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Bhatt P, Sharma M, Sharma S. Prediction and identification of T cell epitopes of COVID-19 with balanced cytokine response for the development of peptide based vaccines. In Silico Pharmacol 2021; 9:40. [PMID: 34221846 PMCID: PMC8237047 DOI: 10.1007/s40203-021-00098-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/05/2021] [Indexed: 12/27/2022] Open
Abstract
Recent outbreak of 2019 novel Corona virus poses serious challenge for the global health system. In lieu of paucity of experimental data, tools and the very basic understanding of host immune responses against SARS-CoV-2, well thought effective measures are needed to control COVID-19 pandemic. We have identified specific overlapping antigenic peptide epitopes (OAPE) within the 4 structural proteins of SARS-CoV-2 predictive of triggering robust CD4 and CD8 T cell responses in host using bio-informatics tools (NetMHC4.0, IEDB, and Vaxijen2.0). We speculate an early release of pro-inflammatory cytokines for protection and later release of anti-inflammatory cytokines for prevention of immunopathology in designing a vaccine for Covid-19. Therefore, the selected immunogenic OAPE were subjected to in silico tools (IL-6-Pred, IFNepitope and PIP-EL) for analyzing their pro-inflammatory response. The OAPEs found to be pro-inflammatory in nature were further subjected to prediction servers (IL-4-Pred, IL-10-Pred, Pre-AIP) to characterize them as inducers of anti-inflammatory response as well. We finally filtered out 12 OAPE which had affinity for both CD4 and CD8 T cells as well as were inducers of pro-inflammatory and anti-inflammatory cytokines. On confirmation of OAPE binding affinity for respective T cell specific MHC allele using docking studies (pepATTRACT, Hex8.0 and Discovery studio) they were found to be have more immunogenic potential than the 3 negative control peptides (NCPs) included in the study. Additionally, we constructed CTxB-adjuvanated multi-epitopic vaccine inclusive of the 12 OAPEs which was non-toxic, non-allergenic and capable of inducing both pro-inflammatory and anti-inflammatory cytokines. A successful in silico cloning and docking of modeled subunit vaccine construct with toll like receptor-2 (TLR-2) confirmed the high efficacy of our multi-epitopic vaccine which can through a balanced interplay of cytokines help in creating a steady-state immune equilibrium. In silico immune simulation studies with the vaccine using C-ImmSim server also showed higher percentage of T cells along with production of pro-inflammatory as well as some anti-inflammatory cytokines. Experimental validation of this prediction based study on Peripheral Blood Mononuclear Cells (PBMCs) of un-infected individuals, patients and recovered individuals will facilitate production of high priority effective SARS -CoV-2 vaccine candidate. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-021-00098-7.
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Affiliation(s)
- Parul Bhatt
- DS Kothari Central Facility for Interdisciplinary Research, Miranda House, University of Delhi, Delhi, 110007 India
- Department of Zoology, Miranda House, University of Delhi, Delhi, 110007 India
| | - Monika Sharma
- DS Kothari Central Facility for Interdisciplinary Research, Miranda House, University of Delhi, Delhi, 110007 India
- Department of Zoology, Miranda House, University of Delhi, Delhi, 110007 India
| | - Sadhna Sharma
- DS Kothari Central Facility for Interdisciplinary Research, Miranda House, University of Delhi, Delhi, 110007 India
- Department of Zoology, Miranda House, University of Delhi, Delhi, 110007 India
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Vazquez C, Swanson SE, Negatu SG, Dittmar M, Miller J, Ramage HR, Cherry S, Jurado KA. SARS-CoV-2 viral proteins NSP1 and NSP13 inhibit interferon activation through distinct mechanisms. PLoS One 2021; 16:e0253089. [PMID: 34166398 PMCID: PMC8224853 DOI: 10.1371/journal.pone.0253089] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating global pandemic, infecting over 43 million people and claiming over 1 million lives, with these numbers increasing daily. Therefore, there is urgent need to understand the molecular mechanisms governing SARS-CoV-2 pathogenesis, immune evasion, and disease progression. Here, we show that SARS-CoV-2 can block IRF3 and NF-κB activation early during virus infection. We also identify that the SARS-CoV-2 viral proteins NSP1 and NSP13 can block interferon activation via distinct mechanisms. NSP1 antagonizes interferon signaling by suppressing host mRNA translation, while NSP13 downregulates interferon and NF-κB promoter signaling by limiting TBK1 and IRF3 activation, as phospho-TBK1 and phospho-IRF3 protein levels are reduced with increasing levels of NSP13 protein expression. NSP13 can also reduce NF-κB activation by both limiting NF-κB phosphorylation and nuclear translocation. Last, we also show that NSP13 binds to TBK1 and downregulates IFIT1 protein expression. Collectively, these data illustrate that SARS-CoV-2 bypasses multiple innate immune activation pathways through distinct mechanisms.
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Affiliation(s)
- Christine Vazquez
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Sydnie E. Swanson
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Seble G. Negatu
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Mark Dittmar
- Department Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jesse Miller
- Department Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Holly R. Ramage
- Department of Microbiology and Immunology, Thomas Jefferson University Sidney Kimmel Medical College, Philadelphia, Pennsylvania, United States of America
| | - Sara Cherry
- Department Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Kellie A. Jurado
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Rai KR, Shrestha P, Yang B, Chen Y, Liu S, Maarouf M, Chen JL. Acute Infection of Viral Pathogens and Their Innate Immune Escape. Front Microbiol 2021; 12:672026. [PMID: 34239508 PMCID: PMC8258165 DOI: 10.3389/fmicb.2021.672026] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/04/2021] [Indexed: 12/15/2022] Open
Abstract
Viral infections can cause rampant disease in human beings, ranging from mild to acute, that can often be fatal unless resolved. An acute viral infection is characterized by sudden or rapid onset of disease, which can be resolved quickly by robust innate immune responses exerted by the host or, instead, may kill the host. Immediately after viral infection, elements of innate immunity, such as physical barriers, various phagocytic cells, group of cytokines, interferons (IFNs), and IFN-stimulated genes, provide the first line of defense for viral clearance. Innate immunity not only plays a critical role in rapid viral clearance but can also lead to disease progression through immune-mediated host tissue injury. Although elements of antiviral innate immunity are armed to counter the viral invasion, viruses have evolved various strategies to escape host immune surveillance to establish successful infections. Understanding complex mechanisms underlying the interaction between viruses and host’s innate immune system would help develop rational treatment strategies for acute viral infectious diseases. In this review, we discuss the pathogenesis of acute infections caused by viral pathogens and highlight broad immune escape strategies exhibited by viruses.
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Affiliation(s)
- Kul Raj Rai
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Prasha Shrestha
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bincai Yang
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhai Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Shasha Liu
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohamed Maarouf
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Ji-Long Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
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Clementi N, Ghosh S, De Santis M, Castelli M, Criscuolo E, Zanoni I, Clementi M, Mancini N. Viral Respiratory Pathogens and Lung Injury. Clin Microbiol Rev 2021; 34:e00103-20. [PMID: 33789928 PMCID: PMC8142519 DOI: 10.1128/cmr.00103-20] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Several viruses target the human respiratory tract, causing different clinical manifestations spanning from mild upper airway involvement to life-threatening acute respiratory distress syndrome (ARDS). As dramatically evident in the ongoing SARS-CoV-2 pandemic, the clinical picture is not always easily predictable due to the combined effect of direct viral and indirect patient-specific immune-mediated damage. In this review, we discuss the main RNA (orthomyxoviruses, paramyxoviruses, and coronaviruses) and DNA (adenoviruses, herpesviruses, and bocaviruses) viruses with respiratory tropism and their mechanisms of direct and indirect cell damage. We analyze the thin line existing between a protective immune response, capable of limiting viral replication, and an unbalanced, dysregulated immune activation often leading to the most severe complication. Our comprehension of the molecular mechanisms involved is increasing and this should pave the way for the development and clinical use of new tailored immune-based antiviral strategies.
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Affiliation(s)
- Nicola Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sreya Ghosh
- Harvard Medical School, Boston Children's Hospital, Division of Immunology, Boston, Massachusetts, USA
| | - Maria De Santis
- Department of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center-IRCCS, Rozzano, Italy
| | - Matteo Castelli
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
| | - Elena Criscuolo
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
| | - Ivan Zanoni
- Harvard Medical School, Boston Children's Hospital, Division of Immunology, Boston, Massachusetts, USA
- Harvard Medical School, Boston Children's Hospital, Division of Gastroenterology, Boston, Massachusetts, USA
| | - Massimo Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nicasio Mancini
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Ramasamy S, Subbian S. Critical Determinants of Cytokine Storm and Type I Interferon Response in COVID-19 Pathogenesis. Clin Microbiol Rev 2021; 34:e00299-20. [PMID: 33980688 PMCID: PMC8142516 DOI: 10.1128/cmr.00299-20] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a rapidly evolving pandemic worldwide with at least 68 million COVID-19-positive cases and a mortality rate of about 2.2%, as of 10 December 2020. About 20% of COVID-19 patients exhibit moderate to severe symptoms. Severe COVID-19 manifests as acute respiratory distress syndrome (ARDS) with elevated plasma proinflammatory cytokines, including interleukin 1β (IL-1β), IL-6, tumor necrosis factor α (TNF-α), C-X-C motif chemokine ligand 10 (CXCL10/IP10), macrophage inflammatory protein 1 alpha (MIP-1α), and chemokine (C-C motif) ligand 2 (CCL2), with low levels of interferon type I (IFN-I) in the early stage and elevated levels of IFN-I during the advanced stage of COVID-19. Most of the severe and critically ill COVID-19 patients have had preexisting comorbidities, including hypertension, diabetes, cardiovascular diseases, and respiratory diseases. These conditions are known to perturb the levels of cytokines, chemokines, and angiotensin-converting enzyme 2 (ACE2), an essential receptor involved in SARS-CoV-2 entry into the host cells. ACE2 downregulation during SARS-CoV-2 infection activates the angiotensin II/angiotensin receptor (AT1R)-mediated hypercytokinemia and hyperinflammatory syndrome. However, several SARS-CoV-2 proteins, including open reading frame 3b (ORF3b), ORF6, ORF7, ORF8, and the nucleocapsid (N) protein, can inhibit IFN type I and II (IFN-I and -II) production. Thus, hyperinflammation, in combination with the lack of IFN responses against SARS-CoV-2 early on during infection, makes the patients succumb rapidly to COVID-19. Therefore, therapeutic approaches involving anti-cytokine/anti-cytokine-signaling and IFN therapy would favor the disease prognosis in COVID-19. This review describes critical host and viral factors underpinning the inflammatory "cytokine storm" induction and IFN antagonism during COVID-19 pathogenesis. Therapeutic approaches to reduce hyperinflammation and their limitations are also discussed.
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Affiliation(s)
- Santhamani Ramasamy
- Public Health Research Institute (PHRI) at New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Selvakumar Subbian
- Public Health Research Institute (PHRI) at New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
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Li S, Zhu Z, Yang F, Cao W, Yang J, Ma C, Zhao Z, Tian H, Liu X, Ma J, Xiao S, Zheng H. Porcine Epidemic Diarrhea Virus Membrane Protein Interacted with IRF7 to Inhibit Type I IFN Production during Viral Infection. THE JOURNAL OF IMMUNOLOGY 2021; 206:2909-2923. [PMID: 34127522 DOI: 10.4049/jimmunol.2001186] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 04/06/2021] [Indexed: 11/19/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic porcine enteropathogenic coronavirus causing severe enteritis and lethal watery diarrhea in piglets. PEDV infection suppresses the synthesis of type I IFN, and multiple viral proteins of PEDV have been shown to target the adaptors of innate immune pathways to inhibit type I IFN production. In this study, we identified PEDV membrane (M) protein as a new antagonist of type I IFN production in both human embryonic kidney HEK293T cells and porcine kidney PK-15 cells and determined the antagonistic mechanism used by M protein to target IFN regulatory factor 7 (IRF7), an important regulator of type I IFN production. IRF7 is phosphorylated and activated by TBK1 and IKKε in response to viral infection. We found that PEDV M protein interacted with the inhibitory domain of IRF7 and significantly suppressed TBK1/IKKε-induced IRF7 phosphorylation and dimerization of IRF7, leading to the decreased expression of type I IFN, although it did not affect the interaction between TBK1/IKKε and IRF7. As expected, overexpression of M protein significantly increased PEDV replication in porcine cells. The M proteins of both epidemic PEDV strains and vaccine strain showed similar antagonistic effect on type I IFN production, and the 1-55 region of M protein was essential for disruption of IRF7 function by interacting with IRF7. Taken together, our data identified a new, to our knowledge, IFN antagonist of PEDV, as well as a novel, to our knowledge, antagonistic mechanism evolved by PEDV to inhibit type I IFN production.
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Affiliation(s)
- Shasha Li
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Zixiang Zhu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Fan Yang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Weijun Cao
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Jinping Yang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Caina Ma
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Zhenxiang Zhao
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Hong Tian
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Xiangtao Liu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Junwu Ma
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
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57
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Chu H, Shuai H, Hou Y, Zhang X, Wen L, Huang X, Hu B, Yang D, Wang Y, Yoon C, Wong BHY, Li C, Zhao X, Poon VKM, Cai JP, Wong KKY, Yeung ML, Zhou J, Au-Yeung RKH, Yuan S, Jin DY, Kok KH, Perlman S, Chan JFW, Yuen KY. Targeting highly pathogenic coronavirus-induced apoptosis reduces viral pathogenesis and disease severity. SCIENCE ADVANCES 2021; 7:7/25/eabf8577. [PMID: 34134991 PMCID: PMC8208716 DOI: 10.1126/sciadv.abf8577] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/04/2021] [Indexed: 05/06/2023]
Abstract
Infection by highly pathogenic coronaviruses results in substantial apoptosis. However, the physiological relevance of apoptosis in the pathogenesis of coronavirus infections is unknown. Here, with a combination of in vitro, ex vivo, and in vivo models, we demonstrated that protein kinase R-like endoplasmic reticulum kinase (PERK) signaling mediated the proapoptotic signals in Middle East respiratory syndrome coronavirus (MERS-CoV) infection, which converged in the intrinsic apoptosis pathway. Inhibiting PERK signaling or intrinsic apoptosis both alleviated MERS pathogenesis in vivo. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and SARS-CoV induced apoptosis through distinct mechanisms but inhibition of intrinsic apoptosis similarly limited SARS-CoV-2- and SARS-CoV-induced apoptosis in vitro and markedly ameliorated the lung damage of SARS-CoV-2-inoculated human angiotensin-converting enzyme 2 (hACE2) mice. Collectively, our study provides the first evidence that virus-induced apoptosis is an important disease determinant of highly pathogenic coronaviruses and demonstrates that this process can be targeted to attenuate disease severity.
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Affiliation(s)
- Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Huiping Shuai
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yuxin Hou
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Xi Zhang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Lei Wen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Xiner Huang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Bingjie Hu
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Dong Yang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yixin Wang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Chaemin Yoon
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Bosco Ho-Yin Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Cun Li
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Xiaoyu Zhao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Vincent Kwok-Man Poon
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jian-Piao Cai
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kenneth Kak-Yuen Wong
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Man-Lung Yeung
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jie Zhou
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Rex Kwok-Him Au-Yeung
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Dong-Yan Jin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kin-Hang Kok
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
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Kehrer T, García-Sastre A, Miorin L. Control of Innate Immune Activation by Severe Acute Respiratory Syndrome Coronavirus 2 and Other Coronaviruses. J Interferon Cytokine Res 2021; 41:205-219. [PMID: 34161170 PMCID: PMC8336211 DOI: 10.1089/jir.2021.0060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 12/25/2022] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represents a public health crisis of unprecedented proportions. After the emergence of SARS-CoV-1 in 2002, and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, this is the third outbreak of a highly pathogenic zoonotic coronavirus (CoV) that the world has witnessed in the last 2 decades. Infection with highly pathogenic human CoVs often results in a severe respiratory disease characterized by a delayed and blunted interferon (IFN) response, accompanied by an excessive production of proinflammatory cytokines. This indicates that CoVs developed effective mechanisms to overcome the host innate immune response and promote viral replication and pathogenesis. In this review, we describe the key innate immune signaling pathways that are activated during infection with SARS-CoV-2 and other well studied pathogenic CoVs. In addition, we summarize the main strategies that these viruses employ to modulate the host immune responses through the antagonism of IFN induction and effector pathways.
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Affiliation(s)
- Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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59
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Galani IE, Andreakos E. Impaired innate antiviral defenses in COVID-19: Causes, consequences and therapeutic opportunities. Semin Immunol 2021; 55:101522. [PMID: 34815163 PMCID: PMC8576141 DOI: 10.1016/j.smim.2021.101522] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently emerged pathogen that has caused coronavirus disease 2019 (COVID-19), the worst pandemic of our times leading to tremendous loss of human life and unprecedented measures of social distancing. COVID-19 symptom manifestations range from asymptomatic disease to severe and lethal outcomes. Lack of previous exposure and immunity to SARS-CoV-2, and high infectivity of the virus have contributed to its broad spread across the globe. In the absence of specific adaptive immunity, innate immune mechanisms are crucial for efficient antiviral defenses and control of the infection. Accumulating evidence now suggests that the remarkable heterogeneity in COVID-19 disease manifestations is due to variable degrees of impairment of innate immune mechanisms. In this review, we summarize recent findings describing both viral and host intrinsic factors that have been linked to defective innate immune responses and account for severe COVID-19. We also discuss emerging therapeutic opportunities for targeting innate immunity for the treatment of COVID-19.
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Affiliation(s)
- Ioanna-Evdokia Galani
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, 11527, Athens, Greece
| | - Evangelos Andreakos
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, 11527, Athens, Greece.
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60
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Dong S, Wang R, Yu R, Chen B, Si F, Xie C, Li Z. Identification of cellular proteins interacting with PEDV M protein through APEX2 labeling. J Proteomics 2021; 240:104191. [PMID: 33757879 PMCID: PMC7980486 DOI: 10.1016/j.jprot.2021.104191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 11/24/2022]
Abstract
Membrane (M) proteins of coronaviruses are the most abundant component of the virus envelope and play crucial roles in virus assembly, virus budding and the regulation of host immunity. To understand more about these functions in the context of PEDV M protein, forty host cell proteins interacting with the M protein were identified in the present study by exploiting the proximity-labeling enzyme APEX2 (a mutant soybean ascorbate peroxidase). Bioinformatic analysis showed that the identified host cell proteins were related to fifty-four signal pathways and a wide diversity of biological processes. Interaction between M and five of the identified proteins (RIG-I, PPID, NHE-RF1, S100A11, CLDN4) was confirmed by co-immunoprecipitation (Co-IP). In addition, knockdown of PPID and S100A11 genes by siRNA significantly improved virus production, indicating that the proteins encoded by the two genes were interfering with or down-regulating virus replication in infected cells. Identification of the host cell proteins accomplished in this study provides new information about the mechanisms underlying PEDV replication and immune evasion. SIGNIFICANCE: PEDV M protein is an essential structural protein implicated in viral infection, replication and assembly although the precise mechanisms underlying these functions remain enigmatic. In this study, we have identified 40 host cell proteins that interact with PEDV M protein using the proximity-labeling enzyme APEX2. Co-immunoprecipitation subsequently confirmed interactions between PEDV M protein and five host cell proteins, two of which (S100A11 and PPID) were involved in down-regulating virus replication in infected cells. This study is significant in that it formulates a strategy to provide new information about the mechanisms relating to the novel functions of PEDV M protein.
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Affiliation(s)
- Shijuan Dong
- Institute of Animal Science and Veterinary Science, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai, PR China,Shanghai Engineering Research Center of Breeding Pigs, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai, PR China
| | - Ruiyang Wang
- Institute of Animal Science and Veterinary Science, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai, PR China
| | - Ruisong Yu
- Institute of Animal Science and Veterinary Science, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai, PR China
| | - Bingqing Chen
- Institute of Animal Science and Veterinary Science, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai, PR China,Shanghai Engineering Research Center of Breeding Pigs, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai, PR China
| | - Fusheng Si
- Institute of Animal Science and Veterinary Science, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai, PR China,Shanghai Engineering Research Center of Breeding Pigs, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai, PR China
| | - Chunfang Xie
- Institute of Animal Science and Veterinary Science, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai, PR China
| | - Zhen Li
- Institute of Animal Science and Veterinary Science, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai, PR China; Shanghai Engineering Research Center of Breeding Pigs, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai, PR China.
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61
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Sui L, Zhao Y, Wang W, Wu P, Wang Z, Yu Y, Hou Z, Tan G, Liu Q. SARS-CoV-2 Membrane Protein Inhibits Type I Interferon Production Through Ubiquitin-Mediated Degradation of TBK1. Front Immunol 2021; 12:662989. [PMID: 34084167 PMCID: PMC8168463 DOI: 10.3389/fimmu.2021.662989] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/31/2021] [Indexed: 12/25/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative pathogen of current COVID-19 pandemic, and insufficient production of type I interferon (IFN-I) is associated with the severe forms of the disease. Membrane (M) protein of SARS-CoV-2 has been reported to suppress host IFN-I production, but the underlying mechanism is not completely understood. In this study, SARS-CoV-2 M protein was confirmed to suppress the expression of IFNβ and interferon-stimulated genes induced by RIG-I, MDA5, IKKϵ, and TBK1, and to inhibit IRF3 phosphorylation and dimerization caused by TBK1. SARS-CoV-2 M could interact with MDA5, TRAF3, IKKϵ, and TBK1, and induce TBK1 degradation via K48-linked ubiquitination. The reduced TBK1 further impaired the formation of TRAF3-TANK-TBK1-IKKε complex that leads to inhibition of IFN-I production. Our study revealed a novel mechanism of SARS-CoV-2 M for negative regulation of IFN-I production, which would provide deeper insight into the innate immunosuppression and pathogenicity of SARS-CoV-2.
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Affiliation(s)
- Liyan Sui
- Laboratory of Emerging Infectious Disease, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China
| | - Yinghua Zhao
- Laboratory of Emerging Infectious Disease, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China
| | - Wenfang Wang
- College of Basic Medical Science, Jilin University, Changchun, China
| | - Ping Wu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Zedong Wang
- Laboratory of Emerging Infectious Disease, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China
| | - Yang Yu
- Hospital of Stomatology, Jilin University, Changchun, China
| | - Zhijun Hou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Guangyun Tan
- Department of Immunology, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China
| | - Quan Liu
- Laboratory of Emerging Infectious Disease, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China
- School of Life Sciences and Engineering, Foshan University, Foshan, China
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62
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Du H, Chen F, Liu H, Hong P. Network-based virus-host interaction prediction with application to SARS-CoV-2. PATTERNS (NEW YORK, N.Y.) 2021; 2:100242. [PMID: 33817672 PMCID: PMC8006187 DOI: 10.1016/j.patter.2021.100242] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/06/2021] [Accepted: 03/24/2021] [Indexed: 12/15/2022]
Abstract
COVID-19, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has quickly become a global health crisis since the first report of infection in December of 2019. However, the infection spectrum of SARS-CoV-2 and its comprehensive protein-level interactions with hosts remain unclear. There is a massive amount of underutilized data and knowledge about RNA viruses highly relevant to SARS-CoV-2 and proteins of their hosts. More in-depth and more comprehensive analyses of that knowledge and data can shed new light on the molecular mechanisms underlying the COVID-19 pandemic and reveal potential risks. In this work, we constructed a multi-layer virus-host interaction network to incorporate these data and knowledge. We developed a machine-learning-based method to predict virus-host interactions at both protein and organism levels. Our approach revealed five potential infection targets of SARS-CoV-2 and 19 highly possible interactions between SARS-CoV-2 proteins and human proteins in the innate immune pathway.
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Affiliation(s)
- Hangyu Du
- Department of Computer Science, Brandeis University, Waltham, MA 02453, USA
| | - Feng Chen
- Department of Computer Science, Brandeis University, Waltham, MA 02453, USA
| | - Hongfu Liu
- Department of Computer Science, Brandeis University, Waltham, MA 02453, USA
| | - Pengyu Hong
- Department of Computer Science, Brandeis University, Waltham, MA 02453, USA
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63
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Potential Antiviral Immune Response Against COVID-19: Lessons Learned from SARS-CoV. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1318:149-167. [PMID: 33973177 DOI: 10.1007/978-3-030-63761-3_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Virus and host innate immune system interaction plays a significant role in forming the outcome of viral diseases. Host innate immunity initially recognizes the viral invasion and induces a rapid inflammatory response, and this recognition activates signaling cascades that trigger the release of antiviral mediators. This chapter aims to explore the mechanisms by which newly emerged coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) activates the host immune system. Since SARS-CoV-2 shares similarities with SARS-CoV that caused the epidemic of SARS in 2003, the pathogenesis of both viruses could be at least very similar. For this, this chapter provides a synthesis of literature concerning antiviral immunity in SARS-CoV and SARS-CoV-2. It includes the presentation of epitopes linked to SARS-CoV-2 as well as the ability of SARS-CoV-2 to cause proteolytic activation and interact with angiotensin-converting enzyme 2 (ACE2) via molecular mimicry. This chapter characterizes various mechanisms that this virus may engage in escaping the host immunity, ended by a discussion of humoral immune responses against SARS-CoV-2.
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64
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Kasuga Y, Zhu B, Jang KJ, Yoo JS. Innate immune sensing of coronavirus and viral evasion strategies. Exp Mol Med 2021; 53:723-736. [PMID: 33953325 PMCID: PMC8099713 DOI: 10.1038/s12276-021-00602-1] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/01/2021] [Accepted: 03/03/2021] [Indexed: 12/13/2022] Open
Abstract
The innate immune system is the first line of the host defense program against pathogens and harmful substances. Antiviral innate immune responses can be triggered by multiple cellular receptors sensing viral components. The activated innate immune system produces interferons (IFNs) and cytokines that perform antiviral functions to eliminate invading viruses. Coronaviruses are single-stranded, positive-sense RNA viruses that have a broad range of animal hosts. Coronaviruses have evolved multiple means to evade host antiviral immune responses. Successful immune evasion by coronaviruses may enable the viruses to adapt to multiple species of host organisms. Coronavirus transmission from zoonotic hosts to humans has caused serious illnesses, such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and coronavirus disease-2019 (COVID-19), resulting in global health and economic crises. In this review, we summarize the current knowledge of the mechanisms underlying host sensing of and innate immune responses against coronavirus invasion, as well as host immune evasion strategies of coronaviruses. Understanding how the innate immune system senses coronaviruses and how coronaviruses can escape detection could provide novel approaches to tackle infections. Coronaviruses, including SARS-CoV-2, constantly evolve to manipulate, obstruct and evade host immune responses. A team led by Ji-Seung Yoo, Hokkaido University, Sapporo, Japan, reviewed understanding of innate immune responses to coronaviruses and viral evasion strategies. Two major receptor families recognise RNA viruses upon infection, but how they respond to SARS-CoV-2 is unclear. One receptor, TLR7, plays a critical role in sensing coronavirus infections, and mutations in the TLR7 gene are associated with severe illness and mortality in young Covid-19 patients. Activating host TLR pathways may prove a useful therapeutic approach. Further in-depth investigations are needed into specific coronavirus proteins and viral mechanisms that suppress host immunity.
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Affiliation(s)
- Yusuke Kasuga
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan
| | - Baohui Zhu
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan
| | - Kyoung-Jin Jang
- Department of Pathology, School of Medicine, Institute of Biomedical Science and Technology, Konkuk University, Chungju, 27478, Republic of Korea.
| | - Ji-Seung Yoo
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan.
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65
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Type I and III interferon responses in SARS-CoV-2 infection. Exp Mol Med 2021; 53:750-760. [PMID: 33953323 PMCID: PMC8099704 DOI: 10.1038/s12276-021-00592-0] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), the current pandemic disease, is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Type I and III interferons (IFNs) are innate cytokines that are important in the first-line defense against viruses. Similar to many other viruses, SARS-CoV-2 has evolved mechanisms for evading the antiviral effects of type I and III IFNs at multiple levels, including the induction of IFN expression and cellular responses to IFNs. In this review, we describe the innate sensing mechanisms of SARS-CoV-2 and the mechanisms used by SARS-CoV-2 to evade type I and III IFN responses. We also discuss contradictory reports regarding impaired and robust type I IFN responses in patients with severe COVID-19. Finally, we discuss how delayed but exaggerated type I IFN responses can exacerbate inflammation and contribute to the severe progression of COVID-19. Extensive studies into how SARS-CoV-2 manipulates the immune system and influences the activity of host proteins are needed to improve treatments for COVID-19. SARS-CoV-2 evades or blocks elements of the immune system, including the antiviral activity of type I and type III interferons (IFN). You-Me Kim and Eui-Cheol Shin at the Korea Advanced Institute of Science and Technology, Daejeon, South Korea, reviewed understanding of how SARS-CoV-2 inhibits IFN responses. In infected cells, SARS-CoV-2 proteins use diverse methods to inhibit host IFN pathways, but type I IFN responses are still triggered in non-infected immune cells. The researchers believe this may explain the delayed but exaggerated type I IFN responses that contribute to the hyper-inflammation seen in critically ill patients. They call for further investigations into IFN and inflammatory responses in SARS-CoV-2 infection.
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66
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Zhang J, Zhao C, Zhao W. Virus Caused Imbalance of Type I IFN Responses and Inflammation in COVID-19. Front Immunol 2021; 12:633769. [PMID: 33912161 PMCID: PMC8071932 DOI: 10.3389/fimmu.2021.633769] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/24/2021] [Indexed: 01/18/2023] Open
Abstract
The global expansion of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as one of the greatest public health challenges and imposes a great threat to human health. Innate immunity plays vital roles in eliminating viruses through initiating type I interferons (IFNs)-dependent antiviral responses and inducing inflammation. Therefore, optimal activation of innate immunity and balanced type I IFN responses and inflammation are beneficial for efficient elimination of invading viruses. However, SARS-CoV-2 manipulates the host's innate immune system by multiple mechanisms, leading to aberrant type I IFN responses and excessive inflammation. In this review, we will emphasize the recent advances in the understanding of the crosstalk between host innate immunity and SARS-CoV-2 to explain the imbalance between inflammation and type I IFN responses caused by viral infection, and explore potential therapeutic targets for COVID-19.
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Affiliation(s)
- Jintao Zhang
- Department of Immunology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Chunyuan Zhao
- Department of Immunology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
- Department of Cell Biology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wei Zhao
- Department of Immunology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
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67
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Fung SY, Siu KL, Lin H, Yeung ML, Jin DY. SARS-CoV-2 main protease suppresses type I interferon production by preventing nuclear translocation of phosphorylated IRF3. Int J Biol Sci 2021; 17:1547-1554. [PMID: 33907518 PMCID: PMC8071772 DOI: 10.7150/ijbs.59943] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022] Open
Abstract
Suppression of type I interferon (IFN) response is one pathological outcome of the infection of highly pathogenic human coronaviruses. To effect this, severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 encode multiple IFN antagonists. In this study, we reported on the IFN antagonism of SARS-CoV-2 main protease NSP5. NSP5 proteins of both SARS-CoV and SARS-CoV-2 counteracted Sendai virus-induced IFN production. NSP5 variants G15S and K90R commonly seen in circulating strains of SARS-CoV-2 retained the IFN-antagonizing property. The suppressive effect of NSP5 on IFN-β gene transcription induced by RIG-I, MAVS, TBK1 and IKKϵ suggested that NSP5 likely acts at a step downstream of IRF3 phosphorylation in the cytoplasm. NSP5 did not influence steady-state expression or phosphorylation of IRF3, suggesting that IRF3, regardless of its phosphorylation state, might not be the substrate of NSP5 protease. However, nuclear translocation of phosphorylated IRF3 was severely compromised in NSP5-expressing cells. Taken together, our work revealed a new mechanism by which NSP5 proteins encoded by SARS-CoV and SARS-CoV-2 antagonize IFN production by retaining phosphorylated IRF3 in the cytoplasm. Our findings have implications in rational design and development of antiviral agents against SARS-CoV-2.
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Affiliation(s)
- Sin-Yee Fung
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kam-Leung Siu
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Huayue Lin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Man Lung Yeung
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
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68
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Mohammed MEA. The percentages of SARS-CoV-2 protein similarity and identity with SARS-CoV and BatCoV RaTG13 proteins can be used as indicators of virus origin. ACTA ACUST UNITED AC 2021; 12:81-91. [PMID: 33850392 PMCID: PMC8033097 DOI: 10.1007/s42485-021-00060-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/08/2021] [Accepted: 03/22/2021] [Indexed: 02/08/2023]
Abstract
There are three types of proteins in coronaviruses: nonstructural, structural, and accessory proteins. Coronavirus proteins are essential for viral replication and for the binding and invasion of hosts and the regulation of host cell metabolism and immunity. This study investigated the amino acid sequence similarity and identity percentages of 10 proteins in SARS-CoV-2, SARS-CoV and the Rhinolophus affinis bat coronavirus (BatCoV RaTG13). The investigated proteins were the 1ab polyprotein, spike protein, orf3a, the envelope protein, the membrane protein, orf6, orf7a, orf7b, orf8, and the nucleocapsid protein. The online sequence alignment service of The European Molecular Biology Open Software Suite (EMBOSS) was used to determine the percentages of protein similarity and identity in the three viruses. The results showed that the similarity and identity percentages of the SARS-CoV-2 and BatCoV RaTG13 proteins were both greater than 95%, while the identity and similarity percentages of SARS-CoV-2 and SARS-CoV were both greater than 38%. The proteins of SARS-CoV-2 and BatCoV RaTG13 have high identity and similarity compared to those of SARS-CoV-2 and SARS-CoV.
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Affiliation(s)
- Mohammed Elimam Ahamed Mohammed
- Department of Chemistry, Faculty of Science, King Khalid University, Abha, Saudi Arabia.,Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, Abha, Saudi Arabia
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Evans N, Martinez E, Petrosillo N, Nichols J, Islam E, Pruitt K, Almodovar S. SARS-CoV-2 and Human Immunodeficiency Virus: Pathogen Pincer Attack. HIV AIDS (Auckl) 2021; 13:361-375. [PMID: 33833585 PMCID: PMC8020331 DOI: 10.2147/hiv.s300055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/22/2021] [Indexed: 12/16/2022] Open
Abstract
Paramount efforts worldwide are seeking to increase understanding of the basic virology of SARS-CoV-2, characterize the spectrum of complications associated with COVID-19, and develop vaccines that can protect from new and recurrent infections with SARS-CoV-2. While we continue learning about this new virus, it is clear that 1) the virus is spread via the respiratory route, primarily by droplets and contact with contaminated surfaces and fomites, as well as by aerosol formation during invasive respiratory procedures; 2) the airborne route is still controversial; and 3) that those infected can spread the virus without necessarily developing COVID-19 (ie, asymptomatic). With the number of SARS-CoV-2 infections increasing globally, the possibility of co-infections and/or co-morbidities is becoming more concerning. Co-infection with Human Immunodeficiency Virus (HIV) is one such example of polyparasitism of interest. This military-themed comparative review of SARS-CoV-2 and HIV details their virology and describes them figuratively as separate enemy armies. HIV, an old enemy dug into trenches in individuals already infected, and SARS-CoV-2 the new army, attempting to attack and capture territories, tissues and organs, in order to provide resources for their expansion. This analogy serves to aid in discussion of three main areas of focus and draw attention to how these viruses may cooperate to gain the upper hand in securing a host. Here we compare their target, the key receptors found on those tissues, viral lifecycles and tactics for immune response surveillance. The last focus is on the immune response to infection, addressing similarities in cytokines released. While the majority of HIV cases can be successfully managed with antiretroviral therapy nowadays, treatments for SARS-CoV-2 are still undergoing research given the novelty of this army.
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Affiliation(s)
- Nicholas Evans
- Texas Tech University Health Sciences Center, Department of Immunology & Molecular Microbiology, Lubbock, TX, USA
| | - Edgar Martinez
- Texas Tech University Health Sciences Center, Department of Immunology & Molecular Microbiology, Lubbock, TX, USA
| | - Nicola Petrosillo
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Jacob Nichols
- Texas Tech University Health Sciences Center, Department of Internal Medicine, Lubbock, TX, USA
| | - Ebtesam Islam
- Texas Tech University Health Sciences Center, Department of Internal Medicine, Lubbock, TX, USA
| | - Kevin Pruitt
- Texas Tech University Health Sciences Center, Department of Immunology & Molecular Microbiology, Lubbock, TX, USA
| | - Sharilyn Almodovar
- Texas Tech University Health Sciences Center, Department of Immunology & Molecular Microbiology, Lubbock, TX, USA
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70
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Transcriptional and Non-Transcriptional Activation, Posttranslational Modifications, and Antiviral Functions of Interferon Regulatory Factor 3 and Viral Antagonism by the SARS-Coronavirus. Viruses 2021; 13:v13040575. [PMID: 33805458 PMCID: PMC8066409 DOI: 10.3390/v13040575] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
The immune system defends against invading pathogens through the rapid activation of innate immune signaling pathways. Interferon regulatory factor 3 (IRF3) is a key transcription factor activated in response to virus infection and is largely responsible for establishing an antiviral state in the infected host. Studies in Irf3−/− mice have demonstrated the absence of IRF3 imparts a high degree of susceptibility to a wide range of viral infections. Virus infection causes the activation of IRF3 to transcribe type-I interferon (e.g., IFNβ), which is responsible for inducing the interferon-stimulated genes (ISGs), which act at specific stages to limit virus replication. In addition to its transcriptional function, IRF3 is also activated to trigger apoptosis of virus-infected cells, as a mechanism to restrict virus spread within the host, in a pathway called RIG-I-like receptor-induced IRF3 mediated pathway of apoptosis (RIPA). These dual functions of IRF3 work in concert to mediate protective immunity against virus infection. These two pathways are activated differentially by the posttranslational modifications (PTMs) of IRF3. Moreover, PTMs regulate not only IRF3 activation and function, but also protein stability. Consequently, many viruses utilize viral proteins or hijack cellular enzymes to inhibit IRF3 functions. This review will describe the PTMs that regulate IRF3′s RIPA and transcriptional activities and use coronavirus as a model virus capable of antagonizing IRF3-mediated innate immune responses. A thorough understanding of the cellular control of IRF3 and the mechanisms that viruses use to subvert this system is critical for developing novel therapies for virus-induced pathologies.
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71
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Petro TM. IFN Regulatory Factor 3 in Health and Disease. THE JOURNAL OF IMMUNOLOGY 2021; 205:1981-1989. [PMID: 33020188 DOI: 10.4049/jimmunol.2000462] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/07/2020] [Indexed: 12/14/2022]
Abstract
Immunity to viruses requires an array of critical cellular proteins that include IFN regulatory factor 3 (IRF3). Consequently, most viruses that infect vertebrates encode proteins that interfere with IRF3 activation. This review describes the cellular pathways linked to IRF3 activation and where those pathways are targeted by human viral pathogens. Moreover, key regulatory pathways that control IRF3 are discussed. Besides viral infections, IRF3 is also involved in resistance to some bacterial infections, in anticancer immunity, and in anticancer therapies involving DNA damage agents. A recent finding shows that IRF3 is needed for T cell effector functions that are involved in anticancer immunity and also in T cell autoimmune diseases. In contrast, unregulated IRF3 activity is clearly not beneficial, considering it is implicated in certain interferonopathies, in which heightened IRF3 activity leads to IFN-β-induced disease. Therefore, IRF3 is involved largely in maintaining health but sometimes contributing to disease.
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Affiliation(s)
- Thomas M Petro
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE 68583; and Nebraska Center for Virology, University of Nebraska Medical Center, Lincoln, NE 68583
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Garcia-del-Barco D, Risco-Acevedo D, Berlanga-Acosta J, Martos-Benítez FD, Guillén-Nieto G. Revisiting Pleiotropic Effects of Type I Interferons: Rationale for Its Prophylactic and Therapeutic Use Against SARS-CoV-2. Front Immunol 2021; 12:655528. [PMID: 33841439 PMCID: PMC8033157 DOI: 10.3389/fimmu.2021.655528] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/08/2021] [Indexed: 12/11/2022] Open
Abstract
The pandemic distribution of SARS-CoV-2 together with its particular feature of inactivating the interferon-based endogenous response and accordingly, impairing the innate immunity, has become a challenge for the international scientific and medical community. Fortunately, recombinant interferons as therapeutic products have accumulated a long history of beneficial therapeutic results in the treatment of chronic and acute viral diseases and also in the therapy of some types of cancer. One of the first antiviral treatments during the onset of COVID-19 in China was based on the use of recombinant interferon alfa 2b, so many clinicians began to use it, not only as therapy but also as a prophylactic approach, mainly in medical personnel. At the same time, basic research on interferons provided new insights that have contributed to a much better understanding of how treatment with interferons, initially considered as antivirals, actually has a much broader pharmacological scope. In this review, we briefly describe interferons, how they are induced in the event of a viral infection, and how they elicit signaling after contact with their specific receptor on target cells. Additionally, some of the genes stimulated by type I interferons are described, as well as the way interferon-mediated signaling is torpedoed by coronaviruses and in particular by SARS-CoV-2. Angiotensin converting enzyme 2 (ACE2) gene is one of the interferon response genes. Although for many scientists this fact could result in an adverse effect of interferon treatment in COVID-19 patients, ACE2 expression contributes to the balance of the renin-angiotensin system, which is greatly affected by SARS-CoV-2 in its internalization into the cell. This manuscript also includes the relationship between type I interferons and neutrophils, NETosis, and interleukin 17. Finally, under the subtitle of "take-home messages", we discuss the rationale behind a timely treatment with interferons in the context of COVID-19 is emphasized.
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Affiliation(s)
- Diana Garcia-del-Barco
- Neuroprotection Project, Center for Genetic Engineering and Biotechnology, Pharmaceutical Division, Havana, Cuba
| | - Daniela Risco-Acevedo
- Neuroprotection Project, Center for Genetic Engineering and Biotechnology, Pharmaceutical Division, Havana, Cuba
| | - Jorge Berlanga-Acosta
- Cytoprotection Project, Center for Genetic Engineering and Biotechnology, Pharmaceutical Division, Havana, Cuba
| | | | - Gerardo Guillén-Nieto
- Biomedical Research Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
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Song LG, Xie QX, Lao HL, Lv ZY. Human coronaviruses and therapeutic drug discovery. Infect Dis Poverty 2021; 10:28. [PMID: 33726861 PMCID: PMC7962087 DOI: 10.1186/s40249-021-00812-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
Background Coronaviruses (CoVs) are distributed worldwide and have various susceptible hosts; CoVs infecting humans are called human coronaviruses (HCoVs). Although HCoV-specific drugs are still lacking, many potent targets for drug discovery are being explored, and many vigorously designed clinical trials are being carried out in an orderly manner. The aim of this review was to gain a comprehensive understanding of the current status of drug development against HCoVs, particularly severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Main text A scoping review was conducted by electronically searching research studies, reviews, and clinical trials in PubMed and the CNKI. Studies on HCoVs and therapeutic drug discovery published between January 2000 and October 2020 and in English or Chinese were included, and the information was summarized. Of the 3248 studies identified, 159 publication were finally included. Advances in drug development against HCoV, especially SARS-CoV-2, are summarized under three categories: antiviral drugs aimed at inhibiting the HCoV proliferation process, drugs acting on the host's immune system, and drugs derived from plants with potent activity. Furthermore, clinical trials of drugs targeting SARS-CoV-2 are summarized. Conclusions During the spread of COVID-19 outbreak, great efforts have been made in therapeutic drug discovery against the virus, although the pharmacological effects and adverse reactions of some drugs under study are still unclear. However, well-designed high-quality studies are needed to further study the effectiveness and safety of these potential drugs so as to provide valid recommendations for better control of the COVID-19 pandemic. ![]()
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Affiliation(s)
- Lan-Gui Song
- The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, China.
| | - Qing-Xing Xie
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Hui-Lin Lao
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zhi-Yue Lv
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China. .,NHC Key Laboratory of Control of Tropical Diseases, the First Affiliated Hospital, Hainan Medical University, Haikou, China. .,Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, China.
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74
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Pei J, Wagner ND, Zou AJ, Chatterjee S, Borek D, Cole AR, Kim PJ, Basler CF, Otwinowski Z, Gross ML, Amarasinghe GK, Leung DW. Structural basis for IFN antagonism by human respiratory syncytial virus nonstructural protein 2. Proc Natl Acad Sci U S A 2021; 118:e2020587118. [PMID: 33649232 PMCID: PMC7958447 DOI: 10.1073/pnas.2020587118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Human respiratory syncytial virus (RSV) nonstructural protein 2 (NS2) inhibits host interferon (IFN) responses stimulated by RSV infection by targeting early steps in the IFN-signaling pathway. But the molecular mechanisms related to how NS2 regulates these processes remain incompletely understood. To address this gap, here we solved the X-ray crystal structure of NS2. This structure revealed a unique fold that is distinct from other known viral IFN antagonists, including RSV NS1. We also show that NS2 directly interacts with an inactive conformation of the RIG-I-like receptors (RLRs) RIG-I and MDA5. NS2 binding prevents RLR ubiquitination, a process critical for prolonged activation of downstream signaling. Structural analysis, including by hydrogen-deuterium exchange coupled to mass spectrometry, revealed that the N terminus of NS2 is essential for binding to the RIG-I caspase activation and recruitment domains. N-terminal mutations significantly diminish RIG-I interactions and result in increased IFNβ messenger RNA levels. Collectively, our studies uncover a previously unappreciated regulatory mechanism by which NS2 further modulates host responses and define an approach for targeting host responses.
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Affiliation(s)
- Jingjing Pei
- John T. Milliken Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Nicole D Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63110
| | - Angela J Zou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Srirupa Chatterjee
- John T. Milliken Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Dominika Borek
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Aidan R Cole
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Preston J Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303
| | - Zbyszek Otwinowski
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63110
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Daisy W Leung
- John T. Milliken Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110;
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
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75
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Vieira C, Nery L, Martins L, Jabour L, Dias R, Simões E Silva AC. Downregulation of Membrane-bound Angiotensin Converting Enzyme 2 (ACE2) Receptor has a Pivotal Role in COVID-19 Immunopathology. Curr Drug Targets 2021; 22:254-281. [PMID: 33081670 DOI: 10.2174/1389450121666201020154033] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/06/2020] [Accepted: 09/22/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The Coronavirus Disease 2019 (COVID-19) is becoming the major health issue in recent human history with thousands of deaths and millions of cases worldwide. Newer research and old experience with other coronaviruses highlighted a probable underlying mechanism of disturbance of the renin-angiotensin system (RAS) that is associated with the intrinsic effects of SARS-CoV-2 infection. OBJECTIVE In this review, we aimed to describe the intimate connections between the RAS components, the immune system and COVID-19 pathophysiology. METHODS This non-systematic review article summarizes recent evidence on the relationship between COVID-19 and the RAS. RESULTS Several studies have indicated that the downregulation of membrane-bound ACE2 may exert a key role for the impairment of immune functions and for COVID-19 patients' outcomes. The downregulation may occur by distinct mechanisms, particularly: (1) the shedding process induced by the SARS-CoV-2 fusion pathway, which reduces the amount of membrane-bound ACE2, stimulating more shedding by the high levels of Angiotensin II; (2) the endocytosis of ACE2 receptor with the virus itself and (3) by the interferon inhibition caused by SARS-CoV-2 effects on the immune system, which leads to a reduction of ACE2 receptor expression. CONCLUSION Recent research provides evidence of a reduction of the components of the alternative RAS axis, including ACE2 and Angiotensin-(1-7). In contrast, increased levels of Angiotensin II can activate the AT1 receptor in several organs. Consequently, increased inflammation, thrombosis and angiogenesis occur in patients infected with SARS-COV-2. Attention should be paid to the interactions of the RAS and COVID-19, mainly in the context of novel vaccines and proposed medications.
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Affiliation(s)
- Cristina Vieira
- Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Lucas Nery
- Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Ludimila Martins
- Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Luiz Jabour
- Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Raphael Dias
- Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Ana Cristina Simões E Silva
- Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
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76
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Teodorescu M. An Overview of a Year with COVID-19: What We Know? ELECTRONIC JOURNAL OF GENERAL MEDICINE 2021. [DOI: 10.29333/ejgm/9765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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77
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Mehrzadi S, Karimi MY, Fatemi A, Reiter RJ, Hosseinzadeh A. SARS-CoV-2 and other coronaviruses negatively influence mitochondrial quality control: beneficial effects of melatonin. Pharmacol Ther 2021; 224:107825. [PMID: 33662449 PMCID: PMC7919585 DOI: 10.1016/j.pharmthera.2021.107825] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/25/2020] [Accepted: 02/22/2021] [Indexed: 12/19/2022]
Abstract
Coronaviruses (CoVs) are a group of single stranded RNA viruses, of which some of them such as SARS-CoV, MERS-CoV, and SARS-CoV-2 are associated with deadly worldwide human diseases. Coronavirus disease-2019 (COVID-19), a condition caused by SARS-CoV-2, results in acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) associated with high mortality in the elderly and in people with underlying comorbidities. Results from several studies suggest that CoVs localize in mitochondria and interact with mitochondrial protein translocation machinery to target their encoded products to mitochondria. Coronaviruses encode a number of proteins; this process is essential for viral replication through inhibiting degradation of viral proteins and host misfolded proteins including those in mitochondria. These viruses seem to maintain their replication by altering mitochondrial dynamics and targeting mitochondrial-associated antiviral signaling (MAVS), allowing them to evade host innate immunity. Coronaviruses infections such as COVID-19 are more severe in aging patients. Since endogenous melatonin levels are often dramatically reduced in the aged and because it is a potent anti-inflammatory agent, melatonin has been proposed to be useful in CoVs infections by altering proteasomal and mitochondrial activities. Melatonin inhibits mitochondrial fission due to its antioxidant and inhibitory effects on cytosolic calcium overload. The collective data suggests that melatonin may mediate mitochondrial adaptations through regulating both mitochondrial dynamics and biogenesis. We propose that melatonin may inhibit SARS-CoV-2-induced cell damage by regulating mitochondrial physiology.
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Affiliation(s)
- Saeed Mehrzadi
- Razi Drug Research Center, Iran University of Medical Sciences, Tehran, Iran
| | | | - Alireza Fatemi
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Russel J Reiter
- Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Azam Hosseinzadeh
- Razi Drug Research Center, Iran University of Medical Sciences, Tehran, Iran.
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78
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Tabibzadeh A, Esghaei M, Soltani S, Yousefi P, Taherizadeh M, Safarnezhad Tameshkel F, Golahdooz M, Panahi M, Ajdarkosh H, Zamani F, Karbalaie Niya MH. Evolutionary study of COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as an emerging coronavirus: Phylogenetic analysis and literature review. Vet Med Sci 2021; 7:559-571. [PMID: 33210477 PMCID: PMC7753621 DOI: 10.1002/vms3.394] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/12/2020] [Accepted: 10/25/2020] [Indexed: 12/22/2022] Open
Abstract
Since emerging coronaviruses have always become a human health concern globally especially severe acute respiratory syndrome coronavirus 2 (SARS-CoV) and Middle East respiratory syndrome coronavirus and a novel coronavirus was introduced in Wuhan, China, in December 2019 (called SARS-CoV-2), many researchers focused on its epidemics, virological and clinical features. SARS-CoV-2 is classified as Betacoronaviruses genus and Sarbecovirus subgenus (lineage B). The virus shows a great similarity with SARS-CoV and bat SARS-like coronaviruses. In this study, we evaluate SARS-CoV-2 virus phylogeny and evolution by using current virus and related sequences.
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Affiliation(s)
- Alireza Tabibzadeh
- Department of VirologyFaculty of MedicineIran University of Medical SciencesTehranIran
| | - Maryam Esghaei
- Department of VirologyFaculty of MedicineIran University of Medical SciencesTehranIran
| | - Saber Soltani
- Department of VirologyFaculty of Public HealthTehran University of Medical SciencesTehranIran
| | - Parastoo Yousefi
- Department of VirologyFaculty of MedicineIran University of Medical SciencesTehranIran
| | - Mahsa Taherizadeh
- Department of VirologyRabies Research CenterPasteur Institute of IranTehranIran
| | | | - Mahsa Golahdooz
- Department of VirologyRabies Research CenterPasteur Institute of IranTehranIran
| | - Mahshid Panahi
- Gastrointestinal and Liver Diseases Research CenterIran University of Medical SciencesTehranIran
| | - Hossein Ajdarkosh
- Gastrointestinal and Liver Diseases Research CenterIran University of Medical SciencesTehranIran
| | - Farhad Zamani
- Gastrointestinal and Liver Diseases Research CenterIran University of Medical SciencesTehranIran
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79
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Fu YZ, Wang SY, Zheng ZQ, Yi Huang, Li WW, Xu ZS, Wang YY. SARS-CoV-2 membrane glycoprotein M antagonizes the MAVS-mediated innate antiviral response. Cell Mol Immunol 2021; 18:613-620. [PMID: 33110251 PMCID: PMC7588591 DOI: 10.1038/s41423-020-00571-x] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/29/2020] [Indexed: 12/30/2022] Open
Abstract
A novel SARS-related coronavirus (SARS-CoV-2) has recently emerged as a serious pathogen that causes high morbidity and substantial mortality. However, the mechanisms by which SARS-CoV-2 evades host immunity remain poorly understood. Here, we identified SARS-CoV-2 membrane glycoprotein M as a negative regulator of the innate immune response. We found that the M protein interacted with the central adaptor protein MAVS in the innate immune response pathways. This interaction impaired MAVS aggregation and its recruitment of downstream TRAF3, TBK1, and IRF3, leading to attenuation of the innate antiviral response. Our findings reveal a mechanism by which SARS-CoV-2 evades the innate immune response and suggest that the M protein of SARS-CoV-2 is a potential target for the development of SARS-CoV-2 interventions.
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Affiliation(s)
- Yu-Zhi Fu
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071, Wuhan, China.
| | - Su-Yun Wang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071, Wuhan, China
| | - Zhou-Qin Zheng
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071, Wuhan, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yi Huang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071, Wuhan, China
| | - Wei-Wei Li
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071, Wuhan, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhi-Sheng Xu
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071, Wuhan, China
| | - Yan-Yi Wang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071, Wuhan, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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Khorramdelazad H, Kazemi MH, Najafi A, Keykhaee M, Zolfaghari Emameh R, Falak R. Immunopathological similarities between COVID-19 and influenza: Investigating the consequences of Co-infection. Microb Pathog 2021; 152:104554. [PMID: 33157216 PMCID: PMC7607235 DOI: 10.1016/j.micpath.2020.104554] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a global public health emergency since December 2019, and so far, more than 980,000 people (until September 24, 2020) around the world have died. SARS-CoV-2 mimics the influenza virus regarding methods and modes of transmission, clinical features, related immune responses, and seasonal coincidence. Accordingly, co-infection by these viruses is imaginable because some studies have reported several cases with SARS-CoV-2 and influenza virus co-infection. Given the importance of the mentioned co-infection and the coming influenza season, it is essential to recognize the similarities and differences between the symptoms, immunopathogenesis and treatment of SARS-CoV-2 and influenza virus. Therefore, we reviewed the virology, clinical features, and immunopathogenesis of both influenza virus and SARS-CoV-2 and evaluated outcomes in cases with SARS-CoV-2 and influenza virus co-infection.
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Affiliation(s)
- Hossein Khorramdelazad
- Department of Immunology, School of Medicine, Molecular Medicine Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran; Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hossein Kazemi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Najafi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Keykhaee
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 14965/161, Tehran, Iran
| | - Reza Falak
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran.
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Triggle CR, Bansal D, Ding H, Islam MM, Farag EABA, Hadi HA, Sultan AA. A Comprehensive Review of Viral Characteristics, Transmission, Pathophysiology, Immune Response, and Management of SARS-CoV-2 and COVID-19 as a Basis for Controlling the Pandemic. Front Immunol 2021; 12:631139. [PMID: 33717166 PMCID: PMC7952616 DOI: 10.3389/fimmu.2021.631139] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/26/2021] [Indexed: 12/15/2022] Open
Abstract
COVID-19 emerged from China in December 2019 and during 2020 spread to every continent including Antarctica. The coronavirus, SARS-CoV-2, has been identified as the causative pathogen, and its spread has stretched the capacities of healthcare systems and negatively affected the global economy. This review provides an update on the virus, including the genome, the risks associated with the emergence of variants, mode of transmission, immune response, COVID-19 in children and the elderly, and advances made to contain, prevent and manage the disease. Although our knowledge of the mechanics of virus transmission and the immune response has been substantially demystified, concerns over reinfection, susceptibility of the elderly and whether asymptomatic children promote transmission remain unanswered. There are also uncertainties about the pathophysiology of COVID-19 and why there are variations in clinical presentations and why some patients suffer from long lasting symptoms-"the long haulers." To date, there are no significantly effective curative drugs for COVID-19, especially after failure of hydroxychloroquine trials to produce positive results. The RNA polymerase inhibitor, remdesivir, facilitates recovery of severely infected cases but, unlike the anti-inflammatory drug, dexamethasone, does not reduce mortality. However, vaccine development witnessed substantial progress with several being approved in countries around the globe.
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Affiliation(s)
- Chris R. Triggle
- Department of Pharmacology, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Devendra Bansal
- Department of Health Protection & Communicable Diseases Control, Ministry of Public Health, Doha, Qatar
| | - Hong Ding
- Department of Pharmacology, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Md Mazharul Islam
- Department of Animal Resources, Ministry of Municipality and Environment, Doha, Qatar
| | | | - Hamad Abdel Hadi
- Communicable Diseases Centre, Hamad Medical Corporations, Doha, Qatar
| | - Ali A. Sultan
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Doha, Qatar
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Kalhori MR, Saadatpour F, Arefian E, Soleimani M, Farzaei MH, Aneva IY, Echeverría J. The Potential Therapeutic Effect of RNA Interference and Natural Products on COVID-19: A Review of the Coronaviruses Infection. Front Pharmacol 2021; 12:616993. [PMID: 33716745 PMCID: PMC7953353 DOI: 10.3389/fphar.2021.616993] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/14/2021] [Indexed: 01/08/2023] Open
Abstract
The SARS-CoV-2 virus was reported for the first time in Wuhan, Hubei Province, China, and causes respiratory infection. This pandemic pneumonia killed about 1,437,835 people out of 61,308,161cases up to November 27, 2020. The disease's main clinical complications include fever, recurrent coughing, shortness of breath, acute respiratory syndrome, and failure of vital organs that could lead to death. It has been shown that natural compounds with antioxidant, anticancer, and antiviral activities and RNA interference agents could play an essential role in preventing or treating coronavirus infection by inhibiting the expression of crucial virus genes. This study aims to introduce a summary of coronavirus's genetic and morphological structure and determine the role of miRNAs, siRNAs, chemical drugs, and natural compounds in stimulating the immune system or inhibiting the virus's structural and non-structural genes that are essential for replication and infection of SARS-CoV-2.
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Affiliation(s)
- Mohammad Reza Kalhori
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Fatemeh Saadatpour
- Molecular Virology Lab, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Ehsan Arefian
- Molecular Virology Lab, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Masoud Soleimani
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Hosien Farzaei
- Medical Technology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ina Yosifova Aneva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Javier Echeverría
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
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83
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Mohammed MEA. SARS-CoV-2 proteins: Are they useful as targets for COVID-19 drugs and vaccines? Curr Mol Med 2021; 22:50-66. [PMID: 33622224 DOI: 10.2174/1566524021666210223143243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 11/22/2022]
Abstract
The proteins of coronavirus are classified to nonstructural, structural, and accessory. There are 16 nonstructural viral proteins beside their precursors (1a and 1ab polyproteins). The nonstructural proteins are named as nsp1 to nsp16 and they act as enzymes, coenzymes, and binding proteins to facilitate the replication, transcription, and translation of the virus. The structural proteins are bound to the RNA in the nucleocapsid (N- protein) or to the lipid bilayer membrane of the viral envelope. The lipid bilayer proteins include the membrane protein (M), envelope protein (E), and spike protein (S). Beside their role as structural proteins, they are essential for the host cells binding and invasion. The SARS-CoV-2 contains six accessory proteins which participates in the viral replication, assembly and virus- host interactions. The SARS-CoV-2 accessory proteins are orf3a, orf6, orf7a, orf7b, orf8, and orf10. The functions of the SARS-CoV-2 are not well known, while the functions of their corresponding proteins in SARS-CoV are either well known or poorly studied. Recently, the Oxford University and Pfizer and BioNTech made SARS-CoV-2 vaccines through targeting the spike protein gene. The US Food and Drug Administration (FDA) and the health authorities of the United Kingdom approved and started vaccination using the Pfizer and BioNTech mRNA vaccine. Also, The FDA of USA approved the treatment of COVID-19 using two monoclonal antibodies produced by Regeneron pharmaceuticals to target the spike protein. The SARS-CoV-2 proteins can be used for the diagnosis, as drug targets and in vaccination trials for COVID-19. For future COVID-19 research, more efforts should be done to elaborate the functions and structure of the SARS-CoV-2 proteins so as to use them as targets for COVID-19 drug and vaccines. Special attention should be drawn to extensive research on the SARS-CoV-2 nsp3, orf8, and orf10.
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84
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Zhou Z, Sun Y, Xu J, Tang X, Zhou L, Li Q, Lan T, Ma J. Swine Acute Diarrhea Syndrome Coronavirus Nucleocapsid Protein Antagonizes Interferon- β Production via Blocking the Interaction Between TRAF3 and TBK1. Front Immunol 2021; 12:573078. [PMID: 33692778 PMCID: PMC7937869 DOI: 10.3389/fimmu.2021.573078] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/15/2021] [Indexed: 01/19/2023] Open
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV), first discovered in 2017, is a porcine enteric coronavirus that can cause acute diarrhea syndrome (SADS) in piglets. Here, we studied the role of SADS-CoV nucleocapsid (N) protein in innate immunity. Our results showed that SADS-CoV N protein could inhibit type I interferon (IFN) production mediated by Sendai virus (Sev) and could block the phosphorylation and nuclear translocation of interferon regulatory factor 3 (IRF3). Simultaneously, the IFN-β promoter activity mediated by TANK binding kinase 1 (TBK1) or its upstream molecules in the RLRs signal pathway was inhibited by SADS-CoV N protein. Further investigations revealed that SADS-CoV N protein could counteract interaction between TNF receptor-associated factor 3 (TRAF3) and TBK1, which led to reduced TBK1 activation and IFN-β production. Our study is the first report of the interaction between SADS-CoV N protein and the host antiviral innate immune responses, and the mechanism utilized by SADS-CoV N protein provides a new insight of coronaviruses evading host antiviral innate immunity.
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Affiliation(s)
- Zhihai Zhou
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Yuan Sun
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Jingya Xu
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Xiaoyu Tang
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Ling Zhou
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Qianniu Li
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Tian Lan
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Jingyun Ma
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
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85
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Wahl A, Gralinski LE, Johnson CE, Yao W, Kovarova M, Dinnon KH, Liu H, Madden VJ, Krzystek HM, De C, White KK, Gully K, Schäfer A, Zaman T, Leist SR, Grant PO, Bluemling GR, Kolykhalov AA, Natchus MG, Askin FB, Painter G, Browne EP, Jones CD, Pickles RJ, Baric RS, Garcia JV. SARS-CoV-2 infection is effectively treated and prevented by EIDD-2801. Nature 2021; 591:451-457. [PMID: 33561864 PMCID: PMC7979515 DOI: 10.1038/s41586-021-03312-w] [Citation(s) in RCA: 269] [Impact Index Per Article: 89.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/29/2021] [Indexed: 12/31/2022]
Abstract
All known recently emerged human coronaviruses likely originated in bats1. Here, we used a single experimental platform based on human lung-only mice (LoM) to demonstrate efficient in vivo replication of all recently emerged human coronaviruses (SARS-CoV, MERS-CoV, SARS-CoV-2) and two highly relevant endogenous pre-pandemic SARS-like bat coronaviruses. Virus replication in this model occurs in bona fide human lung tissue and does not require any type of adaptation of the virus or the host. Our results indicate that bats harbor endogenous coronaviruses capable of direct transmission into humans. Further detailed analysis of pandemic SARS-CoV-2 in vivo infection of LoM human lung tissue showed predominant infection of human lung epithelial cells, including type II pneumocytes present in alveoli and ciliated airway cells. Acute SARS-CoV-2 infection was highly cytopathic and induced a robust and sustained Type I interferon and inflammatory cytokine/chemokine response. Finally, we evaluated a therapeutic and pre-exposure prophylaxis strategy for coronavirus infection. Our results show that therapeutic and prophylactic administration of EIDD-2801, an oral broad spectrum antiviral currently in phase II-III clinical trials, dramatically inhibited SARS-CoV-2 replication in vivo and thus has significant potential for the prevention and treatment of COVID-19.
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Affiliation(s)
- Angela Wahl
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Claire E Johnson
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wenbo Yao
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Martina Kovarova
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth H Dinnon
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hongwei Liu
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Victoria J Madden
- Microscopy Services Laboratory, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Halina M Krzystek
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chandrav De
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kristen K White
- Microscopy Services Laboratory, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kendra Gully
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tanzila Zaman
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paul O Grant
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gregory R Bluemling
- Emory Institute of Drug Development (EIDD), Emory University, Atlanta, GA, USA.,Drug Innovation Ventures at Emory (DRIVE), Atlanta, GA, USA
| | - Alexander A Kolykhalov
- Emory Institute of Drug Development (EIDD), Emory University, Atlanta, GA, USA.,Drug Innovation Ventures at Emory (DRIVE), Atlanta, GA, USA
| | | | - Frederic B Askin
- Department of Pathology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - George Painter
- Emory Institute of Drug Development (EIDD), Emory University, Atlanta, GA, USA.,Drug Innovation Ventures at Emory (DRIVE), Atlanta, GA, USA.,Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA, USA
| | - Edward P Browne
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Raymond J Pickles
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Marsico Lung Institute, University of North Carolina at Chapel, Chapel Hill, NC, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J Victor Garcia
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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86
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Prates ET, Garvin MR, Pavicic M, Jones P, Shah M, Demerdash O, Amos BK, Geiger A, Jacobson D. Potential Pathogenicity Determinants Identified from Structural Proteomics of SARS-CoV and SARS-CoV-2. Mol Biol Evol 2021; 38:702-715. [PMID: 32941612 PMCID: PMC7543629 DOI: 10.1093/molbev/msaa231] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Despite SARS-CoV and SARS-CoV-2 being equipped with highly similar protein arsenals, the corresponding zoonoses have spread among humans at extremely different rates. The specific characteristics of these viruses that led to such distinct outcomes remain unclear. Here, we apply proteome-wide comparative structural analysis aiming to identify the unique molecular elements in the SARS-CoV-2 proteome that may explain the differing consequences. By combining protein modeling and molecular dynamics simulations, we suggest nonconservative substitutions in functional regions of the spike glycoprotein (S), nsp1, and nsp3 that are contributing to differences in virulence. Particularly, we explain why the substitutions at the receptor-binding domain of S affect the structure–dynamics behavior in complexes with putative host receptors. Conservation of functional protein regions within the two taxa is also noteworthy. We suggest that the highly conserved main protease, nsp5, of SARS-CoV and SARS-CoV-2 is part of their mechanism of circumventing the host interferon antiviral response. Overall, most substitutions occur on the protein surfaces and may be modulating their antigenic properties and interactions with other macromolecules. Our results imply that the striking difference in the pervasiveness of SARS-CoV-2 and SARS-CoV among humans seems to significantly derive from molecular features that modulate the efficiency of viral particles in entering the host cells and blocking the host immune response.
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Affiliation(s)
- Erica T Prates
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN.,National Virtual Biotechnology Laboratory, US Department of Energy, TN
| | - Michael R Garvin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN.,National Virtual Biotechnology Laboratory, US Department of Energy, TN
| | - Mirko Pavicic
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN.,National Virtual Biotechnology Laboratory, US Department of Energy, TN
| | - Piet Jones
- National Virtual Biotechnology Laboratory, US Department of Energy, TN.,The Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee Knoxville, Knoxville, TN
| | - Manesh Shah
- Genome Science and Technology, The University of Tennessee Knoxville, Knoxville, TN
| | - Omar Demerdash
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - B Kirtley Amos
- Department of Horticulture, N-318 Ag Sciences Center, University of Kentucky, Lexington, KY
| | - Armin Geiger
- National Virtual Biotechnology Laboratory, US Department of Energy, TN.,The Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee Knoxville, Knoxville, TN
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN.,National Virtual Biotechnology Laboratory, US Department of Energy, TN.,The Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee Knoxville, Knoxville, TN.,Genome Science and Technology, The University of Tennessee Knoxville, Knoxville, TN.,Department of Psychology, The University of Tennessee Knoxville, Knoxville, TN
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87
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Woodby B, Arnold MM, Valacchi G. SARS-CoV-2 infection, COVID-19 pathogenesis, and exposure to air pollution: What is the connection? Ann N Y Acad Sci 2021; 1486:15-38. [PMID: 33022781 PMCID: PMC7675684 DOI: 10.1111/nyas.14512] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/11/2020] [Accepted: 09/21/2020] [Indexed: 12/20/2022]
Abstract
Exposure to air pollutants has been previously associated with respiratory viral infections, including influenza, measles, mumps, rhinovirus, and respiratory syncytial virus. Epidemiological studies have also suggested that air pollution exposure is associated with increased cases of SARS-CoV-2 infection and COVID-19-associated mortality, although the molecular mechanisms by which pollutant exposure affects viral infection and pathogenesis of COVID-19 remain unknown. In this review, we suggest potential molecular mechanisms that could account for this association. We have focused on the potential effect of exposure to nitrogen dioxide (NO2 ), ozone (O3 ), and particulate matter (PM) since there are studies investigating how exposure to these pollutants affects the life cycle of other viruses. We have concluded that pollutant exposure may affect different stages of the viral life cycle, including inhibition of mucociliary clearance, alteration of viral receptors and proteases required for entry, changes to antiviral interferon production and viral replication, changes in viral assembly mediated by autophagy, prevention of uptake by macrophages, and promotion of viral spread by increasing epithelial permeability. We believe that exposure to pollutants skews adaptive immune responses toward bacterial/allergic immune responses, as opposed to antiviral responses. Exposure to air pollutants could also predispose exposed populations toward developing COIVD-19-associated immunopathology, enhancing virus-induced tissue inflammation and damage.
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Affiliation(s)
- Brittany Woodby
- Animal Science DepartmentPlants for Human Health Institute, N.C. Research Campus, North Carolina State UniversityKannapolisNorth Carolina
| | - Michelle M. Arnold
- Department of Microbiology and ImmunologyCenter for Molecular and Tumor VirologyLouisiana State University Health Sciences CenterShreveportLouisiana
| | - Giuseppe Valacchi
- Animal Science DepartmentPlants for Human Health Institute, N.C. Research Campus, North Carolina State UniversityKannapolisNorth Carolina
- Department of Life Sciences and BiotechnologyUniversity of FerraraFerraraItaly
- Department of Food and NutritionKyung Hee UniversitySeoulSouth Korea
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88
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Mdkhana B, Saheb Sharif-Askari N, Ramakrishnan RK, Goel S, Hamid Q, Halwani R. Nucleic Acid-Sensing Pathways During SARS-CoV-2 Infection: Expectations versus Reality. J Inflamm Res 2021; 14:199-216. [PMID: 33531826 PMCID: PMC7847386 DOI: 10.2147/jir.s277716] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/16/2020] [Indexed: 12/22/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has affected millions of people and crippled economies worldwide. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for this pandemic has triggered avid research on its pathobiology to better understand the pathophysiology of COVID-19. In the absence of approved antiviral therapeutic strategies or vaccine platforms capable of effectively targeting this global threat, the hunt for effective therapeutics has led to many candidates being actively evaluated for their efficacy in controlling or preventing COVID-19. In this review, we gathered current evidence on the innate nucleic acid-sensing pathways expected to be elicited by SARS-CoV-2 and the immune evasion mechanisms they have developed to promote viral replication and infection. Within the nucleic acid-sensing pathways, SARS-CoV-2 infection and evasion mechanisms trigger the activation of NOD-signaling and NLRP3 pathways leading to the production of inflammatory cytokines, IL-1β and IL-6, while muting or blocking cGAS-STING and interferon type I and III pathways, resulting in decreased production of antiviral interferons and delayed innate response. Therefore, blocking the inflammatory arm and boosting the interferon production arm of nucleic acid-sensing pathways could facilitate early control of viral replication and dissemination, prevent disease progression, and cytokine storm development. We also discuss the rationale behind therapeutic modalities targeting these sensing pathways and their implications in the treatment of COVID-19.
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Affiliation(s)
- Bushra Mdkhana
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Narjes Saheb Sharif-Askari
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Rakhee K Ramakrishnan
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Swati Goel
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Qutayba Hamid
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Meakins-Christie Laboratories, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Rabih Halwani
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
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89
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Ng CS, Stobart CC, Luo H. Innate immune evasion mediated by picornaviral 3C protease: Possible lessons for coronaviral 3C-like protease? Rev Med Virol 2021; 31:1-22. [PMID: 33624382 PMCID: PMC7883238 DOI: 10.1002/rmv.2206] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 01/10/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 is the etiological agent of the ongoing pandemic of coronavirus disease-2019, a multi-organ disease that has triggered an unprecedented global health and economic crisis. The virally encoded 3C-like protease (3CLpro ), which is named after picornaviral 3C protease (3Cpro ) due to their similarities in substrate recognition and enzymatic activity, is essential for viral replication and has been considered as the primary drug target. However, information regarding the cellular substrates of 3CLpro and its interaction with the host remains scarce, though recent work has begun to shape our understanding more clearly. Here we summarized and compared the mechanisms by which picornaviruses and coronaviruses have evolved to evade innate immune surveillance, with a focus on the established role of 3Cpro in this process. Through this comparison, we hope to highlight the potential action and mechanisms that are conserved and shared between 3Cpro and 3CLpro . In this review, we also briefly discussed current advances in the development of broad-spectrum antivirals targeting both 3Cpro and 3CLpro .
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Affiliation(s)
- Chen Seng Ng
- Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, Canada.,Department of Pathology and Laboratory of Medicine, University of British Columbia, Vancouver, Canada
| | | | - Honglin Luo
- Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, Canada.,Department of Pathology and Laboratory of Medicine, University of British Columbia, Vancouver, Canada
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90
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Bakadia BM, He F, Souho T, Lamboni L, Ullah MW, Boni BO, Ahmed AAQ, Mukole BM, Yang G. Prevention and treatment of COVID-19: Focus on interferons, chloroquine/hydroxychloroquine, azithromycin, and vaccine. Biomed Pharmacother 2021; 133:111008. [PMID: 33227708 PMCID: PMC7831445 DOI: 10.1016/j.biopha.2020.111008] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/03/2020] [Accepted: 11/08/2020] [Indexed: 12/16/2022] Open
Abstract
The ongoing pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has drawn the attention of researchers and clinicians from several disciplines and sectors who are trying to find durable solutions both at preventive and treatment levels. To date, there is no approved effective treatment or vaccine available to control the coronavirus disease-2019 (COVID-19). The preliminary in vitro studies on viral infection models showed potential antiviral activities of type I and III interferons (IFNs), chloroquine (CQ)/hydroxychloroquine (HCQ), and azithromycin (AZM); however, the clinical studies on COVID-19 patients treated with CQ/HCQ and AZM led to controversies in different regions due to their adverse side effects, as well as their combined treatment could prolong the QT interval. Interestingly, the treatment with type I IFNs showed encouraging results. Moreover, the different preliminary reports of COVID-19 candidate vaccines showcase promising results by inducing the production of a high level of neutralizing antibodies (NAbs) and specific T cell-mediated immune response in almost all participants. The present review aims to summarize and analyze the recent progress evidence concerning the use of IFNs, CQ/HCQ, and AZM for the treatment of COVID-19. The available data on immunization options to prevent the COVID-19 are also analyzed with the aim to present the promising options which could be investigated in future for sustainable control of the pandemic.
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Affiliation(s)
- Bianza Moise Bakadia
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China; Institut Supérieur des Techniques Médicales de Lubumbashi, Lubumbashi, Democratic Republic of the Congo
| | - Feng He
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang 43800, PR China.
| | - Tiatou Souho
- Laboratoire de Biochimie des Aliments et Nutrition, Faculté des Sciences et Techniques, Université de Kara, Kara, Togo
| | - Lallepak Lamboni
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China; Laboratoire de Biologie Moléculaire et Virologie, Institut National d'Hygiène-Togo, 26 Rue Nangbéto, Quartier Administratif- PO. Box 1396, Lomé, Togo
| | - Muhammad Wajid Ullah
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China.
| | - Biaou Ode Boni
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Abeer Ahmed Qaed Ahmed
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Biampata Mutu Mukole
- Institut National de Recherche Biomédicale, Ministère de la Santé, Democratic Republic of the Congo
| | - Guang Yang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China.
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91
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Xu D, Biswal M, Neal A, Hai R. Review Devil's tools: SARS-CoV-2 antagonists against innate immunity. CURRENT RESEARCH IN VIROLOGICAL SCIENCE 2021; 2:100013. [PMID: 34812428 PMCID: PMC8598260 DOI: 10.1016/j.crviro.2021.100013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 04/22/2023]
Abstract
The unprecedented Coronavirus pandemic of 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Like other coronaviruses, to establish its infection, SARS-CoV-2 is required to overcome the innate interferon (IFN) response, which is the first line of host defense. SARS-CoV-2 has also developed complex antagonism approaches involving almost all its encoding viral proteins. Here, we summarize our current understanding of these different viral factors and their roles in suppressing IFN responses. Some of them are conserved IFN evasion strategies used by SARS-CoV; others are novel countermeasures only employed by SARS-CoV-2. The filling of gaps in understanding these underlying mechanisms will provide rationale guidance for applying IFN treatment against SARS-CoV-2 infection.
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Affiliation(s)
- Duo Xu
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA, USA
| | - Mahamaya Biswal
- Department of Biochemistry, University of California-Riverside, Riverside, CA, USA
| | - Arrmund Neal
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA, USA
| | - Rong Hai
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA, USA
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92
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Zheng Y, Zhuang MW, Han L, Zhang J, Nan ML, Zhan P, Kang D, Liu X, Gao C, Wang PH. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) membrane (M) protein inhibits type I and III interferon production by targeting RIG-I/MDA-5 signaling. Signal Transduct Target Ther 2020; 5:299. [PMID: 33372174 PMCID: PMC7768267 DOI: 10.1038/s41392-020-00438-7] [Citation(s) in RCA: 213] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 11/05/2020] [Accepted: 11/16/2020] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has quickly spread worldwide and has affected more than 10 million individuals. A typical feature of COVID-19 is the suppression of type I and III interferon (IFN)-mediated antiviral immunity. However, the molecular mechanism by which SARS-CoV-2 evades antiviral immunity remains elusive. Here, we reported that the SARS-CoV-2 membrane (M) protein inhibits the production of type I and III IFNs induced by the cytosolic dsRNA-sensing pathway mediated by RIG-I/MDA-5-MAVS signaling. In addition, the SARS-CoV-2 M protein suppresses type I and III IFN induction stimulated by SeV infection or poly (I:C) transfection. Mechanistically, the SARS-CoV-2 M protein interacts with RIG-I, MAVS, and TBK1, thus preventing the formation of the multiprotein complex containing RIG-I, MAVS, TRAF3, and TBK1 and subsequently impeding the phosphorylation, nuclear translocation, and activation of IRF3. Consequently, ectopic expression of the SARS-CoV-2 M protein facilitates the replication of vesicular stomatitis virus. Taken together, these results indicate that the SARS-CoV-2 M protein antagonizes type I and III IFN production by targeting RIG-I/MDA-5 signaling, which subsequently attenuates antiviral immunity and enhances viral replication. This study provides insight into the interpretation of SARS-CoV-2-induced antiviral immune suppression and illuminates the pathogenic mechanism of COVID-19.
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Affiliation(s)
- Yi Zheng
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, 250012, Jinan, China
| | - Meng-Wei Zhuang
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, 250012, Jinan, China
| | - Lulu Han
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, 250012, Jinan, China
| | - Jing Zhang
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, 250012, Jinan, China
| | - Mei-Ling Nan
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, 250012, Jinan, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Chengjiang Gao
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, 250012, Jinan, China.
| | - Pei-Hui Wang
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, 250012, Jinan, China.
- Suzhou Research Institute, Shandong University, Shandong University, Suzhou, Jiangsu, 215123, China.
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93
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Garvin MR, T Prates E, Pavicic M, Jones P, Amos BK, Geiger A, Shah MB, Streich J, Felipe Machado Gazolla JG, Kainer D, Cliff A, Romero J, Keith N, Brown JB, Jacobson D. Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Genome Biol 2020; 21:304. [PMID: 33357233 PMCID: PMC7756312 DOI: 10.1186/s13059-020-02191-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/29/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND A mechanistic understanding of the spread of SARS-CoV-2 and diligent tracking of ongoing mutagenesis are of key importance to plan robust strategies for confining its transmission. Large numbers of available sequences and their dates of transmission provide an unprecedented opportunity to analyze evolutionary adaptation in novel ways. Addition of high-resolution structural information can reveal the functional basis of these processes at the molecular level. Integrated systems biology-directed analyses of these data layers afford valuable insights to build a global understanding of the COVID-19 pandemic. RESULTS Here we identify globally distributed haplotypes from 15,789 SARS-CoV-2 genomes and model their success based on their duration, dispersal, and frequency in the host population. Our models identify mutations that are likely compensatory adaptive changes that allowed for rapid expansion of the virus. Functional predictions from structural analyses indicate that, contrary to previous reports, the Asp614Gly mutation in the spike glycoprotein (S) likely reduced transmission and the subsequent Pro323Leu mutation in the RNA-dependent RNA polymerase led to the precipitous spread of the virus. Our model also suggests that two mutations in the nsp13 helicase allowed for the adaptation of the virus to the Pacific Northwest of the USA. Finally, our explainable artificial intelligence algorithm identified a mutational hotspot in the sequence of S that also displays a signature of positive selection and may have implications for tissue or cell-specific expression of the virus. CONCLUSIONS These results provide valuable insights for the development of drugs and surveillance strategies to combat the current and future pandemics.
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Affiliation(s)
- Michael R Garvin
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Erica T Prates
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Mirko Pavicic
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Piet Jones
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - B Kirtley Amos
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- Department of Horticulture, N-318 Ag Sciences Center, University of Kentucky, Lexington, KY, USA
| | - Armin Geiger
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Manesh B Shah
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Jared Streich
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | | | - David Kainer
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Ashley Cliff
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Jonathon Romero
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Nathan Keith
- Lawrence Berkeley National Laboratory, Environmental Genomics & Systems Biology, Berkeley, CA, USA
| | - James B Brown
- Lawrence Berkeley National Laboratory, Environmental Genomics & Systems Biology, Berkeley, CA, USA
| | - Daniel Jacobson
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA.
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA.
- Department of Psychology, University of Tennessee Knoxville, Knoxville, TN, USA.
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94
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Wang P, Deng Y, Guo Y, Xu Z, Li Y, Ou X, Xie L, Lu M, Zhong J, Li B, Hu L, Deng S, Peng T, Cai M, Li M. Epstein-Barr Virus Early Protein BFRF1 Suppresses IFN-β Activity by Inhibiting the Activation of IRF3. Front Immunol 2020; 11:513383. [PMID: 33391252 PMCID: PMC7774019 DOI: 10.3389/fimmu.2020.513383] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 09/15/2020] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV) is the causative agent of infectious mononucleosis that is closely associated with several human malignant diseases, while type I interferon (IFN-I) plays an important role against EBV infection. As we all know, EBV can encode some proteins to inhibit the production of IFN-I, but it’s not clear whether other proteins also take part in this progress. EBV early lytic protein BFRF1 is shown to be involved in viral maturation, however, whether BFRF1 participates in the host innate immune response is still not well known. In this study, we found BFRF1 could down-regulate sendai virus-induced IFN-β promoter activity and mRNA expression of IFN-β and ISG54 during BFRF1 plasmid transfection and EBV lytic infection, but BFRF1 could not affect the promoter activity of NF-κB or IRF7. Specifically, BFRF1 could co-localize and interact with IKKi. Although BFRF1 did not interfere the interaction between IKKi and IRF3, it could block the kinase activity of IKKi, which finally inhibited the phosphorylation, dimerization, and nuclear translocation of IRF3. Taken together, BFRF1 may play a critical role in disrupting the host innate immunity by suppressing IFN-β activity during EBV lytic cycle.
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Affiliation(s)
- Ping Wang
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Yangxi Deng
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Yingjie Guo
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Zuo Xu
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Yiwen Li
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Xiaowen Ou
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Li Xie
- Centralab, Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Manjiao Lu
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Jiayi Zhong
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Bolin Li
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Li Hu
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Shenyu Deng
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Tao Peng
- State Key Laboratory of Respiratory Diseases, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China.,South China Vaccine Corporation Limited, Guangzhou, China
| | - Mingsheng Cai
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Meili Li
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
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95
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Yao C, Bora SA, Parimon T, Zaman T, Friedman OA, Palatinus JA, Surapaneni NS, Matusov YP, Cerro Chiang G, Kassar AG, Patel N, Green CER, Aziz AW, Suri H, Suda J, Lopez AA, Martins GA, Stripp BR, Gharib SA, Goodridge HS, Chen P. Cell-Type-Specific Immune Dysregulation in Severely Ill COVID-19 Patients. Cell Rep 2020; 34:108590. [PMID: 33357411 PMCID: PMC7744012 DOI: 10.1016/j.celrep.2020.108590] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/03/2020] [Accepted: 12/10/2020] [Indexed: 12/12/2022] Open
Abstract
Recent studies have demonstrated immunologic dysfunction in severely ill coronavirus disease 2019 (COVID-19) patients. We use single-cell RNA sequencing (scRNA-seq) to analyze the transcriptome of peripheral blood mononuclear cells (PBMCs) from healthy (n = 3) and COVID-19 patients with moderate disease (n = 5), acute respiratory distress syndrome (ARDS, n = 6), or recovering from ARDS (n = 6). Our data reveal transcriptomic profiles indicative of defective antigen presentation and interferon (IFN) responsiveness in monocytes from ARDS patients, which contrasts with higher responsiveness to IFN signaling in lymphocytes. Furthermore, genes involved in cytotoxic activity are suppressed in both natural killer (NK) and CD8 T lymphocytes, and B cell activation is deficient, which is consistent with delayed viral clearance in severely ill COVID-19 patients. Our study demonstrates that COVID-19 patients with ARDS have a state of immune imbalance in which dysregulation of both innate and adaptive immune responses may be contributing to a more severe disease course.
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Affiliation(s)
- Changfu Yao
- Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Stephanie A Bora
- Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Tanyalak Parimon
- Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Tanzira Zaman
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Oren A Friedman
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Joseph A Palatinus
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Nirmala S Surapaneni
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yuri P Matusov
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Giuliana Cerro Chiang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Alexander G Kassar
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Nayan Patel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Chelsi E R Green
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Adam W Aziz
- Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Harshpreet Suri
- Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jo Suda
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Andres A Lopez
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Gislâine A Martins
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Division of Gastroenterology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Barry R Stripp
- Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sina A Gharib
- Computational Medicine Core at Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA 98109, USA.
| | - Helen S Goodridge
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
| | - Peter Chen
- Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
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96
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Xiang Y, Zhang W, Jia P, Lu X, Liu W, Yi M, Jia K. E3 Ubiquitin Ligase RNF114 Inhibits Innate Immune Response to Red-Spotted Grouper Nervous Necrosis Virus Infection in Sea Perch by Targeting MAVS and TRAF3 to Mediate Their Degradation. THE JOURNAL OF IMMUNOLOGY 2020; 206:77-88. [DOI: 10.4049/jimmunol.2000083] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 10/20/2020] [Indexed: 01/25/2023]
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97
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Nainu F, Abidin RS, Bahar MA, Frediansyah A, Emran TB, Rabaan AA, Dhama K, Harapan H. SARS-CoV-2 reinfection and implications for vaccine development. Hum Vaccin Immunother 2020; 16:3061-3073. [PMID: 33393854 PMCID: PMC8641611 DOI: 10.1080/21645515.2020.1830683] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 09/07/2020] [Accepted: 09/25/2020] [Indexed: 12/21/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic continues to constitute a public health emergency of international concern. Multiple vaccine candidates for COVID-19, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have entered clinical trials. However, some evidence suggests that patients who have recovered from COVID-19 can be reinfected. For example, in China, two discharged COVID-19 patients who had recovered and fulfilled the discharge criteria for COVID-19 were retested positive to a reverse transcription polymerase chain reaction (RT-PCR) assay for the virus. This finding is critical and could hamper COVID-19 vaccine development. This review offers literature-based evidence of reinfection with SARS-CoV-2, provides explanation for the possibility of SARS-CoV-2 reinfection both from the agent and host points of view, and discusses its implication for COVID-19 vaccine development.
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Affiliation(s)
- Firzan Nainu
- Faculty of Pharmacy, Hasanuddin University, 90245, Tamalanrea, Makassar, Indonesia
| | - Rufika Shari Abidin
- Faculty of Medicine, Hasanuddin University, 90245, Tamalanrea, Makassar, Indonesia
| | - Muh. Akbar Bahar
- Faculty of Pharmacy, Hasanuddin University, 90245, Tamalanrea, Makassar, Indonesia
| | - Andri Frediansyah
- Research Division for Natural Product Technology (BPTBA), Indonesian Institute of Sciences (LIPI), 55861, Wonosari, Indonesia
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, 72076, Tübingen, Germany
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, 4381, Chittagong, Bangladesh
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, 31311, Dhahran, Saudi Arabia
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, 243122, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Harapan Harapan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, 23111, Banda Aceh, Indonesia
- Tropical Disease Centre, School of Medicine, Universitas Syiah Kuala, 23111, Banda Aceh, Indonesia
- Department of Microbiology, School of Medicine, Universitas Syiah Kuala, 23111, Banda Aceh, Indonesia
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98
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Xia H, Shi PY. Antagonism of Type I Interferon by Severe Acute Respiratory Syndrome Coronavirus 2. J Interferon Cytokine Res 2020; 40:543-548. [PMID: 33337934 PMCID: PMC7757701 DOI: 10.1089/jir.2020.0214] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2008] [Accepted: 11/14/2009] [Indexed: 12/21/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), warranting urgent study of the molecular mechanisms of SARS-CoV-2 infection and host immune response. Type I interferon (IFN-I) is a key component of host innate immune system responsible for eliminating the virus at the early stage of infection. In contrast, SARS-CoV-2 has evolved multiple strategies to evade innate immune response to facilitate viral replication, transmission, and pathogenesis. This review summarizes the recent progresses on SARS-CoV-2 proteins that antagonize host IFN-I production and/or signaling. These progresses have provided knowledge for new vaccine and antiviral development to prevent and control COVID-19.
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Affiliation(s)
- Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, USA
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99
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Lee S, Channappanavar R, Kanneganti TD. Coronaviruses: Innate Immunity, Inflammasome Activation, Inflammatory Cell Death, and Cytokines. Trends Immunol 2020; 41:1083-1099. [PMID: 33153908 PMCID: PMC7561287 DOI: 10.1016/j.it.2020.10.005] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022]
Abstract
The innate immune system acts as the first line of defense against pathogens, including coronaviruses (CoVs). Severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV are epidemic zoonotic CoVs that emerged at the beginning of the 21st century. The recently emerged virus SARS-CoV-2 is a novel strain of CoV that has caused the coronavirus 2019 (COVID-19) pandemic. Scientific advancements made by studying the SARS-CoV and MERS-CoV outbreaks have provided a foundation for understanding pathogenesis and innate immunity against SARS-CoV-2. In this review, we focus on our present understanding of innate immune responses, inflammasome activation, inflammatory cell death pathways, and cytokine secretion during SARS-CoV, MERS-CoV, and SARS-CoV-2 infection. We also discuss how the pathogenesis of these viruses influences these biological processes.
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Affiliation(s)
- SangJoon Lee
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Rudragouda Channappanavar
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN 38163, USA; Department of Acute and Tertiary Care, University of Tennessee Health Sciences Center, Memphis, TN 38163, USA
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100
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Ahluwalia P, Ahluwalia M, Vaibhav K, Mondal A, Sahajpal N, Islam S, Fulzele S, Kota V, Dhandapani K, Baban B, Rojiani AM, Kolhe R. Infections of the lung: a predictive, preventive and personalized perspective through the lens of evolution, the emergence of SARS-CoV-2 and its pathogenesis. EPMA J 2020; 11:581-601. [PMID: 33204369 PMCID: PMC7661834 DOI: 10.1007/s13167-020-00230-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/02/2020] [Indexed: 12/13/2022]
Abstract
The long evolutionary battle between humans and pathogens has played an important role in shaping the current network of host-pathogen interactions. Each organ brings new challenges from the perspective of a pathogen to establish a suitable niche for survival while subverting the protective mechanisms of the host. Lungs, the organ for oxygen exchange, have been an easy target for pathogens due to its accessibility. The organ has evolved diverse capabilities to provide the flexibility required for an organism's health and at the same time maintain protective functionality to prevent and resolve assault by pathogens. The pathogenic invasions are strongly challenged by healthy lung architecture which includes the presence and activity of the epithelium, mucous, antimicrobial proteins, surfactants, and immune cells. Competitively, the pathogens in the form of viruses, bacteria, and fungi have evolved an arsenal of strategies that can over-ride the host's protective mechanisms. While bacteria such as Mycobacterium tuberculosis (M. tuberculosis) can survive in dormant form for years before getting active in humans, novel pathogens can wreak havoc as they pose a high risk of morbidity and mortality in a very short duration of time. Recently, a coronavirus strain SARS-CoV-2 has caused a pandemic which provides us an opportunity to look at the host manipulative strategies used by respiratory pathogens. Their ability to hide, modify, evade, and exploit cell's processes are key to their survival. While pathogens like M. tuberculosis have been infecting humans for thousands of years, SARS-CoV-2 has been the cause of the recent pandemic. Molecular understanding of the strategies used by these pathogens could greatly serve in design of predictive, preventive, personalized medicine (PPPM). In this article, we have emphasized on the clinically relevant evasive strategies of the pathogens in the lungs with emphasis on M. tuberculosis and SARS-CoV-2. The molecular basis of these evasive strategies illuminated through advances in genomics, cell, and structural biology can assist in the mapping of vulnerable molecular networks which can be exploited translationally. These evolutionary approaches can further assist in generating screening and therapeutic options for susceptible populations and could be a promising approach for the prediction, prevention of disease, and the development of personalized medicines. Further, tailoring the clinical data of COVID-19 patients with their physiological responses in light of known host-respiratory pathogen interactions can provide opportunities to improve patient profiling and stratification according to identified therapeutic targets.
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Affiliation(s)
- Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Meenakshi Ahluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Kumar Vaibhav
- Department of Neurosurgery, Medical College of Georgia, Augusta University, Augusta, GA USA
- Department of Oral Biology, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Ashis Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Nikhil Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Shaheen Islam
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Sadanand Fulzele
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Vamsi Kota
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Krishnan Dhandapani
- Department of Neurosurgery, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Babak Baban
- Department of Oral Biology, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Amyn M. Rojiani
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA USA
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