1
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Deng F, Morales-Sosa P, Bernal-Rivera A, Wang Y, Tsuchiya D, Javier JE, Rohner N, Zhao C, Camacho J. Establishing Primary and Stable Cell Lines from Frozen Wing Biopsies for Cellular, Physiological, and Genetic Studies in Bats. Curr Protoc 2024; 4:e1123. [PMID: 39228233 PMCID: PMC11378949 DOI: 10.1002/cpz1.1123] [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] [Indexed: 09/05/2024]
Abstract
Bats stand out among mammalian species for their exceptional traits, including the capacity to navigate through flight and echolocation, conserve energy through torpor/hibernation, harbor a multitude of viruses, exhibit resistance to disease, survive harsh environmental conditions, and demonstrate exceptional longevity compared to other mammals of similar size. In vivo studies of bats are challenging for several reasons, such as difficulty in locating and capturing them in their natural environments, limited accessibility, low sample size, environmental variation, long lifespans, slow reproductive rates, zoonotic disease risks, species protection, and ethical concerns. Thus, establishing alternative laboratory models is crucial for investigating the diverse physiological adaptations observed in bats. Obtaining quality cells from tissues is a critical first step for successful primary cell derivation. However, it is often impractical to collect fresh tissue and process the samples immediately for cell culture due to the resources required for isolating and expanding cells. As a result, frozen tissue is typically the starting resource for bat primary cell derivation, but cells in frozen tissue are usually damaged and have low integrity and viability. Isolating primary cells from frozen tissues thus poses a significant challenge. Herein, we present a successfully developed protocol for isolating primary dermal fibroblasts from frozen bat wing biopsies. This protocol marks a significant milestone, as this is the first protocol specifically focused on fibroblast isolation from bat frozen tissue. We also describe methods for primary cell characterization, genetic manipulation of primary cells through lentivirus transduction, and the development of stable cell lines. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Bat wing biopsy collection and preservation Support Protocol 1: Blood collection from bat venipuncture Basic Protocol 2: Isolation of primary fibroblasts from adult bat frozen wing biopsy Support Protocol 2: Primary fibroblast culture and subculture Support Protocol 3: Determination of growth curve and doubling time Support Protocol 4: Cell banking and thawing of primary fibroblasts Basic Protocol 3: Lentiviral transduction of bat primary fibroblasts Basic Protocol 4: Bat stable fibroblast cell line development Support Protocol 5: Bat fibroblast validation by immunofluorescence staining Basic Protocol 5: Chromosome counting.
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Affiliation(s)
- Fengyan Deng
- Stowers Institute for Medical Research, Kansas City, Missouri
| | | | | | - Yan Wang
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Dai Tsuchiya
- Stowers Institute for Medical Research, Kansas City, Missouri
| | | | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, Missouri
- Department of Cell Biology & Physiology, University of Kansas Medical Center, Kansas City, Missouri
| | - Chongbei Zhao
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Jasmin Camacho
- Stowers Institute for Medical Research, Kansas City, Missouri
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2
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Horigan S, Kettenburg G, Kistler A, Ranaivoson HC, Andrianiaina A, Andry S, Raharinosy V, Randriambolamanantsoa TH, Tato CM, Lacoste V, Heraud JM, Dussart P, Brook CE. Detection, characterization, and phylogenetic analysis of novel astroviruses from endemic Malagasy fruit bats. Virol J 2024; 21:195. [PMID: 39180123 PMCID: PMC11344347 DOI: 10.1186/s12985-024-02471-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 08/14/2024] [Indexed: 08/26/2024] Open
Abstract
Bats (order: Chiroptera) are known to host a diverse range of viruses, some of which present a human public health risk. Thorough viral surveillance is therefore essential to predict and potentially mitigate zoonotic spillover. Astroviruses (family: Astroviridae) are an understudied group of viruses with a growing amount of indirect evidence for zoonotic transfer. Astroviruses have been detected in bats with significant prevalence and diversity, suggesting that bats may act as important astrovirus hosts. Most astrovirus surveillance in wild bat hosts has, to date, been restricted to single-gene PCR detection and concomitant Sanger sequencing; additionally, many bat species and many geographic regions have not yet been surveyed for astroviruses at all. Here, we use metagenomic Next Generation Sequencing (mNGS) to detect astroviruses in three species of Madagascar fruit bats, Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis. We detect numerous partial sequences from all three species and one near-full length astrovirus sequence from Rousettus madagascariensis, which we use to characterize the evolutionary history of astroviruses both within bats and the broader mammalian clade, Mamastrovirus. Taken together, applications of mNGS implicate bats as important astrovirus hosts and demonstrate novel patterns of bat astrovirus evolutionary history, particularly in the Southwest Indian Ocean region.
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Affiliation(s)
- Sophia Horigan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
| | | | - Amy Kistler
- Chan Zuckerburg Biohub, San Francisco, CA, USA
| | - Hafaliana C Ranaivoson
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
| | - Angelo Andrianiaina
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
| | - Santino Andry
- Department of Entomology, University of Antananarivo, Antananarivo, Madagascar
| | | | | | | | - Vincent Lacoste
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jean-Michel Heraud
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Epidemic and Pandemic Preparedness and Prevention, Global Influenza Programme, World Health Organization, Geneva, Switzerland
| | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Cara E Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
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3
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Apoorva, Singh SK. A tale of endurance: bats, viruses and immune dynamics. Future Microbiol 2024; 19:841-856. [PMID: 38648093 DOI: 10.2217/fmb-2023-0233] [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: 10/21/2023] [Accepted: 02/09/2024] [Indexed: 04/25/2024] Open
Abstract
The emergence of highly zoonotic viral infections has propelled bat research forward. The viral outbreaks including Hendra virus, Nipah virus, Marburg virus, Ebola virus, Rabies virus, Middle East respiratory syndrome coronavirus, SARS-CoV and the latest SARS-CoV-2 have been epidemiologically linked to various bat species. Bats possess unique immunological characteristics that allow them to serve as a potential viral reservoir. Bats are also known to protect themselves against viruses and maintain their immunity. Therefore, there is a need for in-depth understanding into bat-virus biology to unravel the major factors contributing to the coexistence and spread of viruses.
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Affiliation(s)
- Apoorva
- Molecular Biology Unit, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Sunit Kumar Singh
- Molecular Biology Unit, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
- Dr. B R Ambedkar Center for Biomedical Research, University of Delhi (North Campus), New Delhi, 110007, India
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4
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Deng F, Morales-Sosa P, Bernal-Rivera A, Wang Y, Tsuchiya D, Javier JE, Rohner N, Zhao C, Camacho J. Establishing Primary and Stable Cell Lines from Frozen Wing Biopsies for Cellular, Physiological, and Genetic Studies in Bats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586286. [PMID: 38585913 PMCID: PMC10996558 DOI: 10.1101/2024.03.22.586286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Bats stand out among mammalian species for their exceptional traits, including the capacity to navigate through flight and echolocation, conserve energy through torpor/hibernation, harbor a multitude of viruses, exhibit resistance to disease, survive harsh environmental conditions, and demonstrate exceptional longevity compared to other mammals of similar size. In vivo studies of bats can be challenging for several reasons such as ability to locate and capture them in their natural environments, limited accessibility, low sample size, environmental variation, long lifespans, slow reproductive rates, zoonotic disease risks, species protection, and ethical concerns. Thus, establishing alternative laboratory models is crucial for investigating the diverse physiological adaptations observed in bats. Obtaining quality cells from tissues is a critical first step for successful primary cell derivation. However, it is often impractical to collect fresh tissue and process the samples immediately for cell culture due to the resources required for isolating and expanding cells. As a result, frozen tissue is typically the starting resource for bat primary cell derivation. Yet, cells in frozen tissue are usually damaged and represent low integrity and viability. As a result, isolating primary cells from frozen tissues poses a significant challenge. Herein, we present a successfully developed protocol for isolating primary dermal fibroblasts from frozen bat wing biopsies. This protocol marks a significant milestone, as this the first protocol specially focused on fibroblasts isolation from bat frozen tissue. We also describe methods for primary cell characterization, genetic manipulation of primary cells through lentivirus transduction, and the development of stable cell lines. Basic Protocol 1: Bat wing biopsy collection and preservation Support Protocol 1: Blood collection from bat- venipuncture Basic Protocol 2: Isolation of primary fibroblasts from adult bat frozen wing biopsy Support Protocol 2: Maintenance of primary fibroblasts Support Protocol 3: Cell banking and thawing of primary fibroblasts Support Protocol 4: Growth curve and doubling time Support Protocol 5: Lentiviral transduction of bat primary fibroblasts Basic Protocol 3: Bat stable fibroblasts cell lines development Support Protocol 6: Bat fibroblasts validation by immunofluorescence staining Support Protocol 7: Chromosome counting.
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Affiliation(s)
- Fengyan Deng
- Stowers Institute for Medical Research, Kansas City, MO, USA, 64110
| | | | | | - Yan Wang
- Stowers Institute for Medical Research, Kansas City, MO, USA, 64110
| | - Dai Tsuchiya
- Stowers Institute for Medical Research, Kansas City, MO, USA, 64110
| | | | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO, USA, 64110
- Department of Cell Biology & Physiology, University of Kansas Medical Center, Kansas City, KS, USA, 66103
| | - Chongbei Zhao
- Stowers Institute for Medical Research, Kansas City, MO, USA, 64110
| | - Jasmin Camacho
- Stowers Institute for Medical Research, Kansas City, MO, USA, 64110
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5
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Wang Z, Pei S, Ye R, Chen J, Cheng N, Zhao M, Cao W, Jia Z. Increasing evolution, prevalence, and outbreaks for rift valley fever virus in the process of breaking geographical barriers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170302. [PMID: 38272089 DOI: 10.1016/j.scitotenv.2024.170302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
BACKGROUND Rift valley fever (RVF) is listed as one of prioritized diseases by WHO. This study aims to describe RVF virus' landscape distribution globally, and to insight dynamics change of its evolution, prevalence, and outbreaks in the process of breaking geographical barriers. METHODS A systematic literature review and meta-analyses was conducted to estimate RVF prevalence by hosts using a random-effect model. Molecular clock-based phylogenetic analyses were performed to estimate RVF virus nucleotide substitution rates using nucleotide sequences in NCBI database. RVF virus prevalence, nucleotide substitution rates, and outbreaks were compared before and after breaking geographical barriers twice, respectively. RESULTS RVF virus was reported from 26 kinds of hosts covering 48 countries from 1930 to 2022. Since RVF broke geographical barriers, (1) nucleotide substitution rates significantly increased after firstly spreading out of Africa in 2000, (2) prevalence in humans significantly increased from 1.92 % (95 % CI: 0.86-3.25 %) to 3.03 % (95 % CI: 2.09-4.12 %) after it broke Sahara Desert geographical barriers in 1977, and to 5.24 % (95 % CI: 3.81-6.82 %) after 2000, (3) RVF outbreaks in humans and the number of wildlife hosts presented increasing trends. RVF virus spillover may exist between bats and humans, and accelerate viral substitution rates in humans. During outbreaks, the RVF virus substitution rates accelerated in humans. 60.00 % RVF outbreaks occurred 0-2 months after floods and (or) heavy rainfall. CONCLUSION RVF has the increasing risk to cause pandemics, and global collaboration on "One Health" is needed to prevent potential pandemics.
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Affiliation(s)
- Zekun Wang
- School of Public Health, Peking University, Beijing, China
| | - Shaojun Pei
- School of Public Health, Peking University, Beijing, China
| | - Runze Ye
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyuan Chen
- School of Public Health, Peking University, Beijing, China
| | - Nuo Cheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Mingchen Zhao
- School of Public Health, Peking University, Beijing, China
| | - Wuchun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhongwei Jia
- School of Public Health, Peking University, Beijing, China; Center for Intelligent Public Health, Institute for Artificial Intelligence, Peking University, Beijing, China; Center for Drug Abuse Control and Prevention, National Institute of Health Data Science, Peking University, Beijing, China; Peking University Clinical Research Institute, Beijing, China.
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6
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Sánchez CA, Phelps KL, Frank HK, Geldenhuys M, Griffiths ME, Jones DN, Kettenburg G, Lunn TJ, Moreno KR, Mortlock M, Vicente-Santos A, Víquez-R LR, Kading RC, Markotter W, Reeder DM, Olival KJ. Advances in understanding bat infection dynamics across biological scales. Proc Biol Sci 2024; 291:20232823. [PMID: 38444339 PMCID: PMC10915549 DOI: 10.1098/rspb.2023.2823] [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: 12/13/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
Over the past two decades, research on bat-associated microbes such as viruses, bacteria and fungi has dramatically increased. Here, we synthesize themes from a conference symposium focused on advances in the research of bats and their microbes, including physiological, immunological, ecological and epidemiological research that has improved our understanding of bat infection dynamics at multiple biological scales. We first present metrics for measuring individual bat responses to infection and challenges associated with using these metrics. We next discuss infection dynamics within bat populations of the same species, before introducing complexities that arise in multi-species communities of bats, humans and/or livestock. Finally, we outline critical gaps and opportunities for future interdisciplinary work on topics involving bats and their microbes.
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Affiliation(s)
| | | | - Hannah K. Frank
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Marike Geldenhuys
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | | | - Devin N. Jones
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | | | - Tamika J. Lunn
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Kelsey R. Moreno
- Department of Psychology, Saint Xavier University, Chicago, IL 60655, USA
| | - Marinda Mortlock
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | | | - Luis R. Víquez-R
- Department of Biology, Bucknell University, Lewisburg, PA 17837, USA
| | - Rebekah C. Kading
- Department of Microbiology, Immunology and Pathology, Center for Vector-borne and Infectious Diseases, Colorado State University, Fort Collins, CO 80523, USA
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - DeeAnn M. Reeder
- Department of Biology, Bucknell University, Lewisburg, PA 17837, USA
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7
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Strahan EK, Witherbee J, Bergl R, Lonsdorf EV, Mwacha D, Mjungu D, Arandjelovic M, Ikfuingei R, Terio K, Travis DA, Gillespie TR. Potentially Zoonotic Enteric Infections in Gorillas and Chimpanzees, Cameroon and Tanzania. Emerg Infect Dis 2024; 30:577-580. [PMID: 38407249 PMCID: PMC10902540 DOI: 10.3201/eid3003.230318] [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] [Indexed: 02/27/2024] Open
Abstract
Despite zoonotic potential, data are lacking on enteric infection diversity in wild apes. We employed a novel molecular diagnostic platform to detect enteric infections in wild chimpanzees and gorillas. Prevalent Cryptosporidium parvum, adenovirus, and diarrheagenic Escherichia coli across divergent sites and species demonstrates potential widespread circulation among apes in Africa.
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8
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Abu Mazen N, Luc J, Lobb B, Hirota JA, Banerjee A, Doxey AC. Metatranscriptomic RNA-Seq Data Analysis of Virus-Infected Host Cells. Methods Mol Biol 2024; 2813:79-94. [PMID: 38888771 DOI: 10.1007/978-1-0716-3890-3_5] [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] [Indexed: 06/20/2024]
Abstract
RNA sequencing (RNA-seq) analysis of virus-infected host cells enables researchers to study a wide range of phenomena involving host-virus interactions. This includes genomic analysis of the viral population itself, as well as analysis of the transcriptional dynamics of the virus and host during infection. In this chapter, we provide a guide for researchers interested in performing RNA-seq data analysis of virus-infected host cells or cell lines. We outline several bioinformatic protocols for quantifying viral abundance, assembling viral genomes from mixed samples, and performing differential expression analysis, among other common workflows. These workflows can be used as starting points for researchers aiming to analyze RNA-seq datasets of mixed samples containing both host and viral RNA, such as virus-infected cell lines or clinical samples.
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Affiliation(s)
- Nooran Abu Mazen
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Jessica Luc
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Briallen Lobb
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Jeremy Alexander Hirota
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- Firestone Institute for Respiratory Health - Division of Respirology, Department of Medicine, McMaster University, Hamilton, ON, Canada
- School of Biomedical Engineering, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Michael G. DeGroote Centre for Learning and Discovery, Hamilton, ON, Canada
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Arinjay Banerjee
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
- Firestone Institute for Respiratory Health - Division of Respirology, Department of Medicine, McMaster University, Hamilton, ON, Canada.
- Waterloo Centre for Microbial Research, Waterloo, ON, Canada.
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9
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Horigan S, Kistler A, Ranaivoson HC, Andrianianina A, Andry S, Kettenburg G, Raharinosy V, Randriambolamanantsoa TH, Tato CM, Lacoste V, Heraud JM, Dussart P, Brook CE. Detection, characterization, and phylogenetic analysis of a near-whole genome sequence of a novel astrovirus in an endemic Malagasy fruit bat, Rousettus madagascariensis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.564436. [PMID: 37961349 PMCID: PMC10635015 DOI: 10.1101/2023.10.27.564436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Bats (order: Chiroptera ) are known to host a diverse range of viruses, some of which present a public health risk. Thorough viral surveillance is therefore essential to predict and potentially mitigate zoonotic spillover. Astroviruses (family: Astroviridae ) are an understudied group of viruses with a growing amount of indirect evidence for zoonotic transfer. Astroviruses have been detected in bats with significant prevalence and diversity, suggesting that bats may act as important astrovirus hosts. Most astrovirus surveillance in wild bat hosts has, to date, been restricted to single-gene PCR detection and concomitant Sanger sequencing; additionally, many bat species and many geographic regions have not yet been surveyed for astroviruses at all. Here, we use metagenomic Next Generation Sequencing (mNGS) to detect astroviruses in three species of Madagascar fruit bats, Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis . We detect numerous partial sequences from all three species and one near-full length astrovirus sequence from Rousettus madagascariensis , which we use to characterize the evolutionary history of astroviruses both within bats and the broader mammalian clade, Mamastrovirus . Taken together, applications of mNGS implicate bats as important astrovirus hosts and demonstrate novel patterns of bat astrovirus evolutionary history, particularly in the Southwest Indian Ocean region.
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10
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Li S, Vazquez JM, Sudmant PH. The evolution of aging and lifespan. Trends Genet 2023; 39:830-843. [PMID: 37714733 PMCID: PMC11147682 DOI: 10.1016/j.tig.2023.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/17/2023]
Abstract
Aging is a nearly inescapable trait among organisms yet lifespan varies tremendously across different species and spans several orders of magnitude in vertebrates alone. This vast phenotypic diversity is driven by distinct evolutionary trajectories and tradeoffs that are reflected in patterns of diversification and constraint in organismal genomes. Age-specific impacts of selection also shape allele frequencies in populations, thus impacting disease susceptibility and environment-specific mortality risk. Further, the mutational processes that spawn this genetic diversity in both germline and somatic cells are strongly influenced by age and life history. We discuss recent advances in our understanding of the evolution of aging and lifespan at organismal, population, and cellular scales, and highlight outstanding questions that remain unanswered.
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Affiliation(s)
- Stacy Li
- Department of Integrative Biology, University of California, Berkeley, CA, USA; Center for Computational Biology, University of California, Berkeley, CA. USA
| | - Juan Manuel Vazquez
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Peter H Sudmant
- Department of Integrative Biology, University of California, Berkeley, CA, USA; Center for Computational Biology, University of California, Berkeley, CA. USA.
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11
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Hashimi M, Sebrell TA, Hedges JF, Snyder D, Lyon KN, Byrum SD, Mackintosh SG, Crowley D, Cherne MD, Skwarchuk D, Robison A, Sidar B, Kunze A, Loveday EK, Taylor MP, Chang CB, Wilking JN, Walk ST, Schountz T, Jutila MA, Bimczok D. Antiviral responses in a Jamaican fruit bat intestinal organoid model of SARS-CoV-2 infection. Nat Commun 2023; 14:6882. [PMID: 37898615 PMCID: PMC10613288 DOI: 10.1038/s41467-023-42610-x] [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: 12/03/2022] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
Bats are natural reservoirs for several zoonotic viruses, potentially due to an enhanced capacity to control viral infection. However, the mechanisms of antiviral responses in bats are poorly defined. Here we established a Jamaican fruit bat (JFB, Artibeus jamaicensis) intestinal organoid model of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Upon infection with SARS-CoV-2, increased viral RNA and subgenomic RNA was detected, but no infectious virus was released, indicating that JFB organoids support only limited viral replication but not viral reproduction. SARS-CoV-2 replication was associated with significantly increased gene expression of type I interferons and inflammatory cytokines. Interestingly, SARS-CoV-2 also caused enhanced formation and growth of JFB organoids. Proteomics revealed an increase in inflammatory signaling, cell turnover, cell repair, and SARS-CoV-2 infection pathways. Collectively, our findings suggest that primary JFB intestinal epithelial cells mount successful antiviral interferon responses and that SARS-CoV-2 infection in JFB cells induces protective regenerative pathways.
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Affiliation(s)
- Marziah Hashimi
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - T Andrew Sebrell
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Jodi F Hedges
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Deann Snyder
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Katrina N Lyon
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Stephanie D Byrum
- University of Arkansas for Medical Sciences, Department of Biochemistry and Molecular Biology, Little Rock, AR, USA
- Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Samuel G Mackintosh
- University of Arkansas for Medical Sciences, Department of Biochemistry and Molecular Biology, Little Rock, AR, USA
| | - Dan Crowley
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
- Department of Public & Ecosystem Health, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Michelle D Cherne
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - David Skwarchuk
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Amanda Robison
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Barkan Sidar
- Montana State University, Chemical and Biological Engineering Department, Bozeman, MT, USA
- Center for Biofilm Engineering, Bozeman, MT, USA
| | - Anja Kunze
- Montana State University, Electrical and Computer Engineering Department, Bozeman, MT, USA
| | - Emma K Loveday
- Montana State University, Chemical and Biological Engineering Department, Bozeman, MT, USA
- Center for Biofilm Engineering, Bozeman, MT, USA
| | - Matthew P Taylor
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Connie B Chang
- Montana State University, Chemical and Biological Engineering Department, Bozeman, MT, USA
- Center for Biofilm Engineering, Bozeman, MT, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - James N Wilking
- Montana State University, Chemical and Biological Engineering Department, Bozeman, MT, USA
- Center for Biofilm Engineering, Bozeman, MT, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Seth T Walk
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology and Center of Vector-Borne Infectious Diseases, Colorado State University, Fort, Collins, CO, USA
| | - Mark A Jutila
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Diane Bimczok
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA.
- Center for Biofilm Engineering, Bozeman, MT, USA.
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12
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Brook CE, Rozins C, Guth S, Boots M. Reservoir host immunology and life history shape virulence evolution in zoonotic viruses. PLoS Biol 2023; 21:e3002268. [PMID: 37676899 PMCID: PMC10484437 DOI: 10.1371/journal.pbio.3002268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 07/21/2023] [Indexed: 09/09/2023] Open
Abstract
The management of future pandemic risk requires a better understanding of the mechanisms that determine the virulence of emerging zoonotic viruses. Meta-analyses suggest that the virulence of emerging zoonoses is correlated with but not completely predictable from reservoir host phylogeny, indicating that specific characteristics of reservoir host immunology and life history may drive the evolution of viral traits responsible for cross-species virulence. In particular, bats host viruses that cause higher case fatality rates upon spillover to humans than those derived from any other mammal, a phenomenon that cannot be explained by phylogenetic distance alone. In order to disentangle the fundamental drivers of these patterns, we develop a nested modeling framework that highlights mechanisms that underpin the evolution of viral traits in reservoir hosts that cause virulence following cross-species emergence. We apply this framework to generate virulence predictions for viral zoonoses derived from diverse mammalian reservoirs, recapturing trends in virus-induced human mortality rates reported in the literature. Notably, our work offers a mechanistic hypothesis to explain the extreme virulence of bat-borne zoonoses and, more generally, demonstrates how key differences in reservoir host longevity, viral tolerance, and constitutive immunity impact the evolution of viral traits that cause virulence following spillover to humans. Our theoretical framework offers a series of testable questions and predictions designed to stimulate future work comparing cross-species virulence evolution in zoonotic viruses derived from diverse mammalian hosts.
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Affiliation(s)
- Cara E. Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Carly Rozins
- Department of Science, Technology, and Society, York University, Toronto, Canada
| | - Sarah Guth
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Mike Boots
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
- Biosciences, University of Exeter, Penryn, United Kingdom
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13
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Colella JP, Cobos ME, Salinas I, Cook JA. Advancing the central role of non-model biorepositories in predictive modeling of emerging pathogens. PLoS Pathog 2023; 19:e1011410. [PMID: 37319170 DOI: 10.1371/journal.ppat.1011410] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Affiliation(s)
- Jocelyn P Colella
- University of Kansas Biodiversity Institute and Department of Ecology & Evolutionary Biology, Lawrence, Kansas, United States of America
| | - Marlon E Cobos
- University of Kansas Biodiversity Institute and Department of Ecology & Evolutionary Biology, Lawrence, Kansas, United States of America
| | - Irene Salinas
- University of New Mexico, Department of Biology, Albuquerque, New Mexico, United States of America
- Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Joseph A Cook
- University of New Mexico, Department of Biology, Albuquerque, New Mexico, United States of America
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
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14
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Déjosez M, Marin A, Hughes GM, Morales AE, Godoy-Parejo C, Gray JL, Qin Y, Singh AA, Xu H, Juste J, Ibáñez C, White KM, Rosales R, Francoeur NJ, Sebra RP, Alcock D, Volkert TL, Puechmaille SJ, Pastusiak A, Frost SDW, Hiller M, Young RA, Teeling EC, García-Sastre A, Zwaka TP. Bat pluripotent stem cells reveal unusual entanglement between host and viruses. Cell 2023; 186:957-974.e28. [PMID: 36812912 PMCID: PMC10085545 DOI: 10.1016/j.cell.2023.01.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/06/2022] [Accepted: 01/09/2023] [Indexed: 02/23/2023]
Abstract
Bats are distinctive among mammals due to their ability to fly, use laryngeal echolocation, and tolerate viruses. However, there are currently no reliable cellular models for studying bat biology or their response to viral infections. Here, we created induced pluripotent stem cells (iPSCs) from two species of bats: the wild greater horseshoe bat (Rhinolophus ferrumequinum) and the greater mouse-eared bat (Myotis myotis). The iPSCs from both bat species showed similar characteristics and had a gene expression profile resembling that of cells attacked by viruses. They also had a high number of endogenous viral sequences, particularly retroviruses. These results suggest that bats have evolved mechanisms to tolerate a large load of viral sequences and may have a more intertwined relationship with viruses than previously thought. Further study of bat iPSCs and their differentiated progeny will provide insights into bat biology, virus host relationships, and the molecular basis of bats' special traits.
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Affiliation(s)
- Marion Déjosez
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Paratus Sciences, 430 East 29th Street, Suite 600, New York, NY 10016, USA
| | - Arturo Marin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Graham M Hughes
- School of Biology and Environmental Science, University College Dublin, Ireland
| | - Ariadna E Morales
- Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany; Faculty of Biosciences, Goethe University, Max-von-Laue-Str, 60438 Frankfurt, Germany
| | - Carlos Godoy-Parejo
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Jonathan L Gray
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Yiren Qin
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Arun A Singh
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Hui Xu
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Javier Juste
- Estación biológica de doñana (CSIC), Avda. Américo Vespucio 26, Seville 41092, Spain; CIBER Epidemiology and Public Health, CIBERESP, Madrid, Spain
| | - Carlos Ibáñez
- Estación biológica de doñana (CSIC), Avda. Américo Vespucio 26, Seville 41092, Spain
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Robert P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Institute for Genomics, New York, NY, USA
| | - Dominic Alcock
- School of Biology and Environmental Science, University College Dublin, Ireland
| | - Thomas L Volkert
- Paratus Sciences, 430 East 29th Street, Suite 600, New York, NY 10016, USA
| | | | - Andrzej Pastusiak
- Microsoft Premonition, Microsoft Building 99, 14820 NE 36th Street, Redmond, WA 98052, USA
| | - Simon D W Frost
- Microsoft Premonition, Microsoft Building 99, 14820 NE 36th Street, Redmond, WA 98052, USA; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany; Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany; Faculty of Biosciences, Goethe University, Max-von-Laue-Str, 60438 Frankfurt, Germany
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Ireland.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Molecular and Cell-Based Medicine and the Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Thomas P Zwaka
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Paratus Sciences, 430 East 29th Street, Suite 600, New York, NY 10016, USA.
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15
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Novel Chaphamaparvovirus in Insectivorous Molossus molossus Bats, from the Brazilian Amazon Region. Viruses 2023; 15:v15030606. [PMID: 36992315 PMCID: PMC10054343 DOI: 10.3390/v15030606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/17/2023] [Accepted: 02/18/2023] [Indexed: 02/25/2023] Open
Abstract
Chaphamaparvovirus (CHPV) is a recently characterized genus of the Parvoviridae family whose members can infect different hosts, including bats, which constitute the second most diverse order of mammals and are described worldwide as important transmitters of zoonotic diseases. In this study, we identified a new CHPV in bat samples from the municipality of Santarém (Pará state, North Brazil). A total of 18 Molossus molossus bats were analyzed using viral metagenomics. In five animals, we identified CHPVs. These CHPV sequences presented the genome with a size ranging from 3797 to 4284 bp. Phylogenetic analysis-based nucleotide and amino acid sequences of the VP1 and NS1 regions showed that all CHPV sequences are monophyletic. They are also closely related to CHPV sequences previously identified in bats in southern and southeast Brazil. According to the International Committee on Taxonomy of Viruses (ICTV) classification criteria for this species (the CHPV NS1 gene region must have 85% identity to be classified in the same species), our sequences are likely a new specie within the genus Chaphamaparvovirus, since they have less than 80% identity with other CHPV described earlier in bats. We also make some phylogenetic considerations about the interaction between CHPV and their host. We suggest a high level of specificity of CPHV and its hosts. Thus, the findings contribute to improving information about the viral diversity of parvoviruses and show the importance of better investigating bats, considering that they harbor a variety of viruses that may favor zoonotic events.
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16
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Hashimi M, Sebrell T, Hedges J, Snyder D, Lyon K, Byrum S, Mackintosh SG, Cherne M, Skwarchuk D, Crowley D, Robison A, Sidar B, Kunze A, Loveday E, Taylor M, Chang C, Wilking J, Walk S, Schountz T, Jutila M, Bimczok D. Antiviral response mechanisms in a Jamaican Fruit Bat intestinal organoid model of SARS-CoV-2 infection. RESEARCH SQUARE 2022:rs.3.rs-2340919. [PMID: 36561186 PMCID: PMC9774215 DOI: 10.21203/rs.3.rs-2340919/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bats are natural reservoirs for several zoonotic viruses, potentially due to an enhanced capacity to control viral infection. However, the mechanisms of antiviral responses in bats are poorly defined. Here we established a Jamaican fruit bat (JFB) intestinal organoid model of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. JFB organoids were susceptible to SARS-CoV-2 infection, with increased viral RNA and subgenomic RNA detected in cell lysates and supernatants. Gene expression of type I interferons and inflammatory cytokines was induced in response to SARS-CoV-2 but not in response to TLR agonists. Interestingly, SARS-CoV-2 did not lead to cytopathic effects in JFB organoids but caused enhanced organoid growth. Proteomic analyses revealed an increase in inflammatory signaling, cell turnover, cell repair, and SARS-CoV-2 infection pathways. Collectively, our findings suggest that primary JFB intestinal epithelial cells can mount a successful antiviral interferon response and that SARS-CoV-2 infection in JFB cells induces protective regenerative pathways.
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17
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Thakor JC, Dinesh M, Manikandan R, Bindu S, Sahoo M, Sahoo D, Dhawan M, Pandey MK, Tiwari R, Emran TB, Dhama K, Chaicumpa W. Swine coronaviruses (SCoVs) and their emerging threats to swine population, inter-species transmission, exploring the susceptibility of pigs for SARS-CoV-2 and zoonotic concerns. Vet Q 2022; 42:125-147. [PMID: 35584308 PMCID: PMC9225692 DOI: 10.1080/01652176.2022.2079756] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 03/23/2022] [Accepted: 05/16/2022] [Indexed: 12/23/2022] Open
Abstract
Swine coronaviruses (SCoVs) are one of the most devastating pathogens affecting the livelihoods of farmers and swine industry across the world. These include transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), porcine respiratory coronavirus (PRCV), porcine hemagglutinating encephalomyelitis virus (PHEV), swine acute diarrhea syndrome coronavirus (SADS-CoV), and porcine delta coronavirus (PDCoV). Coronaviruses infect a wide variety of animal species and humans because these are having single stranded-RNA that accounts for high mutation rates and thus could break the species barrier. The gastrointestinal, cardiovascular, and nervous systems are the primary organ systems affected by SCoVs. Infection is very common in piglets compared to adult swine causing high mortality in the former. Bat is implicated to be the origin of all CoVs affecting animals and humans. Since pig is the only domestic animal in which CoVs cause a wide range of diseases; new coronaviruses with high zoonotic potential could likely emerge in the future as observed in the past. The recently emerged severe acute respiratory syndrome coronavirus virus-2 (SARS-CoV-2), causing COVID-19 pandemic in humans, has been implicated to have animal origin, also reported from few animal species, though its zoonotic concerns are still under investigation. This review discusses SCoVs and their epidemiology, virology, evolution, pathology, wildlife reservoirs, interspecies transmission, spill-over events and highlighting their emerging threats to swine population. The role of pigs amid ongoing SARS-CoV-2 pandemic will also be discussed. A thorough investigation should be conducted to rule out zoonotic potential of SCoVs and to design appropriate strategies for their prevention and control.
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Affiliation(s)
- Jigarji C. Thakor
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Murali Dinesh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Rajendran Manikandan
- Immunology Section, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Suresh Bindu
- Immunology Section, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Monalisa Sahoo
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Diptimayee Sahoo
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana, India
- The Trafford Group of Colleges, Manchester, United Kingdom
| | - Megha Katare Pandey
- Department of Translational Medicine Center, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU), Mathura, India
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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18
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Tyrkalska SD, Candel S, Pedoto A, García-Moreno D, Alcaraz-Pérez F, Sánchez-Ferrer Á, Cayuela ML, Mulero V. Zebrafish models of COVID-19. FEMS Microbiol Rev 2022; 47:6794271. [PMID: 36323404 PMCID: PMC9841970 DOI: 10.1093/femsre/fuac042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/23/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022] Open
Abstract
Although COVID-19 has only recently appeared, research studies have already developed and implemented many animal models for deciphering the secrets of the disease and provided insights into the biology of SARS-CoV-2. However, there are several major factors that complicate the study of this virus in model organisms, such as the poor infectivity of clinical isolates of SARS-CoV-2 in some model species, and the absence of persistent infection, immunopathology, severe acute respiratory distress syndrome, and, in general, all the systemic complications which characterize COVID-19 clinically. Another important limitation is that SARS-CoV-2 mainly causes severe COVID-19 in older people with comorbidities, which represents a serious problem when attempting to use young and immunologically naïve laboratory animals in COVID-19 testing. We review here the main animal models developed so far to study COVID-19 and the unique advantages of the zebrafish model that may help to contribute to understand this disease, in particular to the identification and repurposing of drugs to treat COVID-19, to reveal the mechanism of action and side-effects of Spike-based vaccines, and to decipher the high susceptibility of aged people to COVID-19.
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Affiliation(s)
| | | | - Annamaria Pedoto
- Departmento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain,Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Diana García-Moreno
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Francisca Alcaraz-Pérez
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain,Grupo de Telomerasa, Cáncer y Envejecimiento (TCAG), Hospital Clínico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain
| | - Álvaro Sánchez-Ferrer
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain,Departmento de Bioloquímica y Biología Molecular A, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | | | - Victoriano Mulero
- Corresponding author: Departmento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain. E-mail:
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19
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Mitra J, Kodavati M, Provasek VE, Rao KS, Mitra S, Hamilton DJ, Horner PJ, Vahidy FS, Britz GW, Kent TA, Hegde ML. SARS-CoV-2 and the central nervous system: Emerging insights into hemorrhage-associated neurological consequences and therapeutic considerations. Ageing Res Rev 2022; 80:101687. [PMID: 35843590 PMCID: PMC9288264 DOI: 10.1016/j.arr.2022.101687] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/20/2022] [Accepted: 07/07/2022] [Indexed: 01/27/2023]
Abstract
Coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to impact our lives by causing widespread illness and death and poses a threat due to the possibility of emerging strains. SARS-CoV-2 targets angiotensin-converting enzyme 2 (ACE2) before entering vital organs of the body, including the brain. Studies have shown systemic inflammation, cellular senescence, and viral toxicity-mediated multi-organ failure occur during infectious periods. However, prognostic investigations suggest that both acute and long-term neurological complications, including predisposition to irreversible neurodegenerative diseases, can be a serious concern for COVID-19 survivors, especially the elderly population. As emerging studies reveal sites of SARS-CoV-2 infection in different parts of the brain, potential causes of chronic lesions including cerebral and deep-brain microbleeds and the likelihood of developing stroke-like pathologies increases, with critical long-term consequences, particularly for individuals with neuropathological and/or age-associated comorbid conditions. Our recent studies linking the blood degradation products to genome instability, leading to cellular senescence and ferroptosis, raise the possibility of similar neurovascular events as a result of SARS-CoV-2 infection. In this review, we discuss the neuropathological consequences of SARS-CoV-2 infection in COVID survivors, focusing on possible hemorrhagic damage in brain cells, its association to aging, and the future directions in developing mechanism-guided therapeutic strategies.
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Affiliation(s)
- Joy Mitra
- Division of DNA Repair Research, Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA.
| | - Manohar Kodavati
- Division of DNA Repair Research, Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Vincent E Provasek
- Division of DNA Repair Research, Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA; College of Medicine, Texas A&M University, College Station, TX, USA
| | - K S Rao
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation Deemed to be University, Green Fields, Vaddeswaram, Andhra Pradesh 522502, India
| | - Sankar Mitra
- Division of DNA Repair Research, Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Dale J Hamilton
- Center for Bioenergetics, Houston Methodist Research Institute, Houston, TX 77030, USA; Weill Cornell Medical College, New York, USA
| | - Philip J Horner
- Division of DNA Repair Research, Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA; Weill Cornell Medical College, New York, USA
| | - Farhaan S Vahidy
- Center for Outcomes Research, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Gavin W Britz
- Division of DNA Repair Research, Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA; Weill Cornell Medical College, New York, USA
| | - Thomas A Kent
- Center for Genomics and Precision Medicine, Department of Translational Medical Sciences, Institute of Biosciences and Technology, College of Medicine, Texas A&M Health Science Center, Houston, TX, USA
| | - Muralidhar L Hegde
- Division of DNA Repair Research, Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA; Weill Cornell Medical College, New York, USA.
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20
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Aicher SM, Streicher F, Chazal M, Planas D, Luo D, Buchrieser J, Nemcova M, Seidlova V, Zukal J, Serra-Cobo J, Pontier D, Pain B, Zimmer G, Schwartz O, Roingeard P, Pikula J, Dacheux L, Jouvenet N. Species-Specific Molecular Barriers to SARS-CoV-2 Replication in Bat Cells. J Virol 2022; 96:e0060822. [PMID: 35862713 PMCID: PMC9327701 DOI: 10.1128/jvi.00608-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/07/2022] [Indexed: 11/20/2022] Open
Abstract
Bats are natural reservoirs of numerous coronaviruses, including the potential ancestor of SARS-CoV-2. Knowledge concerning the interaction between coronaviruses and bat cells is sparse. We investigated the ability of primary cells from Rhinolophus and Myotis species, as well as of established and novel cell lines from Myotis myotis, Eptesicus serotinus, Tadarida brasiliensis, and Nyctalus noctula, to support SARS-CoV-2 replication. None of these cells were permissive to infection, not even the ones expressing detectable levels of angiotensin-converting enzyme 2 (ACE2), which serves as the viral receptor in many mammalian species. The resistance to infection was overcome by expression of human ACE2 (hACE2) in three cell lines, suggesting that the restriction to viral replication was due to a low expression of bat ACE2 (bACE2) or the absence of bACE2 binding in these cells. Infectious virions were produced but not released from hACE2-transduced M. myotis brain cells. E. serotinus brain cells and M. myotis nasal epithelial cells expressing hACE2 efficiently controlled viral replication, which correlated with a potent interferon response. Our data highlight the existence of species-specific and cell-specific molecular barriers to viral replication in bat cells. These novel chiropteran cellular models are valuable tools to investigate the evolutionary relationships between bats and coronaviruses. IMPORTANCE Bats are host ancestors of several viruses that cause serious disease in humans, as illustrated by the ongoing SARS-CoV-2 pandemic. Progress in investigating bat-virus interactions has been hampered by a limited number of available bat cellular models. We have generated primary cells and cell lines from several bat species that are relevant for coronavirus research. The various permissivities of the cells to SARS-CoV-2 infection offered the opportunity to uncover some species-specific molecular restrictions to viral replication. All bat cells exhibited a potent entry-dependent restriction. Once this block was overcome by overexpression of human ACE2, which serves at the viral receptor, two bat cell lines controlled well viral replication, which correlated with the inability of the virus to counteract antiviral responses. Other cells potently inhibited viral release. Our novel bat cellular models contribute to a better understanding of the molecular interplays between bat cells and viruses.
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Affiliation(s)
- Sophie-Marie Aicher
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
| | - Felix Streicher
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
| | - Maxime Chazal
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
| | - Delphine Planas
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus and Immunity Unit, Paris, France
- Vaccine Research Institute, Créteil, France
| | - Dongsheng Luo
- Institut Pasteur, Université de Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, Paris, France
| | - Julian Buchrieser
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus and Immunity Unit, Paris, France
| | - Monika Nemcova
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Veronika Seidlova
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Jan Zukal
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno, Brno, Czech Republic
| | - Jordi Serra-Cobo
- Institut de Recerca de la Biodiversitat (IRBio), Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Dominique Pontier
- Université de Lyon, LabEx Ecofect, Lyon, France
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Villeurbanne, France
| | - Bertrand Pain
- University of Lyon, Université Lyon 1, INSERM, INRAE, Stem Cell and Brain Research Institute, Bron, France
| | - Gert Zimmer
- Institute of Virology and Immunology, Bern & Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Olivier Schwartz
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus and Immunity Unit, Paris, France
- Vaccine Research Institute, Créteil, France
| | - Philippe Roingeard
- INSERM U1259 MAVIVH and Plateforme IBiSA de Microscopie Electronique, Faculté de Médecine, Université de Tours, Tours, France
| | - Jiri Pikula
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Laurent Dacheux
- Institut Pasteur, Université de Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, Paris, France
| | - Nolwenn Jouvenet
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
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21
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Rice BL, Lessler J, McKee C, Metcalf CJE. Why do some coronaviruses become pandemic threats when others do not? PLoS Biol 2022; 20:e3001652. [PMID: 35576224 PMCID: PMC9135331 DOI: 10.1371/journal.pbio.3001652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/26/2022] [Indexed: 11/18/2022] Open
Abstract
Despite multiple spillover events and short chains of transmission on at least 4 continents, Middle East Respiratory Syndrome Coronavirus (MERS-CoV) has never triggered a pandemic. By contrast, its relative, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has, despite apparently little, if any, previous circulation in humans. Resolving the unsolved mystery of the failure of MERS-CoV to trigger a pandemic could help inform how we understand the pandemic potential of pathogens, and probing it underscores a need for a more holistic understanding of the ways in which viral genetic changes scale up to population-level transmission.
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Affiliation(s)
- Benjamin L. Rice
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Justin Lessler
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Clifton McKee
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - C. Jessica E. Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Princeton School of Public and International Affairs, Princeton University, Princeton, New Jersey, United States of America
- Wissenschaftskolleg zu Berlin, Berlin, Germany
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22
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Papies J, Sieberg A, Ritz D, Niemeyer D, Drosten C, Müller MA. Reduced IFN-ß inhibitory activity of Lagos bat virus phosphoproteins in human compared to Eidolon helvum bat cells. PLoS One 2022; 17:e0264450. [PMID: 35259191 PMCID: PMC8903296 DOI: 10.1371/journal.pone.0264450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 02/10/2022] [Indexed: 12/14/2022] Open
Abstract
Eidolon helvum bats are reservoir hosts for highly pathogenic lyssaviruses often showing limited disease upon natural infection. An enhanced antiviral interferon (IFN) response combined with reduced inflammation might be linked to the apparent virus tolerance in bats. Lyssavirus phosphoproteins inhibit the IFN response with virus strain-specific efficiency. To date, little is known regarding the lyssavirus P-dependent anti-IFN countermeasures in bats, mainly due to a lack of in vitro tools. By using E. helvum bat cell cultures in a newly established bat-specific IFN-promoter activation assay, we analyzed the IFN-ß inhibitory activity of multiple lyssavirus P in E. helvum compared to human cells. Initial virus infection studies with a recently isolated E. helvum-borne Lagos bat virus street strain from Ghana showed enhanced LBV propagation in an E. helvum lung cell line compared to human A549 lung cells at later time points suggesting effective viral countermeasures against cellular defense mechanisms. A direct comparison of the IFN-ß inhibitory activity of the LBV-GH P protein with other lyssavirus P proteins showed that LBV-GH P and RVP both strongly inhibited the bat IFN-β promotor activation (range 75–90%) in EidLu/20.2 and an E. helvum kidney cell line. Conversely, LBV-GH P blocked the activation of the human IFN-β promoter less efficiently compared to a prototypic Rabies virus P protein (range LBV P 52–68% vs RVP 71–95%) in two different human cell lines (HEK-293T, A549). The same pattern was seen for two prototypic LBV P variants suggesting an overall reduced LBV P IFN-ß inhibitory activity in human cells as compared to E. helvum bat cells. Increased IFN-ß inhibition by lyssavirus P in reservoir host cells might be a result of host-specific adaptation processes towards an enhanced IFN response in bat cells.
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Affiliation(s)
- Jan Papies
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andrea Sieberg
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Daniel Ritz
- Institute of Virology, Universitätsklinikum Bonn, Bonn, Germany
| | - Daniela Niemeyer
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Berlin, Germany
| | - Marcel A. Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Berlin, Germany
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
- * E-mail:
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23
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Guth S, Mollentze N, Renault K, Streicker DG, Visher E, Boots M, Brook CE. Bats host the most virulent-but not the most dangerous-zoonotic viruses. Proc Natl Acad Sci U S A 2022; 119:e2113628119. [PMID: 35349342 DOI: 10.1101/2021.07.25.453574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
SignificanceThe clear need to mitigate zoonotic risk has fueled increased viral discovery in specific reservoir host taxa. We show that a combination of viral and reservoir traits can predict zoonotic virus virulence and transmissibility in humans, supporting the hypothesis that bats harbor exceptionally virulent zoonoses. However, pandemic prevention requires thinking beyond zoonotic capacity, virulence, and transmissibility to consider collective "burden" on human health. For this, viral discovery targeting specific reservoirs may be inefficient as death burden correlates with viral, not reservoir, traits, and depends on context-specific epidemiological dynamics across and beyond the human-animal interface. These findings suggest that longitudinal studies of viral dynamics in reservoir and spillover host populations may offer the most effective strategy for mitigating zoonotic risk.
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Affiliation(s)
- Sarah Guth
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Nardus Mollentze
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
| | - Katia Renault
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Daniel G Streicker
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Elisa Visher
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Mike Boots
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
- Centre for Ecology and Conservation, University of Exeter, Exeter TR10 9FE, United Kingdom
| | - Cara E Brook
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637
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24
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Guth S, Mollentze N, Renault K, Streicker DG, Visher E, Boots M, Brook CE. Bats host the most virulent-but not the most dangerous-zoonotic viruses. Proc Natl Acad Sci U S A 2022; 119:e2113628119. [PMID: 35349342 PMCID: PMC9168486 DOI: 10.1073/pnas.2113628119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 02/09/2022] [Indexed: 01/06/2023] Open
Abstract
SignificanceThe clear need to mitigate zoonotic risk has fueled increased viral discovery in specific reservoir host taxa. We show that a combination of viral and reservoir traits can predict zoonotic virus virulence and transmissibility in humans, supporting the hypothesis that bats harbor exceptionally virulent zoonoses. However, pandemic prevention requires thinking beyond zoonotic capacity, virulence, and transmissibility to consider collective "burden" on human health. For this, viral discovery targeting specific reservoirs may be inefficient as death burden correlates with viral, not reservoir, traits, and depends on context-specific epidemiological dynamics across and beyond the human-animal interface. These findings suggest that longitudinal studies of viral dynamics in reservoir and spillover host populations may offer the most effective strategy for mitigating zoonotic risk.
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Affiliation(s)
- Sarah Guth
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Nardus Mollentze
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
| | - Katia Renault
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Daniel G. Streicker
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Elisa Visher
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Mike Boots
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
- Centre for Ecology and Conservation, University of Exeter, Exeter TR10 9FE, United Kingdom
| | - Cara E. Brook
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637
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25
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Menter DG, Afshar-Kharghan V, Shen JP, Martch SL, Maitra A, Kopetz S, Honn KV, Sood AK. Of vascular defense, hemostasis, cancer, and platelet biology: an evolutionary perspective. Cancer Metastasis Rev 2022; 41:147-172. [PMID: 35022962 PMCID: PMC8754476 DOI: 10.1007/s10555-022-10019-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/04/2022] [Indexed: 01/08/2023]
Abstract
We have established considerable expertise in studying the role of platelets in cancer biology. From this expertise, we were keen to recognize the numerous venous-, arterial-, microvascular-, and macrovascular thrombotic events and immunologic disorders are caused by severe, acute-respiratory-syndrome coronavirus 2 (SARS-CoV-2) infections. With this offering, we explore the evolutionary connections that place platelets at the center of hemostasis, immunity, and adaptive phylogeny. Coevolutionary changes have also occurred in vertebrate viruses and their vertebrate hosts that reflect their respective evolutionary interactions. As mammals adapted from aquatic to terrestrial life and the heavy blood loss associated with placentalization-based live birth, platelets evolved phylogenetically from thrombocytes toward higher megakaryocyte-blebbing-based production rates and the lack of nuclei. With no nuclei and robust RNA synthesis, this adaptation may have influenced viral replication to become less efficient after virus particles are engulfed. Human platelets express numerous receptors that bind viral particles, which developed from archetypal origins to initiate aggregation and exocytic-release of thrombo-, immuno-, angiogenic-, growth-, and repair-stimulatory granule contents. Whether by direct, evolutionary, selective pressure, or not, these responses may help to contain virus spread, attract immune cells for eradication, and stimulate angiogenesis, growth, and wound repair after viral damage. Because mammalian and marsupial platelets became smaller and more plate-like their biophysical properties improved in function, which facilitated distribution near vessel walls in fluid-shear fields. This adaptation increased the probability that platelets could then interact with and engulf shedding virus particles. Platelets also generate circulating microvesicles that increase membrane surface-area encounters and mark viral targets. In order to match virus-production rates, billions of platelets are generated and turned over per day to continually provide active defenses and adaptation to suppress the spectrum of evolving threats like SARS-CoV-2.
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Affiliation(s)
- David G Menter
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Vahid Afshar-Kharghan
- Division of Internal Medicine, Benign Hematology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - John Paul Shen
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephanie L Martch
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Scott Kopetz
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kenneth V Honn
- Department of Pathology, Bioactive Lipids Research Program, Wayne State University, 5101 Cass Ave. 430 Chemistry, Detroit, MI, 48202, USA
- Department of Pathology, Wayne State University School of Medicine, 431 Chemistry Bldg, Detroit, MI, 48202, USA
- Cancer Biology Division, Wayne State University School of Medicine, 431 Chemistry Bldg, Detroit, MI, 48202, USA
| | - Anil K Sood
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
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26
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Bernstein AS, Ando AW, Loch-Temzelides T, Vale MM, Li BV, Li H, Busch J, Chapman CA, Kinnaird M, Nowak K, Castro MC, Zambrana-Torrelio C, Ahumada JA, Xiao L, Roehrdanz P, Kaufman L, Hannah L, Daszak P, Pimm SL, Dobson AP. The costs and benefits of primary prevention of zoonotic pandemics. SCIENCE ADVANCES 2022; 8:eabl4183. [PMID: 35119921 PMCID: PMC8816336 DOI: 10.1126/sciadv.abl4183] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The lives lost and economic costs of viral zoonotic pandemics have steadily increased over the past century. Prominent policymakers have promoted plans that argue the best ways to address future pandemic catastrophes should entail, "detecting and containing emerging zoonotic threats." In other words, we should take actions only after humans get sick. We sharply disagree. Humans have extensive contact with wildlife known to harbor vast numbers of viruses, many of which have not yet spilled into humans. We compute the annualized damages from emerging viral zoonoses. We explore three practical actions to minimize the impact of future pandemics: better surveillance of pathogen spillover and development of global databases of virus genomics and serology, better management of wildlife trade, and substantial reduction of deforestation. We find that these primary pandemic prevention actions cost less than 1/20th the value of lives lost each year to emerging viral zoonoses and have substantial cobenefits.
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Affiliation(s)
- Aaron S. Bernstein
- Boston Children’s Hospital and the Center for Climate, Health and the Global Environment, Boston, MA 02115, USA
- Corresponding author. (A.S.B.); (S.L.P.); (A.P.D.)
| | - Amy W. Ando
- Department of Agricultural and Consumer Economics, University of Illinois Urbana-Champaign, Champaign, IL 61801, USA
- Resources for the Future, 1616 P Street NW, Washington, DC 20036, USA
| | - Ted Loch-Temzelides
- Department of Economics and Baker Institute for Public Policy, Rice University, Houston, TX 77005, USA
| | - Mariana M. Vale
- Ecology Department, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- National Institute of Science and Technology in Ecology, Evolution and Biodiversity Conservation, Goiania, Brazil
| | - Binbin V. Li
- Environment Research Center, Duke Kunshan University, Kunshan, Jiangsu Province 215317, China
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Hongying Li
- EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018, USA
| | - Jonah Busch
- Moore Center for Science, Conservation International, Arlington, VA 22202, USA
| | - Colin A. Chapman
- Wilson Center, 1300 Pennsylvania Avenue NW, Washington, DC 20004, USA
- Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, DC 20004, USA
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi’an, China
| | - Margaret Kinnaird
- Practice Leader, Wildlife, WWF International, The Mvuli, Mvuli Road, Westlands, Kenya
| | - Katarzyna Nowak
- The Safina Center, 80 North Country Road, Setauket, NY 11733, USA
| | - Marcia C. Castro
- Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | | | - Jorge A. Ahumada
- Moore Center for Science, Conservation International, Arlington, VA 22202, USA
| | - Lingyun Xiao
- Department of Health and Environmental Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu Province 215123, China
| | - Patrick Roehrdanz
- Moore Center for Science, Conservation International, Arlington, VA 22202, USA
| | - Les Kaufman
- Department of Biology and Pardee Center for the Study of the Longer-Range Future, Boston University, Boston, MA 02215, USA
| | - Lee Hannah
- Moore Center for Science, Conservation International, Arlington, VA 22202, USA
| | - Peter Daszak
- EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018, USA
| | - Stuart L. Pimm
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
- Corresponding author. (A.S.B.); (S.L.P.); (A.P.D.)
| | - Andrew P. Dobson
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Santa Fe Institute, Hyde Park Road, Santa Fe, NM 87501, USA
- Corresponding author. (A.S.B.); (S.L.P.); (A.P.D.)
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27
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Head RJ, Lumbers ER, Jarrott B, Tretter F, Smith G, Pringle KG, Islam S, Martin JH. Systems analysis shows that thermodynamic physiological and pharmacological fundamentals drive COVID-19 and response to treatment. Pharmacol Res Perspect 2022; 10:e00922. [PMID: 35106955 PMCID: PMC8929328 DOI: 10.1002/prp2.922] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
Why a systems analysis view of this pandemic? The current pandemic has inflicted almost unimaginable grief, sorrow, loss, and terror at a global scale. One of the great ironies with the COVID‐19 pandemic, particularly early on, is counter intuitive. The speed at which specialized basic and clinical sciences described the details of the damage to humans in COVID‐19 disease has been impressive. Equally, the development of vaccines in an amazingly short time interval has been extraordinary. However, what has been less well understood has been the fundamental elements that underpin the progression of COVID‐19 in an individual and in populations. We have used systems analysis approaches with human physiology and pharmacology to explore the fundamental underpinnings of COVID‐19 disease. Pharmacology powerfully captures the thermodynamic characteristics of molecular binding with an exogenous entity such as a virus and its consequences on the living processes well described by human physiology. Thus, we have documented the passage of SARS‐CoV‐2 from infection of a single cell to species jump, to tropism, variant emergence and widespread population infection. During the course of this review, the recurrent observation was the efficiency and simplicity of one critical function of this virus. The lethality of SARS‐CoV‐2 is due primarily to its ability to possess and use a variable surface for binding to a specific human target with high affinity. This binding liberates Gibbs free energy (GFE) such that it satisfies the criteria for thermodynamic spontaneity. Its binding is the prelude to human host cellular entry and replication by the appropriation of host cell constituent molecules that have been produced with a prior energy investment by the host cell. It is also a binding that permits viral tropism to lead to high levels of distribution across populations with newly formed virions. This thermodynamic spontaneity is repeated endlessly as infection of a single host cell spreads to bystander cells, to tissues, to humans in close proximity and then to global populations. The principal antagonism of this process comes from SARS‐CoV‐2 itself, with its relentless changing of its viral surface configuration, associated with the inevitable emergence of variants better configured to resist immune sequestration and importantly with a greater affinity for the host target and higher infectivity. The great value of this physiological and pharmacological perspective is that it reveals the fundamental thermodynamic underpinnings of SARS‐CoV‐2 infection.
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Affiliation(s)
- Richard J Head
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Eugenie R Lumbers
- School of Biomedical Sciences & Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Bevyn Jarrott
- Florey Institute of Neuroscience & Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Felix Tretter
- Bertalanffy Center for the Study of Systems Science, Vienna, Austria
| | - Gary Smith
- VP System Practice - International Society for System Sciences, Pontypool, UK
| | - Kirsty G Pringle
- School of Biomedical Sciences & Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Saiful Islam
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Jennifer H Martin
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia.,Centre for Drug Repurposing and Medicines Research, Clinical Pharmacology, University of Newcastle, Newcastle, New South Wales, Australia
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28
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Abstract
The twenty-first century has witnessed a wave of severe infectious disease outbreaks, not least the COVID-19 pandemic, which has had a devastating impact on lives and livelihoods around the globe. The 2003 severe acute respiratory syndrome coronavirus outbreak, the 2009 swine flu pandemic, the 2012 Middle East respiratory syndrome coronavirus outbreak, the 2013-2016 Ebola virus disease epidemic in West Africa and the 2015 Zika virus disease epidemic all resulted in substantial morbidity and mortality while spreading across borders to infect people in multiple countries. At the same time, the past few decades have ushered in an unprecedented era of technological, demographic and climatic change: airline flights have doubled since 2000, since 2007 more people live in urban areas than rural areas, population numbers continue to climb and climate change presents an escalating threat to society. In this Review, we consider the extent to which these recent global changes have increased the risk of infectious disease outbreaks, even as improved sanitation and access to health care have resulted in considerable progress worldwide.
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29
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Gupta S, Rouse BT, Sarangi PP. Did Climate Change Influence the Emergence, Transmission, and Expression of the COVID-19 Pandemic? Front Med (Lausanne) 2021; 8:769208. [PMID: 34957147 PMCID: PMC8694059 DOI: 10.3389/fmed.2021.769208] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/19/2021] [Indexed: 12/11/2022] Open
Abstract
The human race has survived many epidemics and pandemics that have emerged and reemerged throughout history. The novel coronavirus Severe Acute Respiratory Syndrome SARS-CoV-2/COVID-19 is the latest pandemic and this has caused major health and socioeconomic problems in almost all communities of the world. The origin of the virus is still in dispute but most likely, the virus emerged from the bats and also may involve an intermediate host before affecting humans. Several other factors also may have affected the emergence and outcome of the infection but in this review, we make a case for a possible role of climate change. The rise in industrialization-related human activities has created a marked imbalance in the homeostasis of environmental factors such as temperature and other weather and these might even have imposed conditions for the emergence of future coronavirus cycles. An attempt is made in this review to explore the effect of ongoing climate changes and discuss if these changes had a role in facilitating the emergence, transmission, and even the expression of the COVID-19 pandemic. We surmise that pandemics will be more frequent in the future and more severely impactful unless climate changes are mitigated.
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Affiliation(s)
- Saloni Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Barry T. Rouse
- Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Pranita P. Sarangi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
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30
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Snell‐Rood EC, Smirnoff D, Cantrell H, Chapman K, Kirscht E, Stretch E. Bioinspiration as a method of problem-based STEM education: A case study with a class structured around the COVID-19 crisis. Ecol Evol 2021; 11:16374-16386. [PMID: 34900221 PMCID: PMC8646331 DOI: 10.1002/ece3.8044] [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: 11/18/2020] [Revised: 07/21/2021] [Accepted: 08/03/2021] [Indexed: 12/23/2022] Open
Abstract
Bioinspiration is a promising lens for biology instruction as it allows the instructor to focus on current issues, such as the COVID-19 pandemic. From social distancing to oxygen stress, organisms have been tackling pandemic-related problems for millions of years. What can we learn from such diverse adaptations in our own applications? This review uses a seminar course on the COVID-19 crisis to illustrate bioinspiration as an approach to teaching biology content. At the start of the class, students mind-mapped the entire problem; this range of subproblems was used to structure the biology content throughout the entire class. Students came to individual classes with a brainstormed list of biological systems that could serve as inspiration for a particular problem (e.g., absorptive leaves in response to the problem of toilet paper shortages). After exploration of relevant biology content, discussion returned to the focal problem. Students dug deeper into the literature in a group project on mask design and biological systems relevant to filtration and transparency. This class structure was an engaging way for students to learn principles from ecology, evolution, behavior, and physiology. Challenges with this course design revolved around the interdisciplinary and creative nature of the structure; for instance, the knowledge of the participants was often stretched by engineering details. While the present class was focused on the COVID-19 crisis, a course structured through a bioinspired approach can be applied to other focal problems, or subject areas, giving instructors a powerful method to deliver interdisciplinary content in an integrated and inquiry-driven way.
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Affiliation(s)
- Emilie C. Snell‐Rood
- Department of Ecology, Evolution and BehaviorUniversity of Minnesota‐Twin CitiesSaint PaulMinnesotaUSA
| | - Dimitri Smirnoff
- Department of Ecology, Evolution and BehaviorUniversity of Minnesota‐Twin CitiesSaint PaulMinnesotaUSA
- Department of Curriculum and InstructionSaint PaulMinnesotaUSA
| | - Hunter Cantrell
- Department of Ecology, Evolution and BehaviorUniversity of Minnesota‐Twin CitiesSaint PaulMinnesotaUSA
| | - Kaila Chapman
- Department of Ecology, Evolution and BehaviorUniversity of Minnesota‐Twin CitiesSaint PaulMinnesotaUSA
| | - Elizabeth Kirscht
- Department of Ecology, Evolution and BehaviorUniversity of Minnesota‐Twin CitiesSaint PaulMinnesotaUSA
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Brintnell E, Gupta M, Anderson DW. Phylogenetic and Ancestral Sequence Reconstruction of SARS-CoV-2 Reveals Latent Capacity to Bind Human ACE2 Receptor. J Mol Evol 2021; 89:656-664. [PMID: 34739551 PMCID: PMC8570237 DOI: 10.1007/s00239-021-10034-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/26/2021] [Indexed: 01/05/2023]
Abstract
SARS-CoV-2 is a unique event, having emerged suddenly as a highly infectious viral pathogen for human populations. Previous phylogenetic analyses show its closest known evolutionary relative to be a virus detected in bats (RaTG13), with a common assumption that SARS-CoV-2 evolved from a zoonotic ancestor via recent genetic changes (likely in the Spike protein receptor-binding domain or RBD) that enabled it to infect humans. We used detailed phylogenetic analysis, ancestral sequence reconstruction, and in situ molecular dynamics simulations to examine the Spike-RBD's functional evolution, finding that the common ancestral virus with RaTG13, dating to no later than 2013, possessed high binding affinity to the human ACE2 receptor. This suggests that SARS-CoV-2 likely possessed a latent capacity to bind to human cellular targets (though this may not have been sufficient for successful infection) and emphasizes the importance of expanding efforts to catalog and monitor viruses circulating in both human and non-human populations.
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Affiliation(s)
- Erin Brintnell
- Bachelor of Health Sciences Program, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Canada
| | - Mehul Gupta
- Bachelor of Health Sciences Program, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada
| | - Dave W Anderson
- Bachelor of Health Sciences Program, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada.
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Bauer S, Zhang F, Linhardt RJ. Implications of Glycosaminoglycans on Viral Zoonotic Diseases. Diseases 2021; 9:85. [PMID: 34842642 PMCID: PMC8628766 DOI: 10.3390/diseases9040085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 11/21/2022] Open
Abstract
Zoonotic diseases are infectious diseases that pass from animals to humans. These include diseases caused by viruses, bacteria, fungi, and parasites and can be transmitted through close contact or through an intermediate insect vector. Many of the world's most problematic zoonotic diseases are viral diseases originating from animal spillovers. The Spanish influenza pandemic, Ebola outbreaks in Africa, and the current SARS-CoV-2 pandemic are thought to have started with humans interacting closely with infected animals. As the human population grows and encroaches on more and more natural habitats, these incidents will only increase in frequency. Because of this trend, new treatments and prevention strategies are being explored. Glycosaminoglycans (GAGs) are complex linear polysaccharides that are ubiquitously present on the surfaces of most human and animal cells. In many infectious diseases, the interactions between GAGs and zoonotic pathogens correspond to the first contact that results in the infection of host cells. In recent years, researchers have made progress in understanding the extraordinary roles of GAGs in the pathogenesis of zoonotic diseases, suggesting potential therapeutic avenues for using GAGs in the treatment of these diseases. This review examines the role of GAGs in the progression, prevention, and treatment of different zoonotic diseases caused by viruses.
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Affiliation(s)
- Sarah Bauer
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA;
| | - Fuming Zhang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA;
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Robert J. Linhardt
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA;
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
- Departments of Biological Science, Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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Selection and stability validation of reference gene candidates for transcriptional analysis in Rousettus aegyptiacus. Sci Rep 2021; 11:21662. [PMID: 34737406 PMCID: PMC8568961 DOI: 10.1038/s41598-021-01260-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/18/2021] [Indexed: 11/08/2022] Open
Abstract
Bats are the only mammals capable of powered flight and their body temperature can reach up to 42 °C during flight. Additionally, bats display robust type I IFN interferon (IFN-I) responses and some species constitutively express IFN-α. Reference genes with stable expression under temperature oscillations and IFN-I release are therefore critical for normalization of quantitative reverse-transcription polymerase chain reaction (qRT-PCR) data in bats. The expression stability of reference genes in Rousettus aegyptiacus remains elusive, although this species is frequently used in the infection research. We selected ACTB, EEF1A1, GAPDH and PGK1 as candidate reference genes and evaluated their expression stability in various tissues and cells from this model bat species upon IFN-I treatment at 35 °C, 37 °C and 40 °C by qRT-PCR. We employed two statistical algorithms, BestKeeper and NormFinder, and found that EEF1A1 exhibited the highest expression stability under all tested conditions. ACTB and GAPDH displayed unstable expression upon temperature change and IFN-I treatment, respectively. By normalizing to EEF1A1, we uncovered that GAPDH expression was significantly induced by IFN-I in R. aegyptiacus. Our study identifies EEF1A1 as the most suitable reference gene for qRT-PCR studies upon temperature changes and IFN-I treatment and unveils the induction of GAPDH expression by IFN-I in R. aegyptiacus. These findings are pertinent to other bat species and may be relevant for non-volant mammals that show physiological fluctuations of core body temperature.
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Roe K. Proposed classifications of immunogenomic editing by cancers and pathogens. INFECTION GENETICS AND EVOLUTION 2021; 96:105126. [PMID: 34715386 DOI: 10.1016/j.meegid.2021.105126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/14/2021] [Accepted: 10/23/2021] [Indexed: 10/20/2022]
Abstract
Several evolutionary mechanisms exist between a lethal disease agent, such as a cancer or a pathogen, and the immune system of a surviving subpopulation of hosts. Immunogenomic editing is herein defined as the evolution of a lethal disease agent genome or the surviving carrier or host subpopulation immune system genomes. One type of immunogenomic editing called immunoediting has already been identified for cancer genomes. The effects of two other types of immunogenomic editing have been observed for pathogens and humans. However, these types of editing are only a few types of a much broader immunogenomic editing process, and some of the other types of immunogenomic editing have not been explicitly recognized. Immunogenomic editing can include seven types, and several types of immunogenomic editing have applications including analysis of subpopulation responses to cancers and pathogens. Applications would also include facilitating analysis of substantial subpopulation vulnerability differences to lethal pathogen epidemics. The need for quicker analysis of the actual transmission chains and the immunogenomic mechanisms for the faster spread of dangerously virulent pathogens can be expected to increase, since modern transportation technology can spread new pathogens very rapidly around the world.
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Affiliation(s)
- Kevin Roe
- San Jose, CA, United States of America.
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35
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Khan AA, Singh H, Bilal M, Ashraf MT. Microbiota, probiotics and respiratory infections: the three musketeers can tip off potential management of COVID-19. Am J Transl Res 2021; 13:10977-10993. [PMID: 34786037 PMCID: PMC8581851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/15/2021] [Indexed: 06/13/2023]
Abstract
Rapid infectivity of SARS-CoV2 with recent viral variants is posing a challenge in the development of robust therapeutic strategies. On the other hand, microbiota is debated for its involvement in SARS-CoV2 infection with varied opinions. Although ample data about the role of microbiota and probiotics in respiratory viral infections are available, their role in COVID-19 is limited albeit emerging rapidly. The utilization of probiotics for the management of COVID-19 is still under investigation in many clinical trials. Existing information coupled with recent COVID-19 related studies can suggest various ways to use microbiota modulation and probiotics for managing this pandemic. Present article indicates the role of microbiota modulation and probiotics in respiratory infections. In addition, scattered evidence was gathered to understand the potential of microbiota and probiotics in the management of SARS-CoV2. Gut-airway microbiota connection is already apparent in respiratory tract viral infections, including SARS-CoV2. Though few clinical trials are evaluating microbiota and probiotics for COVID-19 management, the safety evaluation must be given more serious consideration because of the possibility of opportunistic infections among COVID-19 patients. Nevertheless, the information about microbiota modulation using probiotics and prebiotics can be helpful to manage this outbreak and this review presents different aspects of this idea.
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Affiliation(s)
- Abdul Arif Khan
- Division of Microbiology, Indian Council of Medical Research-National AIDS Research InstitutePune, Maharashtra 411026, India
| | - HariOm Singh
- Division of Molecular Biology, Indian Council of Medical Research-National AIDS Research InstitutePune, Maharashtra 411026, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of TechnologyHuaian 223003, China
| | - Mohd Tashfeen Ashraf
- School of Biotechnology, Gautam Buddha UniversityGautam Budh Nagar, Greater Noida (UP), India
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The Cross-Talk between Thrombosis and Inflammatory Storm in Acute and Long-COVID-19: Therapeutic Targets and Clinical Cases. Viruses 2021; 13:v13101904. [PMID: 34696334 PMCID: PMC8540492 DOI: 10.3390/v13101904] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) commonly complicates with coagulopathy. A syndrome called Long-COVID-19 is emerging recently in COVID-19 survivors, characterized, in addition to the persistence of symptoms typical of the acute phase, by alterations in inflammatory and coagulation parameters due to endothelial damage. The related disseminated intravascular coagulation (DIC) can be associated with high death rates in COVID-19 patients. It is possible to find a prothrombotic state also in Long-COVID-19. Early administration of anticoagulants in COVID-19 was suggested in order to improve patient outcomes, although exact criteria for their application were not well-established. Low-molecular-weight heparin (LMWH) was commonly adopted for counteracting DIC and venous thromboembolism (VTE), due to its pharmacodynamics and anti-inflammatory properties. However, the efficacy of anticoagulant therapy for COVID-19-associated DIC is still a matter of debate. Thrombin and Factor Xa (FXa) are well-known components of the coagulation cascade. The FXa is known to strongly promote inflammation as the consequence of increased cytokine expression. Endothelial cells and mononuclear leucocytes release cytokines, growth factors, and adhesion molecules due to thrombin activation. On the other hand, cytokines can activate coagulation. The cross-talk between coagulation and inflammation is mediated via protease-activated receptors (PARs). These receptors might become potential targets to be considered for counteracting the clinical expressions of COVID-19. SARS-CoV-2 is effectively able to activate local and circulating coagulation factors, thus inducing the generation of disseminated coagula. LMWH may be considered as the new frontier in the treatment of COVID-19 and Long-COVID-19. Indeed, direct oral anticoagulants (DOACs) may be an alternative option for both early and later treatment of COVID-19 patients due to their ability to inhibit PARs. The aim of this report was to evaluate the role of anticoagulants—and DOACs in particular in COVID-19 and Long-COVID-19 patients. We report the case of a COVID-19 patient who, after administration of enoxaparin developed DIC secondary to virosis and positivity for platelet factor 4 (PF4) and a case of Long-COVID with high residual cardiovascular risk and persistence of blood chemistry of inflammation and procoagulative state.
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Seal S, Dharmarajan G, Khan I. Evolution of pathogen tolerance and emerging infections: A missing experimental paradigm. eLife 2021; 10:e68874. [PMID: 34544548 PMCID: PMC8455132 DOI: 10.7554/elife.68874] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/23/2021] [Indexed: 12/11/2022] Open
Abstract
Researchers worldwide are repeatedly warning us against future zoonotic diseases resulting from humankind's insurgence into natural ecosystems. The same zoonotic pathogens that cause severe infections in a human host frequently fail to produce any disease outcome in their natural hosts. What precise features of the immune system enable natural reservoirs to carry these pathogens so efficiently? To understand these effects, we highlight the importance of tracing the evolutionary basis of pathogen tolerance in reservoir hosts, while drawing implications from their diverse physiological and life-history traits, and ecological contexts of host-pathogen interactions. Long-term co-evolution might allow reservoir hosts to modulate immunity and evolve tolerance to zoonotic pathogens, increasing their circulation and infectious period. Such processes can also create a genetically diverse pathogen pool by allowing more mutations and genetic exchanges between circulating strains, thereby harboring rare alive-on-arrival variants with extended infectivity to new hosts (i.e., spillover). Finally, we end by underscoring the indispensability of a large multidisciplinary empirical framework to explore the proposed link between evolved tolerance, pathogen prevalence, and spillover in the wild.
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Affiliation(s)
| | - Guha Dharmarajan
- Savannah River Ecology Laboratory, University of GeorgiaAikenUnited States
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38
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Rice BL, Douek DC, McDermott AB, Grenfell BT, Metcalf CJE. Why are there so few (or so many) circulating coronaviruses? Trends Immunol 2021; 42:751-763. [PMID: 34366247 PMCID: PMC8272969 DOI: 10.1016/j.it.2021.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/11/2022]
Abstract
Despite vast diversity in non-human hosts and conspicuous recent spillover events, only a small number of coronaviruses have been observed to persist in human populations. This puzzling mismatch suggests substantial barriers to establishment. We detail hypotheses that might contribute to explain the low numbers of endemic coronaviruses, despite their considerable evolutionary and emergence potential. We assess possible explanations ranging from issues of ascertainment, historically lower opportunities for spillover, aspects of human demographic changes, and features of pathogen biology and pre-existing adaptive immunity to related viruses. We describe how successful emergent viral species must triangulate transmission, virulence, and host immunity to maintain circulation. Characterizing the factors that might shape the limits of viral persistence can delineate promising research directions to better understand the combinations of pathogens and contexts that are most likely to lead to spillover.
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Affiliation(s)
- Benjamin L Rice
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA; Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA; Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA
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39
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Comparative Computational Modeling of the Bat and Human Immune Response to Viral Infection with the Comparative Biology Immune Agent Based Model. Viruses 2021; 13:v13081620. [PMID: 34452484 PMCID: PMC8402910 DOI: 10.3390/v13081620] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/05/2021] [Accepted: 08/13/2021] [Indexed: 12/22/2022] Open
Abstract
Given the impact of pandemics due to viruses of bat origin, there is increasing interest in comparative investigation into the differences between bat and human immune responses. The practice of comparative biology can be enhanced by computational methods used for dynamic knowledge representation to visualize and interrogate the putative differences between the two systems. We present an agent based model that encompasses and bridges differences between bat and human responses to viral infection: the comparative biology immune agent based model, or CBIABM. The CBIABM examines differences in innate immune mechanisms between bats and humans, specifically regarding inflammasome activity and type 1 interferon dynamics, in terms of tolerance to viral infection. Simulation experiments with the CBIABM demonstrate the efficacy of bat-related features in conferring viral tolerance and also suggest a crucial role for endothelial inflammasome activity as a mechanism for bat systemic viral tolerance and affecting the severity of disease in human viral infections. We hope that this initial study will inspire additional comparative modeling projects to link, compare, and contrast immunological functions shared across different species, and in so doing, provide insight and aid in preparation for future viral pandemics of zoonotic origin.
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40
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A planetary health perspective for kidney disease. Kidney Int 2021; 98:261-265. [PMID: 32709283 PMCID: PMC7372277 DOI: 10.1016/j.kint.2020.03.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 01/06/2023]
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41
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Moreno Santillán DD, Lama TM, Gutierrez Guerrero YT, Brown AM, Donat P, Zhao H, Rossiter SJ, Yohe LR, Potter JH, Teeling EC, Vernes SC, Davies KTJ, Myers E, Hughes GM, Huang Z, Hoffmann F, Corthals AP, Ray DA, Dávalos LM. Large-scale genome sampling reveals unique immunity and metabolic adaptations in bats. Mol Ecol 2021; 30:6449-6467. [PMID: 34146369 DOI: 10.1111/mec.16027] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/27/2021] [Accepted: 06/03/2021] [Indexed: 11/28/2022]
Abstract
Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species, one generated in this study, encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defence receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defence response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance antiviral immune response while dampening inflammatory signalling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored.
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Affiliation(s)
| | - Tanya M Lama
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Yocelyn T Gutierrez Guerrero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Mexico City, Mexico
| | - Alexis M Brown
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Paul Donat
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Huabin Zhao
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Laurel R Yohe
- Department of Earth & Planetary Science, Yale University, New Haven, Connecticut, USA
| | - Joshua H Potter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,School of Biology, The University of St Andrews, Fife, UK
| | - Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Eugene Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Graham M Hughes
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Federico Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA
| | - Angelique P Corthals
- Department of Sciences, John Jay College of Criminal Justice, New York, New York, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Consortium for Inter- Disciplinary Environmental Research, Stony Brook University, Stony Brook, New York, USA
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42
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Hanan N, Doud RL, Park IW, Jones HP, Mathew SO. The Many Faces of Innate Immunity in SARS-CoV-2 Infection. Vaccines (Basel) 2021; 9:vaccines9060596. [PMID: 34199761 PMCID: PMC8228170 DOI: 10.3390/vaccines9060596] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/19/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
The innate immune system is important for initial antiviral response. SARS-CoV-2 can result in overactivity or suppression of the innate immune system. A dysregulated immune response is associated with poor outcomes; with patients having significant Neutrophil-to-Lymphocyte ratios (NLR) due to neutrophilia alongside lymphopenia. Elevated interleukin (IL)-6 and IL-8 leads to overactivity and is a prominent feature of severe COVID-19 patients. IL-6 can result in lymphopenia; where COVID-19 patients typically have significantly altered lymphocyte subsets. IL-8 attracts neutrophils; which may play a significant role in lung tissue damage with the formation of neutrophil extracellular traps leading to cytokine storm or acute respiratory distress syndrome. Several factors like pre-existing co-morbidities, genetic risks, viral pathogenicity, and therapeutic efficacy act as important modifiers of SARS-CoV-2 risks for disease through an interplay with innate host inflammatory responses. In this review, we discuss the role of the innate immune system at play with other important modifiers in SARS-CoV-2 infection.
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Affiliation(s)
- Nicholas Hanan
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (N.H.); (R.L.D.J.); (I.-W.P.); (H.P.J.)
| | - Ronnie L. Doud
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (N.H.); (R.L.D.J.); (I.-W.P.); (H.P.J.)
| | - In-Woo Park
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (N.H.); (R.L.D.J.); (I.-W.P.); (H.P.J.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Harlan P. Jones
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (N.H.); (R.L.D.J.); (I.-W.P.); (H.P.J.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Stephen O. Mathew
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (N.H.); (R.L.D.J.); (I.-W.P.); (H.P.J.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
- Correspondence: ; Tel.: +1-817-735-5407
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43
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Jelinek HF, Mousa M, Alefishat E, Osman W, Spence I, Bu D, Feng SF, Byrd J, Magni PA, Sahibzada S, Tay GK, Alsafar HS. Evolution, Ecology, and Zoonotic Transmission of Betacoronaviruses: A Review. Front Vet Sci 2021; 8:644414. [PMID: 34095271 PMCID: PMC8173069 DOI: 10.3389/fvets.2021.644414] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/25/2021] [Indexed: 12/18/2022] Open
Abstract
Coronavirus infections have been a part of the animal kingdom for millennia. The difference emerging in the twenty-first century is that a greater number of novel coronaviruses are being discovered primarily due to more advanced technology and that a greater number can be transmitted to humans, either directly or via an intermediate host. This has a range of effects from annual infections that are mild to full-blown pandemics. This review compares the zoonotic potential and relationship between MERS, SARS-CoV, and SARS-CoV-2. The role of bats as possible host species and possible intermediate hosts including pangolins, civets, mink, birds, and other mammals are discussed with reference to mutations of the viral genome affecting zoonosis. Ecological, social, cultural, and environmental factors that may play a role in zoonotic transmission are considered with reference to SARS-CoV, MERS, and SARS-CoV-2 and possible future zoonotic events.
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Affiliation(s)
- Herbert F. Jelinek
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center of Heath Engineering Innovation, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mira Mousa
- Nuffield Department of Women's and Reproduction Health, Oxford University, Oxford, United Kingdom
| | - Eman Alefishat
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Pharmacology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Wael Osman
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ian Spence
- Discipline of Pharmacology, University of Sydney, Sydney, NSW, Australia
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Samuel F. Feng
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Mathematics, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Jason Byrd
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Paola A. Magni
- Discipline of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA, Australia
- Murdoch University Singapore, King's Centre, Singapore, Singapore
| | - Shafi Sahibzada
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Guan K. Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Division of Psychiatry, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Habiba S. Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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44
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Yan L, Song Y, Xia K, He P, Zhang F, Chen S, Pouliot R, Weiss DJ, Tandon R, Bates JT, Ederer DR, Mitra D, Sharma P, Davis A, Linhardt RJ. Heparan sulfates from bat and human lung and their binding to the spike protein of SARS-CoV-2 virus. Carbohydr Polym 2021; 260:117797. [PMID: 33712145 PMCID: PMC7882221 DOI: 10.1016/j.carbpol.2021.117797] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/22/2021] [Accepted: 02/06/2021] [Indexed: 12/27/2022]
Abstract
Severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) has resulted in a pandemic and continues to spread at an unprecedented rate around the world. Although a vaccine has recently been approved, there are currently few effective therapeutics to fight its associated disease in humans, COVID-19. SARS-CoV-2 and the related severe acute respiratory syndrome (SARS-CoV-1), and Middle East respiratory syndrome (MERS-CoV) result from zoonotic respiratory viruses that have bats as the primary host and an as yet unknown secondary host. While each of these viruses has different protein-based cell-surface receptors, each rely on the glycosaminoglycan, heparan sulfate as a co-receptor. In this study we compare, for the first time, differences and similarities in the structure of heparan sulfate in human and bat lungs. Furthermore, we show that the spike glycoprotein of COVID-19 binds 3.5 times stronger to human lung heparan sulfate than bat lung heparan sulfate.
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Affiliation(s)
- Lufeng Yan
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou, 310058, China; Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States
| | - Yuefan Song
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States
| | - Ke Xia
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States
| | - Peng He
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States
| | - Fuming Zhang
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States
| | - Shiguo Chen
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou, 310058, China
| | - Robert Pouliot
- Larner College of Medicine, University of Vermont, Burlington, VT, United States
| | - Daniel J Weiss
- Larner College of Medicine, University of Vermont, Burlington, VT, United States
| | - Ritesh Tandon
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, 39216, United States
| | - John T Bates
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, 39216, United States
| | - Dallas R Ederer
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, 39216, United States
| | - Dipanwita Mitra
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, 39216, United States
| | - Poonam Sharma
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, 39216, United States
| | - April Davis
- Rabies Laboratory, New York State Department of Health Wadsworth Center, Albany, New York, United States
| | - Robert J Linhardt
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States; Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States.
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45
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Neely BA, Becker DJ, Janech MG, Fenton MB, Simmons NB, Bland AM. Surveying the Vampire Bat ( Desmodus rotundus) Serum Proteome: A Resource for Identifying Immunological Proteins and Detecting Pathogens. J Proteome Res 2021; 20:2547-2559. [PMID: 33840197 PMCID: PMC9812275 DOI: 10.1021/acs.jproteome.0c00995] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bats are increasingly studied as model systems for longevity and as natural hosts for some virulent viruses. Yet the ability to characterize immune mechanisms of viral tolerance and to quantify infection dynamics in wild bats is often limited by small sample volumes and few species-specific reagents. Here, we demonstrate how proteomics can overcome these limitations by using data-independent acquisition-based shotgun proteomics to survey the serum proteome of 17 vampire bats (Desmodus rotundus) from Belize. Using just 2 μL of sample and relatively short separations of undepleted serum digests, we identified 361 proteins across 5 orders of magnitude. Levels of immunological proteins in vampire bat serum were then compared to human plasma via published databases. Of particular interest were antiviral and antibacterial components, circulating 20S proteasome complex and proteins involved in redox activity. Lastly, we used known virus proteomes to putatively identify Rh186 from Macacine herpesvirus 3 and ORF1a from Middle East respiratory syndrome-related coronavirus, indicating that mass spectrometry-based techniques show promise for pathogen detection. Overall, these results can be used to design targeted mass-spectrometry assays to quantify immunological markers and detect pathogens. More broadly, our findings also highlight the application of proteomics in advancing wildlife immunology and pathogen surveillance.
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Affiliation(s)
- Benjamin A. Neely
- Chemical Sciences Division, National, Institute of Standards and Technology, Charleston, South, Carolina 29412, United States
| | - Daniel J. Becker
- Department of Biology, University of, Oklahoma, Norman, Oklahoma 73019, United States
| | - Michael G. Janech
- Hollings Marine Laboratory, Charleston, South Carolina 29412, United States; Department of, Biology, College of Charleston, Charleston, South Carolina, 29424, United States
| | - M. Brock Fenton
- Department of Biology, Western University, London, Ontario N6A 3K7, Canada
| | - Nancy B. Simmons
- Department of Mammalogy, Division of, Vertebrate Zoology, American Museum of Natural History, New York 10024, United States
| | - Alison M. Bland
- Hollings Marine Laboratory, Charleston, South Carolina 29412, United States; Department of, Biology, College of Charleston, Charleston, South Carolina, 29424, United States
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46
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SARS-CoV-2: Cross-scale Insights from Ecology and Evolution. Trends Microbiol 2021; 29:593-605. [PMID: 33893024 PMCID: PMC7997387 DOI: 10.1016/j.tim.2021.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/19/2022]
Abstract
Ecological and evolutionary processes govern the fitness, propagation, and interactions of organisms through space and time, and viruses are no exception. While coronavirus disease 2019 (COVID-19) research has primarily emphasized virological, clinical, and epidemiological perspectives, crucial aspects of the pandemic are fundamentally ecological or evolutionary. Here, we highlight five conceptual domains of ecology and evolution – invasion, consumer-resource interactions, spatial ecology, diversity, and adaptation – that illuminate (sometimes unexpectedly) the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We describe the applications of these concepts across levels of biological organization and spatial scales, including within individual hosts, host populations, and multispecies communities. Together, these perspectives illustrate the integrative power of ecological and evolutionary ideas and highlight the benefits of interdisciplinary thinking for understanding emerging viruses.
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47
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Martin LB, Hanson HE, Hauber ME, Ghalambor CK. Genes, Environments, and Phenotypic Plasticity in Immunology. Trends Immunol 2021; 42:198-208. [PMID: 33518415 DOI: 10.1016/j.it.2021.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/31/2020] [Accepted: 01/05/2021] [Indexed: 12/30/2022]
Abstract
For most of its history, immunology has sought to control environmental variation to establish genetic causality. As with all biological traits though, variation among individuals arises by three broad pathways: genetic (G), environmental (E), and the interactive between the two (GxE); and immunity is no different. Here, we review the value of applying the evolutionary frameworks of phenotypic plasticity and reaction norms to immunology. Because standardized laboratory environments are vastly different from the conditions under which populations evolved, we hypothesize that immunology might presently be missing important phenotypic variation and even focusing on dysregulated molecular and cellular processes. Modest adjustments to study designs could make model organism immunology more productive, reproducible, and reflective of human physiology.
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Affiliation(s)
- Lynn B Martin
- Center for Global Health and Infectious Disease Research, University of South Florida, Tampa, FL, USA.
| | - Haley E Hanson
- Center for Global Health and Infectious Disease Research, University of South Florida, Tampa, FL, USA
| | - Mark E Hauber
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois, Urbana-Champaign, IL, USA
| | - Cameron K Ghalambor
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Department of Biology, Colorado State University, Fort Collins, CO, USA
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48
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Shankar EM, Che KF, Yong YK, Girija ASS, Velu V, Ansari AW, Larsson M. Asymptomatic SARS-CoV-2 infection: is it all about being refractile to innate immune sensing of viral spare-parts?-Clues from exotic animal reservoirs. Pathog Dis 2021; 79:ftaa076. [PMID: 33289808 PMCID: PMC7799061 DOI: 10.1093/femspd/ftaa076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/04/2020] [Indexed: 01/08/2023] Open
Abstract
A vast proportion of coronavirus disease 2019 (COVID-19) individuals remain asymptomatic and can shed severe acute respiratory syndrome (SARS-CoV) type 2 virus to transmit the infection, which also explains the exponential increase in the number of COVID-19 cases globally. Furthermore, the rate of recovery from clinical COVID-19 in certain pockets of the globe is surprisingly high. Based on published reports and available literature, here, we speculated a few immunovirological mechanisms as to why a vast majority of individuals remain asymptomatic similar to exotic animal (bats and pangolins) reservoirs that remain refractile to disease development despite carrying a huge load of diverse insidious viral species, and whether such evolutionary advantage would unveil therapeutic strategies against COVID-19 infection in humans. Understanding the unique mechanisms that exotic animal species employ to achieve viral control, as well as inflammatory regulation, appears to hold key clues to the development of therapeutic versatility against COVID-19.
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MESH Headings
- Animals
- Animals, Exotic/virology
- Asymptomatic Diseases
- COVID-19/genetics
- COVID-19/immunology
- COVID-19/transmission
- COVID-19/virology
- Chiroptera/virology
- Cytokine Release Syndrome/genetics
- Cytokine Release Syndrome/immunology
- Cytokine Release Syndrome/prevention & control
- Cytokine Release Syndrome/virology
- Disease Reservoirs
- Eutheria/virology
- Gene Expression
- Host Specificity
- Humans
- Immune Tolerance
- Immunity, Innate
- Interferon-beta/deficiency
- Interferon-beta/genetics
- Interferon-beta/immunology
- Killer Cells, Natural/immunology
- Killer Cells, Natural/virology
- Monocytes/immunology
- Monocytes/virology
- NLR Family, Pyrin Domain-Containing 3 Protein/deficiency
- NLR Family, Pyrin Domain-Containing 3 Protein/genetics
- NLR Family, Pyrin Domain-Containing 3 Protein/immunology
- Receptors, KIR/deficiency
- Receptors, KIR/genetics
- Receptors, KIR/immunology
- Receptors, NK Cell Lectin-Like/deficiency
- Receptors, NK Cell Lectin-Like/genetics
- Receptors, NK Cell Lectin-Like/immunology
- SARS-CoV-2/pathogenicity
- Tumor Necrosis Factor-alpha/deficiency
- Tumor Necrosis Factor-alpha/genetics
- Tumor Necrosis Factor-alpha/immunology
- Zoonoses/genetics
- Zoonoses/immunology
- Zoonoses/transmission
- Zoonoses/virology
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Affiliation(s)
- Esaki M Shankar
- Infection Biology, Department of Life Sciences, Central University of Tamil Nadu, Neelakudi, Thiruvarur 610005, India
| | - Karlhans F Che
- Unit for Lung and Airway Research, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yean K Yong
- Laboratory Centre, Xiamen University, Sepang, Malaysia
| | - A S Smiline Girija
- Department of Microbiology, Saveetha Dental College and Hospital, Chennai, India
| | - Vijayakumar Velu
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA USA
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Abdul W Ansari
- Sharjah Institute of Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Marie Larsson
- Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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49
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Irving AT, Ahn M, Goh G, Anderson DE, Wang LF. Lessons from the host defences of bats, a unique viral reservoir. Nature 2021; 589:363-370. [PMID: 33473223 DOI: 10.1038/s41586-020-03128-0] [Citation(s) in RCA: 179] [Impact Index Per Article: 59.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/03/2020] [Indexed: 01/30/2023]
Abstract
There have been several major outbreaks of emerging viral diseases, including Hendra, Nipah, Marburg and Ebola virus diseases, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS)-as well as the current pandemic of coronavirus disease 2019 (COVID-19). Notably, all of these outbreaks have been linked to suspected zoonotic transmission of bat-borne viruses. Bats-the only flying mammal-display several additional features that are unique among mammals, such as a long lifespan relative to body size, a low rate of tumorigenesis and an exceptional ability to host viruses without presenting clinical disease. Here we discuss the mechanisms that underpin the host defence system and immune tolerance of bats, and their ramifications for human health and disease. Recent studies suggest that 64 million years of adaptive evolution have shaped the host defence system of bats to balance defence and tolerance, which has resulted in a unique ability to act as an ideal reservoir host for viruses. Lessons from the effective host defence of bats would help us to better understand viral evolution and to better predict, prevent and control future viral spillovers. Studying the mechanisms of immune tolerance in bats could lead to new approaches to improving human health. We strongly believe that it is time to focus on bats in research for the benefit of both bats and humankind.
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Affiliation(s)
- Aaron T Irving
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore. .,Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China. .,Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Matae Ahn
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Geraldine Goh
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore. .,SingHealth Duke-NUS Global Health Institute, Singapore, Singapore.
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50
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Donnik IM, Popov IV, Sereda SV, Popov IV, Chikindas ML, Ermakov AM. Coronavirus Infections of Animals: Future Risks to Humans. BIOL BULL+ 2021; 48:26-37. [PMID: 33679117 PMCID: PMC7917535 DOI: 10.1134/s1062359021010052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/27/2020] [Accepted: 07/17/2020] [Indexed: 01/31/2023]
Abstract
Coronaviruses have tremendous evolutionary potential, and three major outbreaks of new human coronavirus infections have occurred in the recent history of humankind. In this paper, the patterns of occurrence of new zoonotic coronavirus infections and the role of bioveterinary control in preventing their potential outbreaks in the future are determined. The possibility of SARS-CoV-2 infection in companion animals is considered. Diverse human activities may trigger various interactions between animal species and their viruses, sometimes causing the emergence of new viral pathogens. In addition, the possibility of using probiotics for the control of viral infections in animals is discussed.
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Affiliation(s)
- I. M. Donnik
- Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ig. V. Popov
- Don State Technical University, 344000 Rostov-on-Don, Russia ,Rostov State Medical University, 344022 Rostov-on-Don, Russia
| | - S. V. Sereda
- Don State Technical University, 344000 Rostov-on-Don, Russia
| | - Il. V. Popov
- Rostov State Medical University, 344022 Rostov-on-Don, Russia
| | - M. L. Chikindas
- Don State Technical University, 344000 Rostov-on-Don, Russia ,Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 08901 New Brunswick, NJ USA
| | - A. M. Ermakov
- Don State Technical University, 344000 Rostov-on-Don, Russia
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