm infections, are located in the Chr 1 interval, and the Chr 7 association overlaps with a previously identified QTL peak called Ses2. We identified two new genetic regions on Chr 2 and 4 associated with susceptibility to STm infection. Our data reveal the diversity of responses to STm infection across a range of host genetics and identified new candidate regions for survival of STm infection.
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16
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Robertson SJ, Bedard O, McNally KL, Lewis M, Clancy C, Shaia C, Broeckel RM, Chiramel AI, Sturdevant GL, Forte E, Preuss C, Baker CN, Harder J, Brunton C, Munger S, Sturdevant DE, Martens C, Holland SM, Rosenthal NA, Best SM. Genetically diverse mouse models of SARS-CoV-2 infection reproduce clinical variation and cytokine responses in COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022. [PMID: 35233576 PMCID: PMC8887079 DOI: 10.1101/2021.09.17.460664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Inflammation in response to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection drives severity of coronavirus disease 2019 (COVID-19), with effective versus dysregulated responses influenced by host genetics. To understand mechanisms of inflammation, animal models that reflect genetic diversity and clinical outcomes observed in humans are needed. We report a mouse panel comprising the diverse genetic backgrounds of the Collaborative Cross founder strains crossed to K18-hACE2 transgenic mice that confers high susceptibility to SARS-CoV-2. Infection of CC x K18-hACE2 F1 progeny resulted in a spectrum of weight loss, survival, viral replication kinetics, histopathology, and cytokine profiles, some of which were sex-specific. Importantly, survival was associated with early type I interferon (IFN) expression and a phased proinflammatory response distinct from mice with severe disease. Thus, dynamics of inflammatory responses observed in COVID-19 can be modeled in diverse mouse strains that provide a genetically tractable platform for understanding antiviral immunity and evaluating countermeasures. ONE SENTENCE SUMMARY Genetically diverse mice display a broad spectrum of clinically relevant responses to SARS-CoV-2 infection, reflecting variability in COVID-19 disease.
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17
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Tovar A, Crouse WL, Smith GJ, Thomas JM, Keith BP, McFadden KM, Moran TP, Furey TS, Kelada SNP. Integrative analysis reveals mouse strain-dependent responses to acute ozone exposure associated with airway macrophage transcriptional activity. Am J Physiol Lung Cell Mol Physiol 2022; 322:L33-L49. [PMID: 34755540 PMCID: PMC8721896 DOI: 10.1152/ajplung.00237.2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 01/03/2023] Open
Abstract
Acute ozone (O3) exposure is associated with multiple adverse cardiorespiratory outcomes, the severity of which varies across individuals in human populations and inbred mouse strains. However, molecular determinants of response, including susceptibility biomarkers that distinguish who will develop severe injury and inflammation, are not well characterized. We and others have demonstrated that airway macrophages (AMs) are an important resident immune cell type that are functionally and transcriptionally responsive to O3 inhalation. Here, we sought to explore influences of strain, exposure, and strain-by-O3 exposure interactions on AM gene expression and identify transcriptional correlates of O3-induced inflammation and injury across six mouse strains, including five Collaborative Cross (CC) strains. We exposed adult mice of both sexes to filtered air (FA) or 2 ppm O3 for 3 h and measured inflammatory and injury parameters 21 h later. Mice exposed to O3 developed airway neutrophilia and lung injury with strain-dependent severity. In AMs, we identified a common core O3 transcriptional response signature across all strains, as well as a set of genes exhibiting strain-by-O3 exposure interactions. In particular, a prominent gene expression contrast emerged between a low- (CC017/Unc) and high-responding (CC003/Unc) strain, as reflected by cellular inflammation and injury. Further inspection indicated that differences in their baseline gene expression and chromatin accessibility profiles likely contribute to their divergent post-O3 exposure transcriptional responses. Together, these results suggest that aspects of O3-induced respiratory responses are mediated through altered AM transcriptional signatures and further confirm the importance of gene-environment interactions in mediating differential responsiveness to environmental agents.
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Affiliation(s)
- Adelaide Tovar
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Curriculum in Genetics & Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Wesley L Crouse
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Curriculum in Bioinformatics & Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Gregory J Smith
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Curriculum in Toxicology & Environmental Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Joseph M Thomas
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Benjamin P Keith
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Curriculum in Bioinformatics & Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kathryn M McFadden
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Timothy P Moran
- Department of Pediatrics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Center for Environmental Medicine, Asthma, and Lung Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Terrence S Furey
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Curriculum in Genetics & Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Curriculum in Bioinformatics & Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Samir N P Kelada
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Curriculum in Genetics & Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Curriculum in Bioinformatics & Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Curriculum in Toxicology & Environmental Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Center for Environmental Medicine, Asthma, and Lung Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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18
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Rao D, O'Donnell KL, Carmody A, Weissman IL, Hasenkrug KJ, Marzi A. CD47 expression attenuates Ebola virus-induced immunopathology in mice. Antiviral Res 2022; 197:105226. [PMID: 34923028 PMCID: PMC8748401 DOI: 10.1016/j.antiviral.2021.105226] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 01/03/2023]
Abstract
It has been shown that a very early cell-intrinsic response to infection is the upregulation of CD47 cell surface expression, a molecule known for delivering a "don't eat me signal" that inhibits macrophage-mediated phagocytosis and antigen presentation. Thus, blockade of CD47 signaling during lymphocytic choriomenigitis virus infections of mice has been shown to enhance the kinetics and potency of immune responses, thereby producing faster recovery. It seems counterintuitive that one of the earliest responses to infection would be immunoinhibitory, but it has been hypothesized that CD47 induction acts as an innate immune system checkpoint to prevent immune overactivation and immunopathogenic responses during certain infections. In the current study we examined the effect of CD47 blockade on lethal Ebola virus infection of mice. At 6 days post-infection, CD47 blockade was associated with significantly increased activation of B cells along with increases in recently cytolytic CD8+ T cells. However, the anti-CD47-treated mice exhibited increased weight loss, higher virus titers, and succumbed more rapidly. The anti-CD47-treated mice also had increased inflammatory cytokines in the plasma indicative of a "cytokine storm". Thus, in the context of this rapid hemorrhagic disease, CD47 blockade indeed exacerbated immunopathology and disease severity.
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Affiliation(s)
- Deepashri Rao
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kyle L O'Donnell
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Aaron Carmody
- Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Kim J Hasenkrug
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
| | - Andrea Marzi
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
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19
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Carlson CJ, Farrell MJ, Grange Z, Han BA, Mollentze N, Phelan AL, Rasmussen AL, Albery GF, Bett B, Brett-Major DM, Cohen LE, Dallas T, Eskew EA, Fagre AC, Forbes KM, Gibb R, Halabi S, Hammer CC, Katz R, Kindrachuk J, Muylaert RL, Nutter FB, Ogola J, Olival KJ, Rourke M, Ryan SJ, Ross N, Seifert SN, Sironen T, Standley CJ, Taylor K, Venter M, Webala PW. The future of zoonotic risk prediction. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200358. [PMID: 34538140 PMCID: PMC8450624 DOI: 10.1098/rstb.2020.0358] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2021] [Indexed: 01/26/2023] Open
Abstract
In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges? This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.
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Affiliation(s)
- Colin J. Carlson
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Maxwell J. Farrell
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Zoe Grange
- Public Health Scotland, Glasgow G2 6QE, UK
| | - Barbara A. Han
- Cary Institute of Ecosystem Studies, Millbrook, NY 12545, USA
| | - Nardus Mollentze
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Alexandra L. Phelan
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
- O'Neill Institute for National and Global Health Law, Georgetown University Law Center, Washington, DC 20001, USA
| | - Angela L. Rasmussen
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Gregory F. Albery
- Department of Biology, Georgetown University, Washington, DC 20007, USA
| | - Bernard Bett
- Animal and Human Health Program, International Livestock Research Institute, PO Box 30709-00100, Nairobi, Kenya
| | - David M. Brett-Major
- Department of Epidemiology, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lily E. Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tad Dallas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70806, USA
| | - Evan A. Eskew
- Department of Biology, Pacific Lutheran University, Tacoma, WA, USA
| | - Anna C. Fagre
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kristian M. Forbes
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Rory Gibb
- Centre on Climate Change and Planetary Health, London School of Hygiene and Tropical Medicine, London, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Sam Halabi
- O'Neill Institute for National and Global Health Law, Georgetown University Law Center, Washington, DC 20001, USA
| | - Charlotte C. Hammer
- Centre for the Study of Existential Risk, University of Cambridge, Cambridge, UK
| | - Rebecca Katz
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Jason Kindrachuk
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0J9
| | - Renata L. Muylaert
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Felicia B. Nutter
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
- Department of Public Health and Community Medicine, School of Medicine, Tufts University, Boston, MA 02111, USA
| | | | | | - Michelle Rourke
- Law Futures Centre, Griffith Law School, Griffith University, Nathan, Queensland 4111, Australia
| | - Sadie J. Ryan
- Department of Geography and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Noam Ross
- EcoHealth Alliance, New York, NY 10018, USA
| | - Stephanie N. Seifert
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Tarja Sironen
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Claire J. Standley
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Kishana Taylor
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Marietjie Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Paul W. Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok 20500, Kenya
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20
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Eskew EA, Fraser D, Vonhof MJ, Pinsky ML, Maslo B. Host gene expression in wildlife disease: making sense of species-level responses. Mol Ecol 2021; 30:6517-6530. [PMID: 34516689 DOI: 10.1111/mec.16172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 08/16/2021] [Accepted: 08/31/2021] [Indexed: 12/11/2022]
Abstract
Emerging infectious diseases are significant threats to wildlife conservation, yet the impacts of pathogen exposure and infection can vary widely among host species. As such, conservation biologists and disease ecologists have increasingly aimed to understand species-specific host susceptibility using molecular methods. In particular, comparative gene expression assays have been used to contrast the transcriptomic responses of disease-resistant and disease-susceptible hosts to pathogen exposure. This work usually assumes that the gene expression responses of disease-resistant species will reveal the activation of molecular pathways contributing to host defence. However, results often show that disease-resistant hosts undergo little gene expression change following pathogen challenge. Here, we discuss the mechanistic implications of these "null" findings and offer methodological suggestions for future molecular studies of wildlife disease. First, we highlight that muted transcriptomic responses with minimal immune system recruitment may indeed be protective for nonsusceptible hosts if they limit immunopathology and promote pathogen tolerance in systems where susceptible hosts suffer from genetic dysregulation. Second, we argue that overly narrow investigation of responses to pathogen exposure may overlook important, constitutively active molecular pathways that underlie species-specific defences. Finally, we outline alternative study designs and approaches that complement interspecific transcriptomic comparisons, including intraspecific gene expression studies and genomic methods to detect signatures of selection. Collectively, these insights will help ecologists extract maximal information from conservation-relevant transcriptomic data sets, leading to a deeper understanding of host defences and, ultimately, the implementation of successful conservation interventions.
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Affiliation(s)
- Evan A Eskew
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA.,Department of Biology, Pacific Lutheran University, Tacoma, Washington, USA
| | - Devaughn Fraser
- Wildlife Genetics Research Laboratory, California Department of Fish and Wildlife, Sacramento, California, USA
| | - Maarten J Vonhof
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA
| | - Malin L Pinsky
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Brooke Maslo
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
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21
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Feng E, Balint E, Poznanski SM, Ashkar AA, Loeb M. Aging and Interferons: Impacts on Inflammation and Viral Disease Outcomes. Cells 2021; 10:708. [PMID: 33806810 PMCID: PMC8004738 DOI: 10.3390/cells10030708] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/19/2021] [Accepted: 03/21/2021] [Indexed: 12/16/2022] Open
Abstract
As highlighted by the COVID-19 global pandemic, elderly individuals comprise the majority of cases of severe viral infection outcomes and death. A combined inability to control viral replication and exacerbated inflammatory immune activation in elderly patients causes irreparable immune-mediated tissue pathology in response to infection. Key to these responses are type I, II, and III interferons (IFNs), which are involved in inducing an antiviral response, as well as controlling and suppressing inflammation and immunopathology. IFNs support monocyte/macrophage-stimulated immune responses that clear infection and promote their immunosuppressive functions that prevent excess inflammation and immune-mediated pathology. The timing and magnitude of IFN responses to infection are critical towards their immunoregulatory functions and ability to prevent immunopathology. Aging is associated with multiple defects in the ability of macrophages and dendritic cells to produce IFNs in response to viral infection, leading to a dysregulation of inflammatory immune responses. Understanding the implications of aging on IFN-regulated inflammation will give critical insights on how to treat and prevent severe infection in vulnerable individuals. In this review, we describe the causes of impaired IFN production in aging, and the evidence to suggest that these impairments impact the regulation of the innate and adaptive immune response to infection, thereby causing disease pathology.
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Affiliation(s)
| | | | | | - Ali A. Ashkar
- Department of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada; (E.F.); (E.B.); (S.M.P.); (M.L.)
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22
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Pathogen Dose in Animal Models of Hemorrhagic Fever Virus Infections and the Potential Impact on Studies of the Immune Response. Pathogens 2021; 10:pathogens10030275. [PMID: 33804381 PMCID: PMC7999429 DOI: 10.3390/pathogens10030275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 12/24/2022] Open
Abstract
Viral hemorrhagic fever viruses come from a wide range of virus families and are a significant cause of morbidity and mortality worldwide each year. Animal models of infection with a number of these viruses have contributed to our knowledge of their pathogenesis and have been crucial for the development of therapeutics and vaccines that have been approved for human use. Most of these models use artificially high doses of virus, ensuring lethality in pre-clinical drug development studies. However, this can have a significant effect on the immune response generated. Here I discuss how the dose of antigen or pathogen is a critical determinant of immune responses and suggest that the current study of viruses in animal models should take this into account when developing and studying animal models of disease. This can have implications for determination of immune correlates of protection against disease as well as informing relevant vaccination and therapeutic strategies.
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Muñoz-Fontela C, Dowling WE, Funnell SGP, Gsell PS, Riveros-Balta AX, Albrecht RA, Andersen H, Baric RS, Carroll MW, Cavaleri M, Qin C, Crozier I, Dallmeier K, de Waal L, de Wit E, Delang L, Dohm E, Duprex WP, Falzarano D, Finch CL, Frieman MB, Graham BS, Gralinski LE, Guilfoyle K, Haagmans BL, Hamilton GA, Hartman AL, Herfst S, Kaptein SJF, Klimstra WB, Knezevic I, Krause PR, Kuhn JH, Le Grand R, Lewis MG, Liu WC, Maisonnasse P, McElroy AK, Munster V, Oreshkova N, Rasmussen AL, Rocha-Pereira J, Rockx B, Rodríguez E, Rogers TF, Salguero FJ, Schotsaert M, Stittelaar KJ, Thibaut HJ, Tseng CT, Vergara-Alert J, Beer M, Brasel T, Chan JFW, García-Sastre A, Neyts J, Perlman S, Reed DS, Richt JA, Roy CJ, Segalés J, Vasan SS, Henao-Restrepo AM, Barouch DH. Animal models for COVID-19. Nature 2020; 586:509-515. [PMID: 32967005 PMCID: PMC8136862 DOI: 10.1038/s41586-020-2787-6] [Citation(s) in RCA: 572] [Impact Index Per Article: 143.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the aetiological agent of coronavirus disease 2019 (COVID-19), an emerging respiratory infection caused by the introduction of a novel coronavirus into humans late in 2019 (first detected in Hubei province, China). As of 18 September 2020, SARS-CoV-2 has spread to 215 countries, has infected more than 30 million people and has caused more than 950,000 deaths. As humans do not have pre-existing immunity to SARS-CoV-2, there is an urgent need to develop therapeutic agents and vaccines to mitigate the current pandemic and to prevent the re-emergence of COVID-19. In February 2020, the World Health Organization (WHO) assembled an international panel to develop animal models for COVID-19 to accelerate the testing of vaccines and therapeutic agents. Here we summarize the findings to date and provides relevant information for preclinical testing of vaccine candidates and therapeutic agents for COVID-19.
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Affiliation(s)
- César Muñoz-Fontela
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - William E Dowling
- Centre for Epidemic Preparedness Innovations (CEPI), Washington, DC, USA
| | | | | | | | - Randy A Albrecht
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Miles W Carroll
- National Infection Service, Public Health England, Salisbury, UK
| | | | - Chuan Qin
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking, China
| | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kai Dallmeier
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | | | - Emmie de Wit
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Leen Delang
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Erik Dohm
- Animal Resources Program, University of Alabama at Birmingham, Birmingham, AL, USA
| | - W Paul Duprex
- Department of Microbiology and Molecular Genetics, Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Darryl Falzarano
- VIDO-Intervac, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Courtney L Finch
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Matthew B Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Bart L Haagmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Amy L Hartman
- Department of Microbiology and Molecular Genetics, Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Suzanne J F Kaptein
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - William B Klimstra
- Department of Immunology, Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Philip R Krause
- Center for Biologics Evaluation and Research, FDA, Silver Spring, MD, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Roger Le Grand
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Inserm, CEA, Université Paris-Saclay, Paris, France
| | | | - Wen-Chun Liu
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pauline Maisonnasse
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Inserm, CEA, Université Paris-Saclay, Paris, France
| | - Anita K McElroy
- Division of Pediatric Infectious Diseases, Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Vincent Munster
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Nadia Oreshkova
- Wageningen Bioveterinary Research (WBVR), Wageningen University and Research, Lelystad, The Netherlands
| | - Angela L Rasmussen
- Center for Infection and Immunity, Columbia Mailman |School of Public Health, New York, NY, USA
| | - Joana Rocha-Pereira
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Barry Rockx
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Estefanía Rodríguez
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Thomas F Rogers
- Division of Infectious Diseases, University of California San Diego, San Diego, CA, USA
| | | | - Michael Schotsaert
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Chien-Te Tseng
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Júlia Vergara-Alert
- Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Trevor Brasel
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jasper F W Chan
- Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Adolfo García-Sastre
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Douglas S Reed
- Department of Immunology, Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Juergen A Richt
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Chad J Roy
- Tulane National Primate Research Center, Covington, LA, USA
| | - Joaquim Segalés
- Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, UAB, Bellaterra, Spain
| | - Seshadri S Vasan
- Australian Centre for Disease Preparedness, CSIRO, Geelong, Victoria, Australia
- Department of Health Sciences, University of York, York, UK
| | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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Dong X, Munoz-Basagoiti J, Rickett NY, Pollakis G, Paxton WA, Günther S, Kerber R, Ng LFP, Elmore MJ, Magassouba N, Carroll MW, Matthews DA, Hiscox JA. Variation around the dominant viral genome sequence contributes to viral load and outcome in patients with Ebola virus disease. Genome Biol 2020; 21:238. [PMID: 32894206 PMCID: PMC7475720 DOI: 10.1186/s13059-020-02148-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 08/17/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Viral load is a major contributor to outcome in patients with Ebola virus disease (EVD), with high values leading to a fatal outcome. Evidence from the 2013-2016 Ebola virus (EBOV) outbreak indicated that different genotypes of the virus can have different phenotypes in patients. Additionally, due to the error-prone nature of viral RNA synthesis in an individual patient, the EBOV genome exists around a dominant viral genome sequence. The minor variants within a patient may contribute to the overall phenotype in terms of viral protein function. To investigate the effects of these minor variants, blood samples from patients with acute EVD were deeply sequenced. RESULTS We examine the minor variant frequency between patients with acute EVD who survived infection with those who died. Non-synonymous differences in viral proteins were identified that have implications for viral protein function. The greatest frequency of substitution was identified at three codon sites in the L gene-which encodes the viral RNA-dependent RNA polymerase (RdRp). Recapitulating this in an assay for virus replication, these substitutions result in aberrant viral RNA synthesis and correlate with patient outcome. CONCLUSIONS Together, these findings support the notion that in patients who survived EVD, in some cases, the genetic variability of the virus resulted in deleterious mutations that affected viral protein function, leading to reduced viral load. Such mutations may also lead to persistent strains of the virus and be associated with recrudescent infections.
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Affiliation(s)
- Xiaofeng Dong
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jordana Munoz-Basagoiti
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Natasha Y Rickett
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Georgios Pollakis
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - William A Paxton
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Romy Kerber
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Lisa F P Ng
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK.,Singapore Immunology Network, A*STAR, Singapore, Singapore
| | | | - N'faly Magassouba
- Laboratoire des fièvres hémorragiques en Guinée, Université Gamal Abdel Nasser de Conakry, Conakry, Guinea
| | - Miles W Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK.,Public Health England, Salisbury, UK
| | - David A Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Singapore, Singapore
| | - Julian A Hiscox
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK. .,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK. .,Singapore Immunology Network, A*STAR, Singapore, Singapore.
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