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Shi J, Hu S, Wei H, Zhang L, Lan Y, Guan J, Zhao K, Gao F, He W, Li Z. Dipeptidyl peptidase 4 interacts with porcine coronavirus PHEV spikes and mediates host range expansion. J Virol 2024; 98:e0075324. [PMID: 38829136 PMCID: PMC11265280 DOI: 10.1128/jvi.00753-24] [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: 04/29/2024] [Accepted: 05/08/2024] [Indexed: 06/05/2024] Open
Abstract
Porcine hemagglutinating encephalomyelitis virus (PHEV), a neurotropic betacoronavirus, is prevalent in natural reservoir pigs and infects mice. This raises concerns about host jumping or spillover, but little is known about the cause of occurrence. Here, we revealed that dipeptidyl peptidase 4 (DPP4) is a candidate binding target of PHEV spikes and works as a broad barrier to overcome. Investigations of the host breadth of PHEV confirmed that cells derived from pigs and mice are permissive to virus propagation. Both porcine DPP4 and murine DPP4 have high affinity for the viral spike receptor-binding domain (RBD), independent of their catalytic activity. Loss of DPP4 expression results in limited PHEV infection. Structurally, PHEV spike protein binds to the outer surface of blades IV and V of the DPP4 β-propeller domain, and the DPP4 residues N229 and N321 (relative to human DPP4 numbering) participate in RBD binding via its linked carbohydrate entities. Removal of these N-glycosylations profoundly enhanced the RBD-DPP4 interaction and viral invasion, suggesting they act as shielding in PHEV infection. Furthermore, we found that glycosylation, rather than structural differences or surface charges, is more responsible for DPP4 recognition and species barrier formation. Overall, our findings shed light on virus-receptor interactions and highlight that PHEV tolerance to DPP4 orthologs is a putative determinant of its cross-species transmission or host range expansion.IMPORTANCEPHEV is a neurotropic betacoronavirus that is circulating worldwide and has raised veterinary and economic concerns. In addition to being a reservoir species of pigs, PHEV can also infect wild-type mice, suggesting a "host jump" event. Understanding cross-species transmission is crucial for disease prevention and control but remains to be addressed. Herein, we show that the multifunctional receptor DPP4 plays a pivotal role in the host tropism of PHEV and identifies the conserved glycosylation sites in DPP4 responsible for this restriction. These findings highlight that the ability of PHEV to utilize DPP4 orthologs potentially affects its natural host expansion.
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Affiliation(s)
- Junchao Shi
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Jilin University, Changchun, China
| | - Shiyu Hu
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Hanlu Wei
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Le Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yungang Lan
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jiyu Guan
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Kui Zhao
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Feng Gao
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Wenqi He
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zi Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
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Tse LV, Hou YJ, McFadden E, Lee RE, Scobey TD, Leist SR, Martinez DR, Meganck RM, Schäfer A, Yount BL, Mascenik T, Powers JM, Randell SH, Zhang Y, Wang L, Mascola J, McLellan JS, Baric RS. A MERS-CoV antibody neutralizes a pre-emerging group 2c bat coronavirus. Sci Transl Med 2023; 15:eadg5567. [PMID: 37756379 PMCID: PMC11292784 DOI: 10.1126/scitranslmed.adg5567] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
The repeated emergence of zoonotic human betacoronaviruses (β-CoVs) dictates the need for broad therapeutics and conserved epitope targets for countermeasure design. Middle East respiratory syndrome (MERS)-related coronaviruses (CoVs) remain a pressing concern for global health preparedness. Using metagenomic sequence data and CoV reverse genetics, we recovered a full-length wild-type MERS-like BtCoV/li/GD/2014-422 (BtCoV-422) recombinant virus, as well as two reporter viruses, and evaluated their human emergence potential and susceptibility to currently available countermeasures. Similar to MERS-CoV, BtCoV-422 efficiently used human and other mammalian dipeptidyl peptidase protein 4 (DPP4) proteins as entry receptors and an alternative DPP4-independent infection route in the presence of exogenous proteases. BtCoV-422 also replicated efficiently in primary human airway, lung endothelial, and fibroblast cells, although less efficiently than MERS-CoV. However, BtCoV-422 shows minor signs of infection in 288/330 human DPP4 transgenic mice. Several broad CoV antivirals, including nucleoside analogs and 3C-like/Mpro protease inhibitors, demonstrated potent inhibition against BtCoV-422 in vitro. Serum from mice that received a MERS-CoV mRNA vaccine showed reduced neutralizing activity against BtCoV-422. Although most MERS-CoV-neutralizing monoclonal antibodies (mAbs) had limited activity, one anti-MERS receptor binding domain mAb, JC57-11, neutralized BtCoV-422 potently. A cryo-electron microscopy structure of JC57-11 in complex with BtCoV-422 spike protein revealed the mechanism of cross-neutralization involving occlusion of the DPP4 binding site, highlighting its potential as a broadly neutralizing mAb for group 2c CoVs that use DPP4 as a receptor. These studies provide critical insights into MERS-like CoVs and provide candidates for countermeasure development.
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Affiliation(s)
- Longping V. Tse
- Department of Molecular Microbiology and Immunology, Saint Louis University, St. Louis, MO 63014
| | - Yixuan J. Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Elizabeth McFadden
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Rhianna E Lee
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Trevor D. Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Sarah R. Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - David R. Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Rita M. Meganck
- Department of Molecular Microbiology and Immunology, Saint Louis University, St. Louis, MO 63014
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Boyd L. Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Teresa Mascenik
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - John M. Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Yi Zhang
- National Institute of Allergy and Infectious Disease, National Institute of Health, Bethesda, MD 20892
| | - Lingshu Wang
- National Institute of Allergy and Infectious Disease, National Institute of Health, Bethesda, MD 20892
| | - John Mascola
- National Institute of Allergy and Infectious Disease, National Institute of Health, Bethesda, MD 20892
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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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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Role of Dipeptidyl Peptidase-4 (DPP4) on COVID-19 Physiopathology. Biomedicines 2022; 10:biomedicines10082026. [PMID: 36009573 PMCID: PMC9406088 DOI: 10.3390/biomedicines10082026] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022] Open
Abstract
DPP4/CD26 is a single-pass transmembrane protein with multiple functions on glycemic control, cell migration and proliferation, and the immune system, among others. It has recently acquired an especial relevance due to the possibility to act as a receptor or co-receptor for SARS-CoV-2, as it has been already demonstrated for other coronaviruses. In this review, we analyze the evidence for the role of DPP4 on COVID-19 risk and clinical outcome, and its contribution to COVID-19 physiopathology. Due to the pathogenetic links between COVID-19 and diabetes mellitus and the hyperinflammatory response, with the hallmark cytokine storm developed very often during the disease, we dive deep into the functions of DPP4 on carbohydrate metabolism and immune system regulation. We show that the broad spectrum of functions regulated by DPP4 is performed both as a protease enzyme, as well as an interacting partner of other molecules on the cell surface. In addition, we provide an update of the DPP4 inhibitors approved by the EMA and/or the FDA, together with the newfangled approval of generic drugs (in 2021 and 2022). This review will also cover the effects of DPP4 inhibitors (i.e., gliptins) on the progression of SARS-CoV-2 infection, showing the role of DPP4 in this disturbing disease.
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Niu L, Geyer PE, Gupta R, Santos A, Meier F, Doll S, Wewer Albrechtsen NJ, Klein S, Ortiz C, Uschner FE, Schierwagen R, Trebicka J, Mann M. Dynamic human liver proteome atlas reveals functional insights into disease pathways. Mol Syst Biol 2022; 18:e10947. [PMID: 35579278 PMCID: PMC9112488 DOI: 10.15252/msb.202210947] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/12/2022] Open
Abstract
Deeper understanding of liver pathophysiology would benefit from a comprehensive quantitative proteome resource at cell type resolution to predict outcome and design therapy. Here, we quantify more than 150,000 sequence-unique peptides aggregated into 10,000 proteins across total liver, the major liver cell types, time course of primary cell cultures, and liver disease states. Bioinformatic analysis reveals that half of hepatocyte protein mass is comprised of enzymes and 23% of mitochondrial proteins, twice the proportion of other liver cell types. Using primary cell cultures, we capture dynamic proteome remodeling from tissue states to cell line states, providing useful information for biological or pharmaceutical research. Our extensive data serve as spectral library to characterize a human cohort of non-alcoholic steatohepatitis and cirrhosis. Dramatic proteome changes in liver tissue include signatures of hepatic stellate cell activation resembling liver cirrhosis and providing functional insights. We built a web-based dashboard application for the interactive exploration of our resource (www.liverproteome.org).
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Affiliation(s)
- Lili Niu
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Philipp E Geyer
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- Present address:
OmicEra Diagnostics GmbHPlaneggGermany
| | - Rajat Gupta
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Present address:
Pfizer Worldwide Research and DevelopmentSan DiegoCAUSA
| | - Alberto Santos
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Center for Health Data ScienceFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
- Big Data InstituteNuffield Department of MedicineUniversity of OxfordOxfordUK
| | - Florian Meier
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- Present address:
Functional ProteomicsJena University HospitalJenaGermany
| | - Sophia Doll
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- Present address:
OmicEra Diagnostics GmbHPlaneggGermany
| | - Nicolai J Wewer Albrechtsen
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Department of Clinical BiochemistryRigshospitaletUniversity of CopenhagenCopenhagenDenmark
| | - Sabine Klein
- Department of Internal Medicine IGoethe University Clinic FrankfurtFrankfurtGermany
- Department of Internal Medicine BWW University MünsterMünsterGermany
| | - Cristina Ortiz
- Department of Internal Medicine IGoethe University Clinic FrankfurtFrankfurtGermany
| | - Frank E Uschner
- Department of Internal Medicine IGoethe University Clinic FrankfurtFrankfurtGermany
- Department of Internal Medicine BWW University MünsterMünsterGermany
| | - Robert Schierwagen
- Department of Internal Medicine IGoethe University Clinic FrankfurtFrankfurtGermany
- Department of Internal Medicine BWW University MünsterMünsterGermany
| | - Jonel Trebicka
- Department of Internal Medicine IGoethe University Clinic FrankfurtFrankfurtGermany
- Department of Internal Medicine BWW University MünsterMünsterGermany
- European Foundation for the Study of Chronic Failure, EFCLIFBarcelonaSpain
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
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Functional Reconstitution of the MERS CoV Receptor Binding Motif. Mol Immunol 2022; 145:3-16. [PMID: 35272105 PMCID: PMC8894742 DOI: 10.1016/j.molimm.2022.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/14/2022] [Accepted: 03/01/2022] [Indexed: 01/19/2023]
Abstract
In the early 1960’s the first human coronaviruses (designated 229E and OC43) were identified as etiologic agents of the common cold, to be followed by the subsequent isolation of three more human coronaviruses similarly associated with cold-like diseases. In contrast to these “mild” coronaviruses, over the last 20 years there have been three independent events of emergence of pandemic severe and acute life-threatening respiratory diseases caused by three novel beta-coronaviruses, SARS CoV, MERS CoV and most recently SARS CoV2. Whereas the first SARS CoV appeared in November 2002 and spontaneously disappeared by the summer of 2003, MERS CoV has continued persistently to spill over to humans via an intermediary camel vector, causing tens of cases annually. Although human-to-human transmission is rare, the fatality rate of MERS CoV disease is remarkably higher than 30%. COVID-19 however, is fortunately much less fatal, despite that its etiologic agent, SARS CoV2, is tremendously infectious, particularly with the recent evolution of the Omicron variants of concern (BA.1 and BA.2). Of note, MERS CoV prevalence in camel populations in Africa and the Middle East is extremely high. Moreover, MERS CoV and SARS CoV2 co-exist in the Middle East and especially in Saudi Arabia and the UAE, where sporadic incidences of co-infection have already been reported. Co-infection, either due to reverse spill-over of SARS CoV2 to camels or in double infected humans could lead to recombination between the two viruses, rendering either SARS CoV2 more lethal or MERS CoV more transmittable. In an attempt to prepare for what could develop into a catastrophic event, we have focused on developing a novel epitope-based immunogen for MERS CoV. Implementing combinatorial phage-display conformer libraries, the Receptor Binding Motif (RBM) of the MERS CoV Spike protein has been successfully reconstituted and shown to be recognized by a panel of seven neutralizing monoclonal antibodies.
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Boby N, Cao X, Williams K, Gadila SKG, Shroyer MN, Didier PJ, Srivastav SK, Das A, Baker K, Sha Q, Pahar B. Simian Immunodeficiency Virus Infection Mediated Changes in Jejunum and Peripheral SARS-CoV-2 Receptor ACE2 and Associated Proteins or Genes in Rhesus Macaques. Front Immunol 2022; 13:835686. [PMID: 35281029 PMCID: PMC8914048 DOI: 10.3389/fimmu.2022.835686] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
Angiotensin converting enzyme-2 (ACE2) and associated proteins play a pivotal role in various physiological and pathological events, such as immune activation, inflammation, gut barrier maintenance, intestinal stem cell proliferation, and apoptosis. Although many of these clinical events are quite significant in SIV/HIV infection, expression profiling of these proteins has not been well reported. Considering the different pathological consequences in the gut after HIV infection, we hypothesized that the expression of ACE2 and associated proteins of the Renin-angiotensin system (RAS) could be compromised after SIV/HIV infection. We quantified the gene expression of ACE2 as well as AGTR1/2, ADAM17, and TMPRSS2, and compared between SIV infected and uninfected rhesus macaques (Macaca mulatta; hereafter abbreviated RMs). The gene expression analysis revealed significant downregulation of ACE2 and upregulation of AGTR2 and inflammatory cytokine IL-6 in the gut of infected RMs. Protein expression profiling also revealed significant upregulation of AGTR2 after infection. The expression of ACE2 in protein level was also decreased, but not significantly, after infection. To understand the entirety of the process in newly regenerated epithelial cells, a global transcriptomic study of enteroids raised from intestinal stem cells was performed. Interestingly, most of the genes associated with the RAS, such as DPP4, MME, ANPEP, ACE2, ENPEP, were found to be downregulated in SIV infection. HNFA1 was found to be a key regulator of ACE2 and related protein expression. Jejunum CD4+ T cell depletion and increased IL-6 mRNA, MCP-1 and AGTR2 expression may signal inflammation, monocyte/macrophage accumulation and epithelial apoptosis in accelerating SIV pathogenesis. Overall, the findings in the study suggested a possible impact of SIV/HIV infection on expression of ACE2 and RAS-associated proteins resulting in the loss of gut homeostasis. In the context of the current COVID-19 pandemic, the outcome of SARS-CoV-2 and HIV co-infection remains uncertain and needs further investigation as the significance profile of ACE2, a viral entry receptor for SARS-CoV-2, and its expression in mRNA and protein varied in the current study. There is a concern of aggravated SARS-CoV-2 outcomes due to possible serious pathological events in the gut resulting from compromised expression of RAS- associated proteins in SIV/HIV infection.
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Affiliation(s)
- Nongthombam Boby
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, United States
| | - Xuewei Cao
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI, United States
| | - Kelsey Williams
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, United States
| | - Shiva Kumar Goud Gadila
- Division of Immunology, Tulane National Primate Research Center, Covington, LA, United States
| | - Monica N. Shroyer
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, United States
| | - Peter J. Didier
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, United States
| | - Sudesh K. Srivastav
- Department of Biostatistics, Tulane University, New Orleans, LA, United States
| | - Arpita Das
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA, United States
| | - Kate Baker
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, United States
| | - Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI, United States
| | - Bapi Pahar
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, United States
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, United States
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
- *Correspondence: Bapi Pahar,
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Genetic Insights into the Middle East Respiratory Syndrome Coronavirus Infection among Saudi People. Vaccines (Basel) 2021; 9:vaccines9101193. [PMID: 34696302 PMCID: PMC8539242 DOI: 10.3390/vaccines9101193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/09/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The Middle East respiratory syndrome coronavirus (MERS-CoV) was isolated for the first time in Saudi Arabia from a patient suffering from atypical pneumonia. The Saudi Genome database was built by King Abdulaziz Medical City via the next-generation sequencing of 7000 candidates. METHOD A large list of point mutations were reported in the region of the dipeptidyl peptidase 4 (DPP4) gene. The DPP4 amino acid residues correlated to MERS-CoV entry and the site of activity of DPP4 inhibitors was investigated. We retrieved the SNPs (Single-Nucleotide Polymorphism) with a variation frequency of >0.05. RESULTS SNP 2:162,890,175 and SNP 2:162,891,848 in the intronic region were located within 50 bp of amino acid residues responsible for MERS-CoV entry, amino acids 259-296 and 205-258, respectively. The variation frequency of SNP 2:162,890,175 was 2321 out of 2379 screened individuals. Moreover, mutation of SNP 2:162,891,848, which is located near amino acid residues E205 and E206 (crucial for the activity of DPP4 inhibitors), occurred in 76 out of 2379 screened individuals. CONCLUSIONS Our study shows high variation frequency in the DPP4 region reported in the Saudi Genome database. The identified SNPs are of high significance for MERS-CoV infection in better understanding disease pathogenesis.
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Souza PFN, Mesquita FP, Amaral JL, Landim PGC, Lima KRP, Costa MB, Farias IR, Lima LB, Montenegro RC. The human pandemic coronaviruses on the show: The spike glycoprotein as the main actor in the coronaviruses play. Int J Biol Macromol 2021; 179:1-19. [PMID: 33667553 PMCID: PMC7921731 DOI: 10.1016/j.ijbiomac.2021.02.203] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 01/28/2023]
Abstract
Three coronaviruses (CoVs) have threatened the world population by causing outbreaks in the last two decades. In late 2019, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged and caused the coronaviruses to disease 2019 (COVID-19), leading to the ongoing global outbreak. The other pandemic coronaviruses, SARS-CoV and Middle East respiratory syndrome CoV (MERS-CoV), share a considerable level of similarities at genomic and protein levels. However, the differences between them lead to distinct behaviors. These differences result from the accumulation of mutations in the sequence and structure of spike (S) glycoprotein, which plays an essential role in coronavirus infection, pathogenicity, transmission, and evolution. In this review, we brought together many studies narrating a sequence of events and highlighting the differences among S proteins from SARS-CoV, MERS-CoV, and SARS-CoV-2. It was performed here, analysis of S protein sequences and structures from the three pandemic coronaviruses pointing out the mutations among them and what they come through. Additionally, we investigated the receptor-binding domain (RBD) from all S proteins explaining the mutation and biological importance of all of them. Finally, we discuss the mutation in the S protein from several new isolates of SARS-CoV-2, reporting their difference and importance. This review brings into detail how the variations in S protein that make SARS-CoV-2 more aggressive than its relatives coronaviruses and other differences between coronaviruses.
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Affiliation(s)
- Pedro F N Souza
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Brazil.
| | - Felipe P Mesquita
- Drug research and Development Center, Department of Medicine, Federal University of Ceara, Brazil
| | - Jackson L Amaral
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Brazil
| | - Patrícia G C Landim
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Brazil
| | - Karollyny R P Lima
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Brazil
| | - Marília B Costa
- Drug research and Development Center, Department of Medicine, Federal University of Ceara, Brazil
| | - Izabelle R Farias
- Drug research and Development Center, Department of Medicine, Federal University of Ceara, Brazil
| | - Luina B Lima
- Drug research and Development Center, Department of Medicine, Federal University of Ceara, Brazil
| | - Raquel C Montenegro
- Drug research and Development Center, Department of Medicine, Federal University of Ceara, Brazil
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10
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Abstract
Among the animal superfamily Musteloidea, which includes those commonly known as mustelids, naturally occurring and species-specific alphacoronavirus infections have been observed in both mink (Mustela vison/Neovison vison) and domestic ferrets (Mustela putorius furo). Ferret systemic coronavirus (FRSCV), in particular, has been associated with a rare but fatal systemic disease. In recent months, it has become apparent that both minks and ferrets are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a betacoronavirus and the cause of the coronavirus disease 2019 (COVID-19) pandemic. Several mink farms have experienced SARS-CoV-2 outbreaks, and experimental models have demonstrated susceptibility of ferrets to SARS-CoV-2. The potential for pet ferrets to become infected with SARS-CoV-2, however, remains elusive. During the 2002-2003 SARS epidemic, it was also apparent that ferrets were susceptible to SARS-CoV and could be utilized in vaccine development. From a comparative standpoint, understanding the relationships between different infections and disease pathogenesis in the animal superfamily Musteloidea may help elucidate viral infection and transmission mechanisms, as well as treatment and prevention strategies for coronaviruses.
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Affiliation(s)
- Alison E Stout
- Department of Microbiology & Immunology, Cornell University, Ithaca, New York, USA
| | - Qinghua Guo
- Master of Public Health Program, Cornell University, Ithaca, New York, USA
| | - Jean K Millet
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Ricardo de Matos
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Gary R Whittaker
- Department of Microbiology & Immunology, Cornell University, Ithaca, New York, USA
- Master of Public Health Program, Cornell University, Ithaca, New York, USA
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11
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Jones JE, Le Sage V, Lakdawala SS. Viral and host heterogeneity and their effects on the viral life cycle. Nat Rev Microbiol 2020; 19:272-282. [PMID: 33024309 PMCID: PMC7537587 DOI: 10.1038/s41579-020-00449-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2020] [Indexed: 02/08/2023]
Abstract
Traditionally, the viral replication cycle is envisioned as a single, well-defined loop with four major steps: attachment and entry into a target cell, replication of the viral genome, maturation of viral proteins and genome packaging into infectious progeny, and egress and dissemination to the next target cell. However, for many viruses, a growing body of evidence points towards extreme heterogeneity in each of these steps. In this Review, we reassess the major steps of the viral replication cycle by highlighting recent advances that show considerable variability during viral infection. First, we discuss heterogeneity in entry receptors, followed by a discussion on error-prone and low-fidelity polymerases and their impact on viral diversity. Next, we cover the implications of heterogeneity in genome packaging and assembly on virion morphology. Last, we explore alternative egress mechanisms, including tunnelling nanotubes and host microvesicles. In summary, we discuss the implications of viral phenotypic, morphological and genetic heterogeneity on pathogenesis and medicine. This Review highlights common themes and unique features that give nuance to the viral replication cycle.
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Affiliation(s)
- Jennifer E Jones
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Valerie Le Sage
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Seema S Lakdawala
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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12
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Cadegiani FA. Repurposing existing drugs for COVID-19: an endocrinology perspective. BMC Endocr Disord 2020; 20:149. [PMID: 32993622 PMCID: PMC7523486 DOI: 10.1186/s12902-020-00626-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Coronavirus Disease 2019 (COVID-19) is a multi-systemic infection caused by the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), that has become a pandemic. Although its prevailing symptoms include anosmia, ageusia, dry couch, fever, shortness of brief, arthralgia, myalgia, and fatigue, regional and methodological assessments vary, leading to heterogeneous clinical descriptions of COVID-19. Aging, uncontrolled diabetes, hypertension, obesity, and exposure to androgens have been correlated with worse prognosis in COVID-19. Abnormalities in the renin-angiotensin-aldosterone system (RAAS), angiotensin-converting enzyme-2 (ACE2) and the androgen-driven transmembrane serine protease 2 (TMPRSS2) have been elicited as key modulators of SARS-CoV-2. MAIN TEXT While safe and effective therapies for COVID-19 lack, the current moment of pandemic urges for therapeutic options. Existing drugs should be preferred over novel ones for clinical testing due to four inherent characteristics: 1. Well-established long-term safety profile, known risks and contraindications; 2. More accurate predictions of clinical effects; 3. Familiarity of clinical management; and 4. Affordable costs for public health systems. In the context of the key modulators of SARS-CoV-2 infectivity, endocrine targets have become central as candidates for COVID-19. The only endocrine or endocrine-related drug class with already existing emerging evidence for COVID-19 is the glucocorticoids, particularly for the use of dexamethasone for severely affected patients. Other drugs that are more likely to present clinical effects despite the lack of specific evidence for COVID-19 include anti-androgens (spironolactone, eplerenone, finasteride and dutasteride), statins, N-acetyl cysteine (NAC), ACE inhibitors (ACEi), angiotensin receptor blockers (ARB), and direct TMPRSS-2 inhibitors (nafamostat and camostat). Several other candidates show less consistent plausibility. In common, except for dexamethasone, all candidates have no evidence for COVID-19, and clinical trials are needed. CONCLUSION While dexamethasone may reduce mortality in severely ill patients with COVID-19, in the absence of evidence of any specific drug for mild-to-moderate COVID-19, researchers should consider testing existing drugs due to their favorable safety, familiarity, and cost profile. However, except for dexamethasone in severe COVID-19, drug treatments for COVID-19 patients must be restricted to clinical research studies until efficacy has been extensively proven, with favorable outcomes in terms of reduction in hospitalization, mechanical ventilation, and death.
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Affiliation(s)
- Flavio A Cadegiani
- Adrenal and Hypertension Unit, Division of Endocrinology and Metabolism, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo (EPM/UNIFESP), Rua Pedro de Toledo 781 - 13th floor, São Paulo, SP, 04039-032, Brazil.
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13
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Elrashdy F, Redwan EM, Uversky VN. Why COVID-19 Transmission Is More Efficient and Aggressive Than Viral Transmission in Previous Coronavirus Epidemics? Biomolecules 2020; 10:E1312. [PMID: 32933047 PMCID: PMC7565143 DOI: 10.3390/biom10091312] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing a pandemic of coronavirus disease 2019 (COVID-19). The worldwide transmission of COVID-19 from human to human is spreading like wildfire, affecting almost every country in the world. In the past 100 years, the globe did not face a microbial pandemic similar in scale to COVID-19. Taken together, both previous outbreaks of other members of the coronavirus family (severe acute respiratory syndrome (SARS-CoV) and middle east respiratory syndrome (MERS-CoV)) did not produce even 1% of the global harm already inflicted by COVID-19. There are also four other CoVs capable of infecting humans (HCoVs), which circulate continuously in the human population, but their phenotypes are generally mild, and these HCoVs received relatively little attention. These dramatic differences between infection with HCoVs, SARS-CoV, MERS-CoV, and SARS-CoV-2 raise many questions, such as: Why is COVID-19 transmitted so quickly? Is it due to some specific features of the viral structure? Are there some specific human (host) factors? Are there some environmental factors? The aim of this review is to collect and concisely summarize the possible and logical answers to these questions.
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Affiliation(s)
- Fatma Elrashdy
- Department of Endemic Medicine and Hepatogastroenterology, Kasr Alainy School of Medicine, Cairo University, Cairo 11562, Egypt;
| | - Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Vladimir N. Uversky
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, 142290 Moscow, Russia
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14
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Bassendine MF, Bridge SH, McCaughan GW, Gorrell MD. COVID-19 and comorbidities: A role for dipeptidyl peptidase 4 (DPP4) in disease severity? J Diabetes 2020; 12:649-658. [PMID: 32394639 DOI: 10.1111/1753-0407.13052] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/08/2020] [Indexed: 12/17/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is caused by a novel betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), similar to SARS-CoV and Middle East respiratory syndrome (MERS-CoV), which cause acute respiratory distress syndrome and case fatalities. COVID-19 disease severity is worse in older obese patients with comorbidities such as diabetes, hypertension, cardiovascular disease, and chronic lung disease. Cell binding and entry of betacoronaviruses is via their surface spike glycoprotein; SARS-CoV binds to the metalloprotease angiotensin-converting enzyme 2 (ACE2), MERS-CoV utilizes dipeptidyl peptidase 4 (DPP4), and recent modeling of the structure of SARS-CoV-2 spike glycoprotein predicts that it can interact with human DPP4 in addition to ACE2. DPP4 is a ubiquitous membrane-bound aminopeptidase that circulates in plasma; it is multifunctional with roles in nutrition, metabolism, and immune and endocrine systems. DPP4 activity differentially regulates glucose homeostasis and inflammation via its enzymatic activity and nonenzymatic immunomodulatory effects. The importance of DPP4 for the medical community has been highlighted by the approval of DPP4 inhibitors, or gliptins, for the treatment of type 2 diabetes mellitus. This review discusses the dysregulation of DPP4 in COVID-19 comorbid conditions; DPP4 activity is higher in older individuals and increased plasma DPP4 is a predictor of the onset of metabolic syndrome. DPP4 upregulation may be a determinant of COVID-19 disease severity, which creates interest regarding the use of gliptins in management of COVID-19. Also, knowledge of the chemistry and biology of DPP4 could be utilized to develop novel therapies to block viral entry of some betacoronaviruses, potentially including SARS-CoV-2.
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Affiliation(s)
- Margaret F Bassendine
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Simon H Bridge
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Geoffrey W McCaughan
- Centenary Institute and The University of Sydney Faculty of Medicine and Health, Sydney, Australia
| | - Mark D Gorrell
- Centenary Institute and The University of Sydney Faculty of Medicine and Health, Sydney, Australia
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15
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Khodadadi E, Maroufi P, Khodadadi E, Esposito I, Ganbarov K, Espsoito S, Yousefi M, Zeinalzadeh E, Kafil HS. Study of combining virtual screening and antiviral treatments of the Sars-CoV-2 (Covid-19). Microb Pathog 2020; 146:104241. [PMID: 32387389 PMCID: PMC7199731 DOI: 10.1016/j.micpath.2020.104241] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 02/07/2023]
Abstract
The recent epidemic outbreak of a novel human coronavirus called SARS-CoV-2 and causing the respiratory tract disease COVID-19 has reached worldwide resonance and a global effort is being undertaken to characterize the molecular features and evolutionary origins of this virus. Therefore, rapid and accurate identification of pathogenic viruses plays a vital role in selecting appropriate treatments, saving people's lives and preventing epidemics. Additionally, general treatments, coronavirus-specific treatments, and antiviral treatments useful in fighting COVID-19 are addressed. This review sets out to shed light on the SARS-CoV-2 and host receptor recognition, a crucial factor for successful virus infection and taking immune-informatics approaches to identify B- and T-cell epitopes for surface glycoprotein of SARS-CoV-2. A variety of improved or new approaches also have been developed. It is anticipated that this will assist researchers and clinicians in developing better techniques for timely and effective detection of coronavirus infection. Moreover, the genomic sequence of the virus responsible for COVID-19, as well as the experimentally determined three-dimensional structure of the Main protease (Mpro) is available. The reported structure of the target Mpro was described in this review to identify potential drugs for COVID-19 using virtual high throughput screening.
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Affiliation(s)
- Ehsaneh Khodadadi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Parham Maroufi
- Department of Orthopedy, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Ehsan Khodadadi
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran.
| | | | | | | | - Mehdi Yousefi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Elham Zeinalzadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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16
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Battagello D, Dragunas G, Klein M, Ayub AL, Velloso F, Correa R. Unpuzzling COVID-19: tissue-related signaling pathways associated with SARS-CoV-2 infection and transmission. Clin Sci (Lond) 2020; 134:2137-2160. [PMID: 32820801 PMCID: PMC7443512 DOI: 10.1042/cs20200904] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023]
Abstract
The highly infective coronavirus disease 19 (COVID-19) is caused by a novel strain of coronaviruses - the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) - discovered in December 2019 in the city of Wuhan (Hubei Province, China). Remarkably, COVID-19 has rapidly spread across all continents and turned into a public health emergency, which was ultimately declared as a pandemic by the World Health Organization (WHO) in early 2020. SARS-CoV-2 presents similar aspects to other members of the coronavirus family, mainly regarding its genome, protein structure and intracellular mechanisms, that may translate into mild (or even asymptomatic) to severe infectious conditions. Although the mechanistic features underlying the COVID-19 progression have not been fully clarified, current evidence have suggested that SARS-CoV-2 may primarily behave as other β-coronavirus members. To better understand the development and transmission of COVID-19, unveiling the signaling pathways that may be impacted by SARS-CoV-2 infection, at the molecular and cellular levels, is of crucial importance. In this review, we present the main aspects related to the origin, classification, etiology and clinical impact of SARS-CoV-2. Specifically, here we describe the potential mechanisms of cellular interaction and signaling pathways, elicited by functional receptors, in major targeted tissues/organs from the respiratory, gastrointestinal (GI), cardiovascular, renal, and nervous systems. Furthermore, the potential involvement of these signaling pathways in evoking the onset and progression of COVID-19 symptoms in these organ systems are presently discussed. A brief description of future perspectives related to potential COVID-19 treatments is also highlighted.
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Affiliation(s)
- Daniella S. Battagello
- Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Guilherme Dragunas
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Marianne O. Klein
- Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Ana L.P. Ayub
- Department of Pharmacology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Fernando J. Velloso
- Department of Pharmacology, Physiology and Neurosciences, Rutgers-NJMS, Newark, NJ, U.S.A
| | - Ricardo G. Correa
- NCI-Designated Cancer Center, Sanford Burnham Prebys (SBP) Medical Discovery Institute, La Jolla, CA, U.S.A
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17
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Stout AE, André NM, Jaimes JA, Millet JK, Whittaker GR. Coronaviruses in cats and other companion animals: Where does SARS-CoV-2/COVID-19 fit? Vet Microbiol 2020; 247:108777. [PMID: 32768223 PMCID: PMC7309752 DOI: 10.1016/j.vetmic.2020.108777] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/17/2020] [Accepted: 06/20/2020] [Indexed: 12/26/2022]
Abstract
Coronaviruses (CoVs) cause disease in a range of agricultural and companion animal species, and can be important causes of zoonotic infections. In humans, several coronaviruses circulate seasonally. Recently, a novel zoonotic CoV named SARS-CoV-2 emerged from a bat reservoir, resulting in the COVID-19 pandemic. With a focus on felines, we review here the evidence for SARS-CoV-2 infection in cats, ferrets and dogs, describe the relationship between SARS-CoV-2 and the natural coronaviruses known to infect these species, and provide a rationale for the relative susceptibility of these species to SARS-CoV-2 through comparative analysis of the ACE-2 receptor.
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Affiliation(s)
- Alison E Stout
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, United States
| | - Nicole M André
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, United States
| | - Javier A Jaimes
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, United States
| | - Jean K Millet
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, 78352, Jouy-en-Josas, France
| | - Gary R Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, United States; Master of Public Health Program, Cornell University, Ithaca, NY, 14853, United States; Cornell Feline Health Center, Ithaca, NY, 14853, United States.
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18
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Fam BS, Vargas-Pinilla P, Amorim CEG, Sortica VA, Bortolini MC. ACE2 diversity in placental mammals reveals the evolutionary strategy of SARS-CoV-2. Genet Mol Biol 2020; 43:e20200104. [PMID: 32520981 PMCID: PMC7278419 DOI: 10.1590/1678-4685-gmb-2020-0104] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
The recent emergence of SARS-CoV-2 is responsible for the current pandemic of COVID-19, which uses the human membrane protein ACE2 as a gateway to host-cell infection. We performed a comparative genomic analysis of 70 ACE2 placental mammal orthologues to identify variations and contribute to the understanding of evolutionary dynamics behind this successful adaptation to infect humans. Our results reveal that 4% of the ACE2 sites are under positive selection, all located in the catalytic domain, suggesting possibly taxon-specific adaptations related to the ACE2 function, such as cardiovascular physiology. Considering all variable sites, we selected 30 of them located at the critical ACE2 binding sites to the SARS-CoV-like viruses for analysis in more detail. Our results reveal a relatively high diversity of ACE2 between placental mammal species, while showing no polymorphism within human populations, at least considering the 30 inter-species variable sites. A perfect scenario for natural selection favored this opportunistic new coronavirus in its trajectory of infecting humans. We suggest that SARS-CoV-2 became a specialist coronavirus for human hosts. Differences in the rate of infection and mortality could be related to the innate immune responses, other unknown genetic factors, as well as non-biological factors.
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Affiliation(s)
- Bibiana S.O. Fam
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Porto Alegre, RS, Brazil
| | - Pedro Vargas-Pinilla
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Bioquímica e Imunologia, Ribeirão Preto, SP, Brazil
| | | | - Vinicius A. Sortica
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Porto Alegre, RS, Brazil
| | - Maria Cátira Bortolini
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Porto Alegre, RS, Brazil
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19
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LoPresti M, Beck DB, Duggal P, Cummings DAT, Solomon BD. The Role of Host Genetic Factors in Coronavirus Susceptibility: Review of Animal and Systematic Review of Human Literature. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.05.30.20117788. [PMID: 32511629 PMCID: PMC7276057 DOI: 10.1101/2020.05.30.20117788] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
BACKGROUND The recent SARS-CoV-2 pandemic raises many scientific and clinical questions. One set of questions involves host genetic factors that may affect disease susceptibility and pathogenesis. New work is emerging related to SARS-CoV-2; previous work has been conducted on other coronaviruses that affect different species. OBJECTIVES We aimed to review the literature on host genetic factors related to coronaviruses, with a systematic focus on human studies. METHODS We conducted a PubMed-based search and analysis for articles relevant to host genetic factors in coronavirus. We categorized articles, summarized themes related to animal studies, and extracted data from human studies for analyses. RESULTS We identified 1,187 articles of potential relevance. Forty-five studies were related to human host genetic factors related to coronavirus, of which 35 involved analysis of specific genes or loci; aside from one meta-analysis on respiratory infections, all were candidate-driven studies, typically investigating small number of research subjects and loci. Multiple significant loci were identified, including 16 related to susceptibility to coronavirus (of which 7 identified protective alleles), and 16 related to outcomes or clinical variables (of which 3 identified protective alleles). The types of cases and controls used varied considerably; four studies used traditional replication/validation cohorts. Of the other studies, 28 involved both human and non-human host genetic factors related to coronavirus, 174 involved study of non-human (animal) host genetic factors related to coronavirus, 584 involved study of non-genetic host factors related to coronavirus, including involving immunopathogenesis, 16 involved study of other pathogens (not coronavirus), 321 involved other studies of coronavirus, and 18 studies were assigned to the other categories and removed. KEY FINDINGS We have outlined key genes and loci from animal and human host genetic studies that may bear investigation in the nascent host genetic factor studies of COVID-19. Previous human studies to date have been limited by issues that may be less impactful on current endeavors, including relatively low numbers of eligible participants and limited availability of advanced genomic methods.
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20
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Qi F, Qian S, Zhang S, Zhang Z. Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses. Biochem Biophys Res Commun 2020. [PMID: 32199615 DOI: 10.1016/j.bbrc.2020.03.044pmid:32199615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The new coronavirus (SARS-CoV-2) outbreak from December 2019 in Wuhan, Hubei, China, has been declared a global public health emergency. Angiotensin I converting enzyme 2 (ACE2), is the host receptor by SARS-CoV-2 to infect human cells. Although ACE2 is reported to be expressed in lung, liver, stomach, ileum, kidney and colon, its expressing levels are rather low, especially in the lung. SARS-CoV-2 may use co-receptors/auxiliary proteins as ACE2 partner to facilitate the virus entry. To identify the potential candidates, we explored the single cell gene expression atlas including 119 cell types of 13 human tissues and analyzed the single cell co-expression spectrum of 51 reported RNA virus receptors and 400 other membrane proteins. Consistent with other recent reports, we confirmed that ACE2 was mainly expressed in lung AT2, liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs, rectum ECs, stomach epithelial cells, and kidney proximal tubules. Intriguingly, we found that the candidate co-receptors, manifesting the most similar expression patterns with ACE2 across 13 human tissues, are all peptidases, including ANPEP, DPP4 and ENPEP. Among them, ANPEP and DPP4 are the known receptors for human CoVs, suggesting ENPEP as another potential receptor for human CoVs. We also conducted "CellPhoneDB" analysis to understand the cell crosstalk between CoV-targets and their surrounding cells across different tissues. We found that macrophages frequently communicate with the CoVs targets through chemokine and phagocytosis signaling, highlighting the importance of tissue macrophages in immune defense and immune pathogenesis.
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Affiliation(s)
- Furong Qi
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China
| | - Shen Qian
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center and Institute of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Zheng Zhang
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China; The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, China.
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21
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Qi F, Qian S, Zhang S, Zhang Z. Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses. Biochem Biophys Res Commun 2020. [PMID: 32199615 DOI: 10.1016/j.bbrc.2020.03.044medicine] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
The new coronavirus (SARS-CoV-2) outbreak from December 2019 in Wuhan, Hubei, China, has been declared a global public health emergency. Angiotensin I converting enzyme 2 (ACE2), is the host receptor by SARS-CoV-2 to infect human cells. Although ACE2 is reported to be expressed in lung, liver, stomach, ileum, kidney and colon, its expressing levels are rather low, especially in the lung. SARS-CoV-2 may use co-receptors/auxiliary proteins as ACE2 partner to facilitate the virus entry. To identify the potential candidates, we explored the single cell gene expression atlas including 119 cell types of 13 human tissues and analyzed the single cell co-expression spectrum of 51 reported RNA virus receptors and 400 other membrane proteins. Consistent with other recent reports, we confirmed that ACE2 was mainly expressed in lung AT2, liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs, rectum ECs, stomach epithelial cells, and kidney proximal tubules. Intriguingly, we found that the candidate co-receptors, manifesting the most similar expression patterns with ACE2 across 13 human tissues, are all peptidases, including ANPEP, DPP4 and ENPEP. Among them, ANPEP and DPP4 are the known receptors for human CoVs, suggesting ENPEP as another potential receptor for human CoVs. We also conducted "CellPhoneDB" analysis to understand the cell crosstalk between CoV-targets and their surrounding cells across different tissues. We found that macrophages frequently communicate with the CoVs targets through chemokine and phagocytosis signaling, highlighting the importance of tissue macrophages in immune defense and immune pathogenesis.
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Affiliation(s)
- Furong Qi
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China
| | - Shen Qian
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center and Institute of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Zheng Zhang
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China; The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, China.
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Park MS, Kim JI, Bae JY, Park MS. Animal models for the risk assessment of viral pandemic potential. Lab Anim Res 2020; 36:11. [PMID: 32337177 PMCID: PMC7175453 DOI: 10.1186/s42826-020-00040-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/10/2020] [Indexed: 02/07/2023] Open
Abstract
Pandemics affect human lives severely and globally. Experience predicts that there will be a pandemic for sure although the time is unknown. When a viral epidemic breaks out, assessing its pandemic risk is an important part of the process that characterizes genomic property, viral pathogenicity, transmission in animal model, and so forth. In this review, we intend to figure out how a pandemic may occur by looking into the past influenza pandemic events. We discuss interpretations of the experimental evidences resulted from animal model studies and extend implications of viral pandemic potentials and ingredients to emerging viral epidemics. Focusing on the pandemic potential of viral infectious diseases, we suggest what should be assessed to prevent global catastrophes from influenza virus, Middle East respiratory syndrome coronavirus, dengue and Zika viruses.
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Affiliation(s)
- Mee Sook Park
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea 02841
| | - Jin Il Kim
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea 02841
| | - Joon-Yong Bae
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea 02841
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea 02841
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Qi F, Qian S, Zhang S, Zhang Z. Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses. Biochem Biophys Res Commun 2020; 526:135-140. [PMID: 32199615 PMCID: PMC7156119 DOI: 10.1016/j.bbrc.2020.03.044] [Citation(s) in RCA: 710] [Impact Index Per Article: 177.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 03/08/2020] [Indexed: 11/26/2022]
Abstract
The new coronavirus (SARS-CoV-2) outbreak from December 2019 in Wuhan, Hubei, China, has been declared a global public health emergency. Angiotensin I converting enzyme 2 (ACE2), is the host receptor by SARS-CoV-2 to infect human cells. Although ACE2 is reported to be expressed in lung, liver, stomach, ileum, kidney and colon, its expressing levels are rather low, especially in the lung. SARS-CoV-2 may use co-receptors/auxiliary proteins as ACE2 partner to facilitate the virus entry. To identify the potential candidates, we explored the single cell gene expression atlas including 119 cell types of 13 human tissues and analyzed the single cell co-expression spectrum of 51 reported RNA virus receptors and 400 other membrane proteins. Consistent with other recent reports, we confirmed that ACE2 was mainly expressed in lung AT2, liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs, rectum ECs, stomach epithelial cells, and kidney proximal tubules. Intriguingly, we found that the candidate co-receptors, manifesting the most similar expression patterns with ACE2 across 13 human tissues, are all peptidases, including ANPEP, DPP4 and ENPEP. Among them, ANPEP and DPP4 are the known receptors for human CoVs, suggesting ENPEP as another potential receptor for human CoVs. We also conducted "CellPhoneDB" analysis to understand the cell crosstalk between CoV-targets and their surrounding cells across different tissues. We found that macrophages frequently communicate with the CoVs targets through chemokine and phagocytosis signaling, highlighting the importance of tissue macrophages in immune defense and immune pathogenesis.
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Affiliation(s)
- Furong Qi
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China
| | - Shen Qian
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center and Institute of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Zheng Zhang
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China; The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, China.
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Molecular Basis of Binding between Middle East Respiratory Syndrome Coronavirus and CD26 from Seven Bat Species. J Virol 2020; 94:JVI.01387-19. [PMID: 31776269 PMCID: PMC7022362 DOI: 10.1128/jvi.01387-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/13/2019] [Indexed: 02/05/2023] Open
Abstract
In this study, we found that bat CD26s (bCD26s) from different species exhibit large diversities, especially in the region responsible for binding to the receptor binding domain (RBD) of Middle East respiratory syndrome coronavirus (MERS-CoV). However, they maintain the interaction with MERS-RBD at varied affinities and support the entry of pseudotyped MERS-CoV. These bat receptors polymorphisms seem to confer evolutionary pressure for the adaptation of CD26-binding virus, such as the ancestor of MERS-CoV, and led to the generation of diversified CD26-engaging CoV strains. Thus, our data add more evidence to support that bats are the reservoir of MERS-CoV and similar viruses, as well as further emphasize the necessity to survey MERS-CoV and other CoVs among bats. Continued reports of Middle East respiratory syndrome coronavirus (MERS-CoV) infecting humans have occurred since the identification of this virus in 2012. MERS-CoV is prone to cause endemic disease in the Middle East, with several dozen spillover infections to other continents. It is hypothesized that MERS-CoV originated from bat coronaviruses and that dromedary camels are its natural reservoir. Although gene segments identical to MERS-CoV were sequenced from certain species of bats and one species experimentally shed the virus, it is still unknown whether other bats can transmit the virus. Here, at the molecular level, we found that all purified bat CD26s (bCD26s) from a diverse range of species interact with the receptor binding domain (RBD) of MERS-CoV, with equilibrium dissociation constant values ranging from several to hundreds at the micromolar level. Moreover, all bCD26s expressed in this study mediated the entry of pseudotyped MERS-CoV to receptor-expressing cells, indicating the broad potential engagement of bCD26s as MERS-CoV receptors. Further structural analysis indicated that in the bat receptor, compared to the human receptor, substitutions of key residues and their adjacent amino acids leads to decreased binding affinity to the MERS-RBD. These results add more evidence to the existing belief that bats are the original source of MERS-CoV and suggest that bCD26s in many species can mediate the entry of the virus, which has significant implications for the surveillance and control of MERS-CoV infection. IMPORTANCE In this study, we found that bat CD26s (bCD26s) from different species exhibit large diversities, especially in the region responsible for binding to the receptor binding domain (RBD) of Middle East respiratory syndrome coronavirus (MERS-CoV). However, they maintain the interaction with MERS-RBD at varied affinities and support the entry of pseudotyped MERS-CoV. These bat receptors polymorphisms seem to confer evolutionary pressure for the adaptation of CD26-binding virus, such as the ancestor of MERS-CoV, and led to the generation of diversified CD26-engaging CoV strains. Thus, our data add more evidence to support that bats are the reservoir of MERS-CoV and similar viruses, as well as further emphasize the necessity to survey MERS-CoV and other CoVs among bats.
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25
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Criscitiello MF, Kraev I, Lange S. Deiminated proteins in extracellular vesicles and serum of llama (Lama glama)-Novel insights into camelid immunity. Mol Immunol 2020; 117:37-53. [PMID: 31733447 PMCID: PMC7112542 DOI: 10.1016/j.molimm.2019.10.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/05/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023]
Abstract
Peptidylarginine deiminases (PADs) are phylogenetically conserved calcium-dependent enzymes which post-translationally convert arginine into citrulline in target proteins in an irreversible manner, causing functional and structural changes in target proteins. Protein deimination causes generation of neo-epitopes, affects gene regulation and also allows for protein moonlighting. Furthermore, PADs have been found to be a phylogenetically conserved regulator for extracellular vesicle (EVs) release. EVs are found in most body fluids and participate in cellular communication via transfer of cargo proteins and genetic material. In this study, post-translationally deiminated proteins in serum and serum-EVs are described for the first time in camelids, using the llama (Lama glama L. 1758) as a model animal. We report a poly-dispersed population of llama serum EVs, positive for phylogenetically conserved EV-specific markers and characterised by TEM. In serum, 103 deiminated proteins were overall identified, including key immune and metabolic mediators including complement components, immunoglobulin-based nanobodies, adiponectin and heat shock proteins. In serum, 60 deiminated proteins were identified that were not in EVs, and 25 deiminated proteins were found to be unique to EVs, with 43 shared deiminated protein hits between both serum and EVs. Deiminated histone H3, a marker of neutrophil extracellular trap formation, was also detected in llama serum. PAD homologues were identified in llama serum by Western blotting, via cross reaction with human PAD antibodies, and detected at an expected 70 kDa size. This is the first report of deiminated proteins in serum and EVs of a camelid species, highlighting a hitherto unrecognized post-translational modification in key immune and metabolic proteins in camelids, which may be translatable to and inform a range of human metabolic and inflammatory pathologies.
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Affiliation(s)
- Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA; Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX, 77843, USA.
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes, MK7 6AA, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK.
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26
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Letko M, Miazgowicz K, McMinn R, Seifert SN, Sola I, Enjuanes L, Carmody A, van Doremalen N, Munster V. Adaptive Evolution of MERS-CoV to Species Variation in DPP4. Cell Rep 2019; 24:1730-1737. [PMID: 30110630 PMCID: PMC7104223 DOI: 10.1016/j.celrep.2018.07.045] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/13/2018] [Accepted: 07/12/2018] [Indexed: 01/04/2023] Open
Abstract
Middle East Respiratory Syndrome Coronavirus (MERS-CoV) likely originated in bats and passed to humans through dromedary camels; however, the genetic mechanisms underlying cross-species adaptation remain poorly understood. Variation in the host receptor, dipeptidyl peptidase 4 (DPP4), can block the interaction with the MERS-CoV spike protein and form a species barrier to infection. To better understand the species adaptability of MERS-CoV, we identified a suboptimal species-derived variant of DPP4 to study viral adaption. Passaging virus on cells expressing this DPP4 variant led to accumulation of mutations in the viral spike which increased replication. Parallel passages revealed distinct paths of viral adaptation to the same DPP4 variant. Structural analysis and functional assays showed that these mutations enhanced viral entry with suboptimal DPP4 by altering the surface charge of spike. These findings demonstrate that MERS-CoV spike can utilize multiple paths to rapidly adapt to novel species variation in DPP4.
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MESH Headings
- Adaptation, Physiological
- Amino Acid Sequence
- Animals
- Binding Sites
- Biological Coevolution
- Chiroptera
- Chlorocebus aethiops
- Cricetulus
- Dipeptidyl Peptidase 4/chemistry
- Dipeptidyl Peptidase 4/genetics
- Dipeptidyl Peptidase 4/metabolism
- Gene Expression
- Host Specificity
- Host-Pathogen Interactions/genetics
- Humans
- Middle East Respiratory Syndrome Coronavirus/genetics
- Middle East Respiratory Syndrome Coronavirus/metabolism
- Models, Molecular
- Mutation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Vero Cells
- Virus Internalization
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Affiliation(s)
- Michael Letko
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA.
| | - Kerri Miazgowicz
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA; Department of Infectious Diseases, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA
| | - Rebekah McMinn
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA; Department of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Stephanie N Seifert
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Isabel Sola
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Aaron Carmody
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Neeltje van Doremalen
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Vincent Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA.
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27
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Chen YN, Hsu HC, Wang SW, Lien HC, Lu HT, Peng SK. Entry of Scotophilus Bat Coronavirus-512 and Severe Acute Respiratory Syndrome Coronavirus in Human and Multiple Animal Cells. Pathogens 2019; 8:pathogens8040259. [PMID: 31766704 PMCID: PMC6963420 DOI: 10.3390/pathogens8040259] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/20/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023] Open
Abstract
Bats are natural reservoirs of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV). Scotophilus bat CoV-512 demonstrates potential for cross-species transmission because its viral RNA and specific antibodies have been detected in three bat species of Taiwan. Understanding the cell tropism of Scotophilus bat CoV-512 is the first step for studying the mechanism of cross-species transmission. In this study, a lentivirus-based pseudovirus was produced using the spike (S) protein of Scotophilus bat CoV-512 or SARS-CoV as a surface protein to test the interaction between coronaviral S protein and its cell receptor on 11 different cells. Susceptible cells expressed red fluorescence protein (RFP) after the entry of RFP-bound green fluorescence protein (GFP)-fused S protein of Scotophilus bat CoV-512 (RFP-Sco-S-eGFP) or RFP-SARS-S pseudovirus, and firefly luciferase (FLuc) activity expressed by cells infected with FLuc-Sco-S-eGFP or FLuc-SARS-S pseudovirus was quantified. Scotophilus bat CoV-512 pseudovirus had significantly higher entry efficiencies in Madin Darby dog kidney epithelial cells (MDCK), black flying fox brain cells (Pabr), and rat small intestine epithelial cells (IEC-6). SARS-CoV pseudovirus had significantly higher entry efficiencies in human embryonic kidney epithelial cells (HEK-293T), pig kidney epithelial cells (PK15), and MDCK cells. These findings demonstrated that Scotophilus bat CoV-512 had a broad host range for cross-species transmission like SARS-CoV.
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28
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Leist SR, Cockrell AS. Genetically Engineering a Susceptible Mouse Model for MERS-CoV-Induced Acute Respiratory Distress Syndrome. Methods Mol Biol 2019; 2099:137-159. [PMID: 31883094 PMCID: PMC7123801 DOI: 10.1007/978-1-0716-0211-9_12] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Since 2012, monthly cases of Middle East respiratory syndrome coronavirus (MERS-CoV) continue to cause severe respiratory disease that is fatal in ~35% of diagnosed individuals. The ongoing threat to global public health and the need for novel therapeutic countermeasures have driven the development of animal models that can reproducibly replicate the pathology associated with MERS-CoV in human infections. The inability of MERS-CoV to replicate in the respiratory tracts of mice, hamsters, and ferrets stymied initial attempts to generate small animal models. Identification of human dipeptidyl peptidase IV (hDPP4) as the receptor for MERS-CoV infection opened the door for genetic engineering of mice. Precise molecular engineering of mouse DPP4 (mDPP4) with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology maintained inherent expression profiles, and limited MERS-CoV susceptibility to tissues that naturally express mDPP4, notably the lower respiratory tract wherein MERS-CoV elicits severe pulmonary pathology. Here, we describe the generation of the 288-330+/+ MERS-CoV mouse model in which mice were made susceptible to MERS-CoV by modifying two amino acids on mDPP4 (A288 and T330), and the use of adaptive evolution to generate novel MERS-CoV isolates that cause fatal respiratory disease. The 288-330+/+ mice are currently being used to evaluate novel drug, antibody, and vaccine therapeutic countermeasures for MERS-CoV. The chapter starts with a historical perspective on the emergence of MERS-CoV and animal models evaluated for MERS-CoV pathogenesis, and then outlines the development of the 288-330+/+ mouse model, assays for assessing a MERS-CoV pulmonary infection in a mouse model, and describes some of the challenges associated with using genetically engineered mice.
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Affiliation(s)
- Sarah R Leist
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
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29
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Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are two highly transmissible and pathogenic viruses that emerged in humans at the beginning of the 21st century. Both viruses likely originated in bats, and genetically diverse coronaviruses that are related to SARS-CoV and MERS-CoV were discovered in bats worldwide. In this Review, we summarize the current knowledge on the origin and evolution of these two pathogenic coronaviruses and discuss their receptor usage; we also highlight the diversity and potential of spillover of bat-borne coronaviruses, as evidenced by the recent spillover of swine acute diarrhoea syndrome coronavirus (SADS-CoV) to pigs.
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Affiliation(s)
- Jie Cui
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Fang Li
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.
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30
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Dampened NLRP3-mediated inflammation in bats and implications for a special viral reservoir host. Nat Microbiol 2019; 4:789-799. [PMID: 30804542 PMCID: PMC7096966 DOI: 10.1038/s41564-019-0371-3] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/16/2019] [Indexed: 01/22/2023]
Abstract
Bats are special in their ability to host emerging viruses. As the only flying mammal, bats endure high metabolic rates yet exhibit elongated lifespans. It is currently unclear whether these unique features are interlinked. The important inflammasome sensor, NLR family pyrin domain containing 3 (NLRP3), has been linked to both viral-induced and age-related inflammation. Here, we report significantly dampened activation of the NLRP3 inflammasome in bat primary immune cells compared to human or mouse counterparts. Lower induction of apoptosis-associated speck-like protein containing a CARD (ASC) speck formation and secretion of interleukin-1β in response to both 'sterile' stimuli and infection with multiple zoonotic viruses including influenza A virus (-single-stranded (ss) RNA), Melaka virus (PRV3M, double-stranded RNA) and Middle East respiratory syndrome coronavirus (+ssRNA) was observed. Importantly, this reduction of inflammation had no impact on the overall viral loads. We identified dampened transcriptional priming, a novel splice variant and an altered leucine-rich repeat domain of bat NLRP3 as the cause. Our results elucidate an important mechanism through which bats dampen inflammation with implications for longevity and unique viral reservoir status.
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31
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From SARS to MERS, Thrusting Coronaviruses into the Spotlight. Viruses 2019; 11:v11010059. [PMID: 30646565 PMCID: PMC6357155 DOI: 10.3390/v11010059] [Citation(s) in RCA: 686] [Impact Index Per Article: 137.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/03/2019] [Accepted: 01/09/2019] [Indexed: 11/30/2022] Open
Abstract
Coronaviruses (CoVs) have formerly been regarded as relatively harmless respiratory pathogens to humans. However, two outbreaks of severe respiratory tract infection, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East respiratory syndrome coronavirus (MERS-CoV), as a result of zoonotic CoVs crossing the species barrier, caused high pathogenicity and mortality rates in human populations. This brought CoVs global attention and highlighted the importance of controlling infectious pathogens at international borders. In this review, we focus on our current understanding of the epidemiology, pathogenesis, prevention, and treatment of SARS-CoV and MERS-CoV, as well as provides details on the pivotal structure and function of the spike proteins (S proteins) on the surface of each of these viruses. For building up more suitable animal models, we compare the current animal models recapitulating pathogenesis and summarize the potential role of host receptors contributing to diverse host affinity in various species. We outline the research still needed to fully elucidate the pathogenic mechanism of these viruses, to construct reproducible animal models, and ultimately develop countermeasures to conquer not only SARS-CoV and MERS-CoV, but also these emerging coronaviral diseases.
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32
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Cockrell AS, Leist SR, Douglas MG, Baric RS. Modeling pathogenesis of emergent and pre-emergent human coronaviruses in mice. Mamm Genome 2018; 29:367-383. [PMID: 30043100 PMCID: PMC6132729 DOI: 10.1007/s00335-018-9760-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 07/17/2018] [Indexed: 12/21/2022]
Abstract
The emergence of highly pathogenic human coronaviruses (hCoVs) in the last two decades has illuminated their potential to cause high morbidity and mortality in human populations and disrupt global economies. Global pandemic concerns stem from their high mortality rates, capacity for human-to-human spread by respiratory transmission, and complete lack of approved therapeutic countermeasures. Limiting disease may require the development of virus-directed and host-directed therapeutic strategies due to the acute etiology of hCoV infections. Therefore, understanding how hCoV–host interactions cause pathogenic outcomes relies upon mammalian models that closely recapitulate the pathogenesis of hCoVs in humans. Pragmatism has largely been the driving force underpinning mice as highly effective mammalian models for elucidating hCoV–host interactions that govern pathogenesis. Notably, tractable mouse genetics combined with hCoV reverse genetic systems has afforded the concomitant manipulation of virus and host genetics to evaluate virus–host interaction networks in disease. In addition to assessing etiologies of known hCoVs, mouse models have clinically predictive value as tools to appraise potential disease phenotypes associated with pre-emergent CoVs. Knowledge of CoV pathogenic potential before it crosses the species barrier into the human population provides a highly desirable preclinical platform for addressing global pathogen preparedness, an overarching directive of the World Health Organization. Although we recognize that results obtained in robust mouse models require evaluation in non-human primates, we focus this review on the current state of hCoV mouse models, their use as tractable complex genetic organisms for untangling complex hCoV–host interactions, and as pathogenesis models for preclinical evaluation of novel therapeutic interventions.
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Affiliation(s)
- Adam S Cockrell
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Madeline G Douglas
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, NC, 27599, USA. .,Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, NC, 27599, USA.
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33
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Wang Y, Sun J, Zhu A, Zhao J, Zhao J. Current understanding of middle east respiratory syndrome coronavirus infection in human and animal models. J Thorac Dis 2018; 10:S2260-S2271. [PMID: 30116605 DOI: 10.21037/jtd.2018.03.80] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Middle East respiratory syndrome (MERS) is a highly lethal respiratory disease caused by a novel betacoronavirus (MERS coronavirus, MERS-CoV). Since its first emergence in 2012, multiple transmission events of MERS-CoV (dromedary to human and human to human) have been reported, indicating that MERS-CoV has the potential to cause widespread outbreak. However, the epidemiology of MERS as well as immune responses against the virus in animal models and patients are still not well understood, hindering the vaccine and therapeutic developments. In this review, we summarize recent genetic and epidemic findings of MERS-CoV and the progress in animal model development, immune response studies in both animals and humans. At last, we discussed the breakthrough on vaccine and therapeutic development which are important against potential future MERS outbreak.
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Affiliation(s)
- Yanqun Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital, Guangzhou 510120, China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital, Guangzhou 510120, China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital, Guangzhou 510120, China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital, Guangzhou 510120, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital, Guangzhou 510120, China.,Institute of Infectious disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou 510120, China
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34
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Fung TS, Liu DX. Post-translational modifications of coronavirus proteins: roles and function. Future Virol 2018; 13:405-430. [PMID: 32201497 PMCID: PMC7080180 DOI: 10.2217/fvl-2018-0008] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/13/2018] [Indexed: 12/22/2022]
Abstract
Post-translational modifications (PTMs) refer to the covalent modifications of polypeptides after they are synthesized, adding temporal and spatial regulation to modulate protein functions. Being obligate intracellular parasites, viruses rely on the protein synthesis machinery of host cells to support replication, and not surprisingly, many viral proteins are subjected to PTMs. Coronavirus (CoV) is a group of enveloped RNA viruses causing diseases in both human and animals. Many CoV proteins are modified by PTMs, including glycosylation and palmitoylation of the spike and envelope protein, N- or O-linked glycosylation of the membrane protein, phosphorylation and ADP-ribosylation of the nucleocapsid protein, and other PTMs on nonstructural and accessory proteins. In this review, we summarize the current knowledge on PTMs of CoV proteins, with an emphasis on their impact on viral replication and pathogenesis. The ability of some CoV proteins to interfere with PTMs of host proteins will also be discussed.
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Affiliation(s)
- To Sing Fung
- South China Agricultural University, Guangdong Province Key Laboratory Microbial Signals & Disease Co, & Integrative Microbiology Research Center, Guangzhou 510642, Guangdong, PR China.,South China Agricultural University, Guangdong Province Key Laboratory Microbial Signals & Disease Co, & Integrative Microbiology Research Center, Guangzhou 510642, Guangdong, PR China
| | - Ding Xiang Liu
- South China Agricultural University, Guangdong Province Key Laboratory Microbial Signals & Disease Co, & Integrative Microbiology Research Center, Guangzhou 510642, Guangdong, PR China.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.,South China Agricultural University, Guangdong Province Key Laboratory Microbial Signals & Disease Co, & Integrative Microbiology Research Center, Guangzhou 510642, Guangdong, PR China.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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Zheng J, Perlman S. Immune responses in influenza A virus and human coronavirus infections: an ongoing battle between the virus and host. Curr Opin Virol 2018; 28:43-52. [PMID: 29172107 PMCID: PMC5835172 DOI: 10.1016/j.coviro.2017.11.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/02/2017] [Indexed: 12/25/2022]
Abstract
Respiratory viruses, especially influenza A viruses and coronaviruses such as MERS-CoV, represent continuing global threats to human health. Despite significant advances, much needs to be learned. Recent studies in virology and immunology have improved our understanding of the role of the immune system in protection and in the pathogenesis of these infections and of co-evolution of viruses and their hosts. These findings, together with sophisticated molecular structure analyses, omics tools and computer-based models, have helped delineate the interaction between respiratory viruses and the host immune system, which will facilitate the development of novel treatment strategies and vaccines with enhanced efficacy.
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Affiliation(s)
- Jian Zheng
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242, United States
| | - Stanley Perlman
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242, United States.
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