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Otter CJ, Renner DM, Fausto A, Tan LH, Cohen NA, Weiss SR. Interferon signaling in the nasal epithelium distinguishes among lethal and common cold coronaviruses and mediates viral clearance. Proc Natl Acad Sci U S A 2024; 121:e2402540121. [PMID: 38758698 PMCID: PMC11127059 DOI: 10.1073/pnas.2402540121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/27/2024] [Indexed: 05/19/2024] Open
Abstract
All respiratory viruses establish primary infections in the nasal epithelium, where efficient innate immune induction may prevent dissemination to the lower airway and thus minimize pathogenesis. Human coronaviruses (HCoVs) cause a range of pathologies, but the host and viral determinants of disease during common cold versus lethal HCoV infections are poorly understood. We model the initial site of infection using primary nasal epithelial cells cultured at an air-liquid interface (ALI). HCoV-229E, HCoV-NL63, and human rhinovirus-16 are common cold-associated viruses that exhibit unique features in this model: early induction of antiviral interferon (IFN) signaling, IFN-mediated viral clearance, and preferential replication at nasal airway temperature (33 °C) which confers muted host IFN responses. In contrast, lethal SARS-CoV-2 and MERS-CoV encode antagonist proteins that prevent IFN-mediated clearance in nasal cultures. Our study identifies features shared among common cold-associated viruses, highlighting nasal innate immune responses as predictive of infection outcomes and nasally directed IFNs as potential therapeutics.
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Affiliation(s)
- Clayton J. Otter
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - David M. Renner
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Alejandra Fausto
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Li Hui Tan
- Department of Otorhinolaryngology-Head and Neck Surgery, Division of Rhinology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Noam A. Cohen
- Department of Otorhinolaryngology-Head and Neck Surgery, Division of Rhinology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Surgery, Corporal Michael J. Crescenz Department of Veterans Affairs Medical Center, Philadelphia, PA19104
- Monell Chemical Senses Center, Philadelphia, PA19104
| | - Susan R. Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
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Wang Y, Thaler M, Salgado‐Benvindo C, Ly N, Leijs AA, Ninaber DK, Hansbro PM, Boedijono F, van Hemert MJ, Hiemstra PS, van der Does AM, Faiz A. SARS-CoV-2-infected human airway epithelial cell cultures uniquely lack interferon and immediate early gene responses caused by other coronaviruses. Clin Transl Immunology 2024; 13:e1503. [PMID: 38623540 PMCID: PMC11017760 DOI: 10.1002/cti2.1503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/22/2023] [Accepted: 03/24/2024] [Indexed: 04/17/2024] Open
Abstract
Objectives Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a member of a class of highly pathogenic coronaviruses. The large family of coronaviruses, however, also includes members that cause only mild symptoms, like human coronavirus-229E (HCoV-229E) or OC43 (HCoV-OC43). Unravelling how molecular (and cellular) pathophysiology differs between highly and low pathogenic coronaviruses is important for the development of therapeutic strategies. Methods Here, we analysed the transcriptome of primary human bronchial epithelial cells (PBEC), differentiated at the air-liquid interface (ALI) after infection with SARS-CoV-2, SARS-CoV, Middle East Respiratory Syndrome (MERS)-CoV and HCoV-229E using bulk RNA sequencing. Results ALI-PBEC were efficiently infected by all viruses, and SARS-CoV, MERS-CoV and HCoV-229E infection resulted in a largely similar transcriptional response. The response to SARS-CoV-2 infection differed markedly as it uniquely lacked the increase in expression of immediate early genes, including FOS, FOSB and NR4A1 that was observed with all other coronaviruses. This finding was further confirmed in publicly available experimental and clinical datasets. Interfering with NR4A1 signalling in Calu-3 lung epithelial cells resulted in a 100-fold reduction in extracellular RNA copies of SARS-CoV-2 and MERS-CoV, suggesting an involvement in virus replication. Furthermore, a lack in induction of interferon-related gene expression characterised the main difference between the highly pathogenic coronaviruses and low pathogenic viruses HCoV-229E and HCoV-OC43. Conclusion Our results demonstrate a previously unknown suppression of a host response gene set by SARS-CoV-2 and confirm a difference in interferon-related gene expression between highly pathogenic and low pathogenic coronaviruses.
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Affiliation(s)
- Ying Wang
- PulmoScience Lab, Department of PulmonologyLeiden University Medical CenterLeidenThe Netherlands
| | - Melissa Thaler
- Department of Medical MicrobiologyLeiden University Medical CenterLeidenThe Netherlands
| | | | - Nathan Ly
- Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life SciencesUniversity of Technology SydneySydneyNSWAustralia
| | - Anouk A Leijs
- Department of Medical MicrobiologyLeiden University Medical CenterLeidenThe Netherlands
| | - Dennis K Ninaber
- PulmoScience Lab, Department of PulmonologyLeiden University Medical CenterLeidenThe Netherlands
| | - Philip M Hansbro
- Centre for InflammationCentenary Institute and University of Technology Sydney, Faculty of ScienceSydneyNSWAustralia
| | - Fia Boedijono
- Centre for InflammationCentenary Institute and University of Technology Sydney, Faculty of ScienceSydneyNSWAustralia
| | - Martijn J van Hemert
- Department of Medical MicrobiologyLeiden University Medical CenterLeidenThe Netherlands
| | - Pieter S Hiemstra
- PulmoScience Lab, Department of PulmonologyLeiden University Medical CenterLeidenThe Netherlands
| | - Anne M van der Does
- PulmoScience Lab, Department of PulmonologyLeiden University Medical CenterLeidenThe Netherlands
| | - Alen Faiz
- Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life SciencesUniversity of Technology SydneySydneyNSWAustralia
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3
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Li Z, Lai Y, Qiu R, Tang W, Ren J, Xiao S, Fang P, Fang L. Hyperacetylated microtubules assist porcine deltacoronavirus nsp8 to degrade MDA5 via SQSTM1/p62-dependent selective autophagy. J Virol 2024; 98:e0000324. [PMID: 38353538 PMCID: PMC10949429 DOI: 10.1128/jvi.00003-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 01/21/2024] [Indexed: 03/20/2024] Open
Abstract
The microtubule (MT) is a highly dynamic polymer that functions in various cellular processes through MT hyperacetylation. Thus, many viruses have evolved mechanisms to hijack the MT network of the cytoskeleton to allow intracellular replication of viral genomic material. Coronavirus non-structural protein 8 (nsp8), a component of the viral replication transcriptional complex, is essential for viral survival. Here, we found that nsp8 of porcine deltacoronavirus (PDCoV), an emerging enteropathogenic coronavirus with a zoonotic potential, inhibits interferon (IFN)-β production by targeting melanoma differentiation gene 5 (MDA5), the main pattern recognition receptor for coronaviruses in the cytoplasm. Mechanistically, PDCoV nsp8 interacted with MDA5 and induced autophagy to degrade MDA5 in wild-type cells, but not in autophagy-related (ATG)5 or ATG7 knockout cells. Further screening for autophagic degradation receptors revealed that nsp8 interacts with sequestosome 1/p62 and promotes p62-mediated selective autophagy to degrade MDA5. Importantly, PDCoV nsp8 induced hyperacetylation of MTs, which in turn triggered selective autophagic degradation of MDA5 and subsequent inhibition of IFN-β production. Overall, our study uncovers a novel mechanism employed by PDCoV nsp8 to evade host innate immune defenses. These findings offer new insights into the interplay among viruses, IFNs, and MTs, providing a promising target to develop anti-viral drugs against PDCoV.IMPORTANCECoronavirus nsp8, a component of the viral replication transcriptional complex, is well conserved and plays a crucial role in viral replication. Exploration of the role mechanism of nsp8 is conducive to the understanding of viral pathogenesis and development of anti-viral strategies against coronavirus. Here, we found that nsp8 of PDCoV, an emerging enteropathogenic coronavirus with a zoonotic potential, is an interferon antagonist. Further studies showed that PDCoV nsp8 interacted with MDA5 and sequestosome 1/p62, promoting p62-mediated selective autophagy to degrade MDA5. We further found that PDCoV nsp8 could induce hyperacetylation of MT, therefore triggering selective autophagic degradation of MDA5 and inhibiting IFN-β production. These findings reveal a novel immune evasion strategy used by PDCoV nsp8 and provide insights into potential therapeutic interventions.
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Affiliation(s)
- Zhuang Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Yinan Lai
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Runhui Qiu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Wenbing Tang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Jie Ren
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Shaobo Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Puxian Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Liurong Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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Li Z, Xiao W, Yang Z, Guo J, Zhou J, Xiao S, Fang P, Fang L. Cleavage of HDAC6 to dampen its antiviral activity by nsp5 is a common strategy of swine enteric coronaviruses. J Virol 2024; 98:e0181423. [PMID: 38289103 PMCID: PMC10878235 DOI: 10.1128/jvi.01814-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 12/21/2023] [Indexed: 02/21/2024] Open
Abstract
HDAC6, a structurally and functionally unique member of the histone deacetylase (HDAC) family, is an important host factor that restricts viral infection. The broad-spectrum antiviral activity of HDAC6 makes it a potent antiviral agent. Previously, we found that HDAC6 functions to antagonize porcine deltacoronavirus (PDCoV), an emerging enteropathogenic coronavirus with zoonotic potential. However, the final outcome is typically a productive infection that materializes as cells succumb to viral infection, indicating that the virus has evolved sophisticated mechanisms to combat the antiviral effect of HDAC6. Here, we demonstrate that PDCoV nonstructural protein 5 (nsp5) can cleave HDAC6 at glutamine 519 (Q519), and cleavage of HDAC6 was also detected in the context of PDCoV infection. More importantly, the anti-PDCoV activity of HDAC6 was damaged by nsp5 cleavage. Mechanistically, the cleaved HDAC6 fragments (amino acids 1-519 and 520-1159) lost the ability to degrade PDCoV nsp8 due to their impaired deacetylase activity. Furthermore, nsp5-mediated cleavage impaired the ability of HDAC6 to activate RIG-I-mediated interferon responses. We also tested three other swine enteric coronaviruses (transmissible gastroenteritis virus, porcine epidemic diarrhea virus, and swine acute diarrhea syndrome-coronavirus) and found that all these coronaviruses have adopted similar mechanisms to cleave HDAC6 in both an overexpression system and virus-infected cells, suggesting that cleavage of HDAC6 is a common strategy utilized by swine enteric coronaviruses to antagonize the host's antiviral capacity. Together, these data illustrate how swine enteric coronaviruses antagonize the antiviral function of HDAC6 to maintain their infection, providing new insights to the interaction between virus and host.IMPORTANCEViral infections and host defenses are in constant opposition. Once viruses combat or evade host restriction, productive infection is achieved. HDAC6 is a broad-spectrum antiviral protein that has been demonstrated to inhibit many viruses, including porcine deltacoronavirus (PDCoV). However, whether HDAC6 is reciprocally targeted and disabled by viruses remains unclear. In this study, we used PDCoV as a model and found that HDAC6 is targeted and cleaved by nsp5, a viral 3C-like protease. The cleaved HDAC6 loses its deacetylase activity as well as its ability to degrade viral proteins and activate interferon responses. Furthermore, this cleavage mechanism is shared among other swine enteric coronaviruses. These findings shed light on the intricate interplay between viruses and HDAC6, highlighting the strategies employed by viruses to evade host antiviral defenses.
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Affiliation(s)
- Zhuang Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Wenwen Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Zhixiang Yang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Jiahui Guo
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Junwei Zhou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Shaobo Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Puxian Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Liurong Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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5
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Chen X, Li RT, Chen RY, Shi PD, Liu ZX, Lou YN, Wu M, Zhang RR, Tang W, Li XF, Qin CF. The subgenomic flaviviral RNA suppresses RNA interference through competing with siRNAs for binding RISC components. J Virol 2024; 98:e0195423. [PMID: 38289102 PMCID: PMC10878275 DOI: 10.1128/jvi.01954-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 02/21/2024] Open
Abstract
During the life cycle of mosquito-borne flaviviruses, substantial subgenomic flaviviral RNA (sfRNA) is produced via incomplete degradation of viral genomic RNA by host XRN1. Zika virus (ZIKV) sfRNA has been detected in mosquito and mammalian somatic cells. Human neural progenitor cells (hNPCs) in the developing brain are the major target cells of ZIKV, and antiviral RNA interference (RNAi) plays a critical role in hNPCs. However, whether ZIKV sfRNA was produced in ZIKV-infected hNPCs as well as its function remains not known. In this study, we demonstrate that abundant sfRNA was produced in ZIKV-infected hNPCs. RNA pulldown and mass spectrum assays showed ZIKV sfRNA interacted with host proteins RHA and PACT, both of which are RNA-induced silencing complex (RISC) components. Functionally, ZIKV sfRNA can antagonize RNAi by outcompeting small interfering RNAs (siRNAs) in binding to RHA and PACT. Furthermore, the 3' stem loop (3'SL) of sfRNA was responsible for RISC components binding and RNAi inhibition, and 3'SL can enhance the replication of a viral suppressor of RNAi (VSR)-deficient virus in a RHA- and PACT-dependent manner. More importantly, the ability of binding to RISC components is conversed among multiple flaviviral 3'SLs. Together, our results identified flavivirus 3'SL as a potent VSR in RNA format, highlighting the complexity in virus-host interaction during flavivirus infection.IMPORTANCEZika virus (ZIKV) infection mainly targets human neural progenitor cells (hNPCs) and induces cell death and dysregulated cell-cycle progression, leading to microcephaly and other central nervous system abnormalities. RNA interference (RNAi) plays critical roles during ZIKV infections in hNPCs, and ZIKV has evolved to encode specific viral proteins to antagonize RNAi. Herein, we first show that abundant sfRNA was produced in ZIKV-infected hNPCs in a similar pattern to that in other cells. Importantly, ZIKV sfRNA acts as a potent viral suppressor of RNAi (VSR) by competing with siRNAs for binding RISC components, RHA and PACT. The 3'SL of sfRNA is responsible for binding RISC components, which is a conserved feature among mosquito-borne flaviviruses. As most known VSRs are viral proteins, our findings highlight the importance of viral non-coding RNAs during the antagonism of host RNAi-based antiviral innate immunity.
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Affiliation(s)
- Xiang Chen
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Rui-Ting Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ru-Yi Chen
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Pan-Deng Shi
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zi-Xin Liu
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ya-Nan Lou
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Mei Wu
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Rong-Rong Zhang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wei Tang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiao-Feng Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Cheng-Feng Qin
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, China
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6
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Jiao Z, Wang P, Hu X, Chen Y, Xu J, Zhang J, Wu B, Luo R, Shi Y, Peng G. Feline infectious peritonitis virus ORF7a is a virulence factor involved in inflammatory pathology in cats. Antiviral Res 2024; 222:105794. [PMID: 38176470 DOI: 10.1016/j.antiviral.2024.105794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 12/01/2023] [Accepted: 01/02/2024] [Indexed: 01/06/2024]
Abstract
A hyperinflammatory response is a prominent feature of feline infectious peritonitis (FIP), but the mechanisms behind the feline infectious peritonitis virus (FIPV)-induced cytokine storm in the host have not been clarified. Studies have shown that coronaviruses encode accessory proteins that are involved in viral replication and associated with viral virulence, the inflammatory response and immune regulation. Here, we found that FIPV ORF7a gene plays a key role in viral infection and host proinflammatory responses. The recombinant FIPV strains lacking ORF7a (rQS-79Δ7a) exhibit low replication rates in macrophages and do not induce dramatic upregulation of inflammatory factors. Furthermore, through animal experiments, we found that the rQS-79Δ7a strain is nonpathogenic and do not cause symptoms of FIP in cats. Unexpectedly, after three vaccinations with rQS-79Δ7a strain, humoral and cellular immunity was increased and provided protection against virulent strains in cats, and the protection rate reaches 40%. Importantly, our results demonstrated that ORF7a is a key virulence factor that exacerbates FIPV infection and inflammatory responses. Besides, our findings will provide novel implications for future development of live attenuated FIPV vaccines.
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Affiliation(s)
- Zhe Jiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Lab, Wuhan, China
| | - Pengpeng Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Lab, Wuhan, China
| | - Xiaoshuai Hu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Lab, Wuhan, China
| | - Yixi Chen
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Lab, Wuhan, China
| | - Juan Xu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Lab, Wuhan, China
| | - Jintao Zhang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Lab, Wuhan, China
| | - Benyuan Wu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Lab, Wuhan, China
| | - Ruxue Luo
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Lab, Wuhan, China
| | - Yuejun Shi
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Lab, Wuhan, China.
| | - Guiqing Peng
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Lab, Wuhan, China.
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7
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Corda PO, Bollen M, Ribeiro D, Fardilha M. Emerging roles of the Protein Phosphatase 1 (PP1) in the context of viral infections. Cell Commun Signal 2024; 22:65. [PMID: 38267954 PMCID: PMC10807198 DOI: 10.1186/s12964-023-01468-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/30/2023] [Indexed: 01/26/2024] Open
Abstract
Protein Phosphatase 1 (PP1) is a major serine/threonine phosphatase in eukaryotes, participating in several cellular processes and metabolic pathways. Due to their low substrate specificity, PP1's catalytic subunits do not exist as free entities but instead bind to Regulatory Interactors of Protein Phosphatase One (RIPPO), which regulate PP1's substrate specificity and subcellular localization. Most RIPPOs bind to PP1 through combinations of short linear motifs (4-12 residues), forming highly specific PP1 holoenzymes. These PP1-binding motifs may, hence, represent attractive targets for the development of specific drugs that interfere with a subset of PP1 holoenzymes. Several viruses exploit the host cell protein (de)phosphorylation machinery to ensure efficient virus particle formation and propagation. While the role of many host cell kinases in viral life cycles has been extensively studied, the targeting of phosphatases by viral proteins has been studied in less detail. Here, we compile and review what is known concerning the role of PP1 in the context of viral infections and discuss how it may constitute a putative host-based target for the development of novel antiviral strategies.
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Affiliation(s)
- Pedro O Corda
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Mathieu Bollen
- Department of Cellular and Molecular Medicine, Laboratory of Biosignaling & Therapeutics, Katholieke Universiteit Leuven, Louvain, Belgium
| | - Daniela Ribeiro
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
| | - Margarida Fardilha
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
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8
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Kang S, Xu Z, Liu S, Wu S, Chen H, Xu L, Qin Q, Wei J. Function analysis of fish PACT gene in response to virus infection. FISH & SHELLFISH IMMUNOLOGY 2024; 144:109304. [PMID: 38103849 DOI: 10.1016/j.fsi.2023.109304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/21/2023] [Accepted: 12/13/2023] [Indexed: 12/19/2023]
Abstract
PACT (interferon-inducible double-stranded RNA-dependent protein kinase activator A) is a cellular protein which can activate PKR in dsRNA-independent manner. However, the role of PACT in fish virus infection remains largely unknown. In this study, a PACT homologue from grouper (Epinephelus coioides)(EcPACT) was cloned and characterized. The open reading frame of EcPACT has a full length of 924 bp and encodes a protein of 307 amino acids with a predicted molecular weight of 33.29 kDa. Similar to mammals, EcPACT contains three dsRBD domains. EcPACT shares 99.67 % homology with E. lanceolatus. Real-time fluorescence quantitative PCR results showed that EcPACT mRNA was widely expressed in all tissues and abundantly expressed in brain, blood, head kidney and kidney. In addition, SGIV and RGNNV infection significantly upregulated the transcript levels of EcPACT. Subcellular localization analysis showed that EcPACT was mainly distributed in the nucleus. Overexpression of EcPACT inhibited the replication of SGIV and RGNNV in vitro and positively regulated the expression of interferon (IFN) and pro-inflammatory factors. The results provide a better understanding of the relationship between PACT and viral infection in fish.
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Affiliation(s)
- Shaozhu Kang
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Nansha-South China Agricultural University Fishery Research Institute Guangzhou, Guangzhou, 511400, China
| | - Zhuqing Xu
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Nansha-South China Agricultural University Fishery Research Institute Guangzhou, Guangzhou, 511400, China
| | - Shaoli Liu
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Nansha-South China Agricultural University Fishery Research Institute Guangzhou, Guangzhou, 511400, China
| | - Siting Wu
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Nansha-South China Agricultural University Fishery Research Institute Guangzhou, Guangzhou, 511400, China
| | - Hong Chen
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Nansha-South China Agricultural University Fishery Research Institute Guangzhou, Guangzhou, 511400, China
| | - Linting Xu
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Nansha-South China Agricultural University Fishery Research Institute Guangzhou, Guangzhou, 511400, China
| | - Qiwei Qin
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Nansha-South China Agricultural University Fishery Research Institute Guangzhou, Guangzhou, 511400, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
| | - Jingguang Wei
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Nansha-South China Agricultural University Fishery Research Institute Guangzhou, Guangzhou, 511400, China.
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9
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Sharma N, Kessler P, Sen GC. Cell-type-specific need of Ddx3 and PACT for interferon induction by RNA viruses. J Virol 2023; 97:e0130423. [PMID: 37982645 PMCID: PMC10734550 DOI: 10.1128/jvi.01304-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/23/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Interferon-stimulated genes (ISGs) are induced in response to interferon expression due to viral infections. Role of these ISGs can be variable in different cells or organs. Our study highlights such cell-specific role of an ISG, Ddx3, which regulates the translation of mRNAs essential for interferon induction (PACT) and interferon signaling (STAT1) in a cell-specific manner. Our study also highlights the role of PACT in RNA virus-induced RLR signaling. Our study depicts how Ddx3 regulates innate immune signaling pathways in an indirect manner. Such cell-specific behavior of ISGs helps us to better understand viral pathogenesis and highlights the complexities of viral tropism and innate immune responses.
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Affiliation(s)
- Nikhil Sharma
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Patricia Kessler
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ganes C. Sen
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
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10
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Otter CJ, Renner DM, Fausto A, Tan LH, Cohen NA, Weiss SR. Interferon signaling in the nasal epithelium distinguishes among lethal and common cold respiratory viruses and is critical for viral clearance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.571720. [PMID: 38187597 PMCID: PMC10769301 DOI: 10.1101/2023.12.18.571720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
All respiratory viruses establish primary infections in the nasal epithelium, where efficient innate immune induction may prevent dissemination to the lower airway and thus minimize pathogenesis. Human coronaviruses (HCoVs) cause a range of pathologies, but the host and viral determinants of disease during common cold versus lethal HCoV infections are poorly understood. We model the initial site of infection using primary nasal epithelial cells cultured at air-liquid interface (ALI). HCoV-229E, HCoV-NL63 and human rhinovirus-16 are common cold-associated viruses that exhibit unique features in this model: early induction of antiviral interferon (IFN) signaling, IFN-mediated viral clearance, and preferential replication at nasal airway temperature (33°C) which confers muted host IFN responses. In contrast, lethal SARS-CoV-2 and MERS-CoV encode antagonist proteins that prevent IFN-mediated clearance in nasal cultures. Our study identifies features shared among common cold-associated viruses, highlighting nasal innate immune responses as predictive of infection outcomes and nasally-directed IFNs as potential therapeutics.
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Affiliation(s)
- Clayton J. Otter
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David M. Renner
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alejandra Fausto
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Li Hui Tan
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Noam A. Cohen
- Department of Otorhinolaryngology-Head and Neck Surgery, Division of Rhinology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Monell Chemical Senses Center, Philadelphia, PA, USA
| | - Susan R. Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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11
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Rabaan AA, Alenazy MF, Alshehri AA, Alshahrani MA, Al-Subaie MF, Alrasheed HA, Al Kaabi NA, Thakur N, Bouafia NA, Alissa M, Alsulaiman AM, AlBaadani AM, Alhani HM, Alhaddad AH, Alfouzan WA, Ali BMA, Al-Abdulali KH, Khamis F, Bayahya A, Al Fares MA, Sharma M, Dhawan M. An updated review on pathogenic coronaviruses (CoVs) amid the emergence of SARS-CoV-2 variants: A look into the repercussions and possible solutions. J Infect Public Health 2023; 16:1870-1883. [PMID: 37839310 DOI: 10.1016/j.jiph.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
SARS-CoV-2, responsible for COVID-19, shares 79% and 50% of its identity with SARS-CoV-1 and MERS-CoV, respectively. It uses the same main cell attachment and entry receptor as SARS-CoV-1, which is the ACE-2 receptor. However, key residues in the receptor-binding domain of its S-protein seem to give it a stronger affinity for the receptor and a better ability to hide from the host immune system. Like SARS-CoV-1 and MERS-CoV, cytokine storms in critically ill COVID-19 patients cause ARDS, neurological pathology, multiorgan failure, and increased death. Though many issues remain, the global research effort and lessons from SARS-CoV-1 and MERS-CoV are hopeful. The emergence of novel SARS-CoV-2 variants and subvariants raised serious concerns among the scientific community amid the emergence of other viral diseases like monkeypox and Marburg virus, which are major concerns for healthcare settings worldwide. Hence, an updated review on the comparative analysis of various coronaviruses (CoVs) has been developed, which highlights the evolution of CoVs and their repercussions.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan.
| | - Maha Fahad Alenazy
- Department of Physiology, College of Medicine, King Khalid university hospital, King Saud University, Riyadh 4545, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Mohammed Abdulrahman Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Maha F Al-Subaie
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Research Center, Dr. Sulaiman Alhabib Medical Group, Riyadh 13328, Saudi Arabia; Department of Infectious Diseases, Dr. Sulaiman Alhabib Medical Group, Riyadh 13328, Saudi Arabia
| | - Hayam A Alrasheed
- Department of pharmacy Practice, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia; Pharmacy Department, King Abdullah Bin Abdulaziz University Hospital, Riyadh 11671, Saudi Arabia
| | - Nawal A Al Kaabi
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi, 51900, United Arab Emirates; College of Medicine and Health Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates
| | - Nanamika Thakur
- University Institute of Biotechnology, Department of Biotechnology, Chandigarh University, Mohali 140413, India
| | - Nabiha A Bouafia
- Infection prevention and control centre of Excellence, Prince Sultan Medical Military City, Riyadh 12233, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | | | - Abeer M AlBaadani
- Internal Medicine Department, Infectious Disease Division, London health science Center, London, Ontario N6G0X2, Canada
| | - Hatem M Alhani
- Department of Pediatric Infectious Disease, Maternity and Children Hospital, Dammam 31176, Saudi Arabia; Department of Infection Control, Maternity and Children Hospital, Dammam 31176, Saudi Arabia; Preventive Medicine and Infection Prevention and Control Department, Directorate of Ministry of Health, Dammam 32245, Saudi Arabia
| | - Ali H Alhaddad
- Assistant Agency for Hospital Affairs, Ministry of Health, Riyadh 12382, Saudi Arabia
| | - Wadha A Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait; Microbiology Unit, Department of Laboratories, Farwania Hospital, Farwania 85000, Kuwait
| | - Batool Mohammed Abu Ali
- Infectious disease section, Department of internal medicine, King Fahad Hospital Hofuf, Hofuf 36365, Saudi Arabia
| | - Khadija H Al-Abdulali
- Nursing Department, Home health care, Qatif Health Network, Qatif 31911, Saudi Arabia
| | - Faryal Khamis
- Infection Diseases unit, Department of Internal Medicine, Royal Hospital, Muscat 1331, Oman
| | - Ali Bayahya
- Microbiology Department, Alqunfudah General Hospital, Alqunfudah 28813, Saudi Arabia
| | - Mona A Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia.
| | - Manish Sharma
- University Institute of Biotechnology, Department of Biotechnology, Chandigarh University, Mohali 140413, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, India; Trafford College, Altrincham, Manchester WA14 5PQ, UK.
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12
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Huang M, Liu Y, Xia Y, Wang J, Zheng X, Cao Y. Infectious bronchitis virus nucleocapsid protein suppressed type I interferon production by interfering with the binding of MDA5-dsRNA and interacting with LGP2. Vet Microbiol 2023; 284:109798. [PMID: 37307767 DOI: 10.1016/j.vetmic.2023.109798] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/28/2023] [Accepted: 06/04/2023] [Indexed: 06/14/2023]
Abstract
The type I interferon (IFN-I) is a critical component of the innate immune responses, and Coronaviruses (CoVs) from both the Alphacoronavirus and Betacoronavirus genera interfere with the IFN-I signaling pathway in various ways. Of the gammacoronaviruses that mainly infect birds, little is known about how infectious bronchitis virus (IBV), evades or interferes with the innate immune responses in avian hosts since few IBV strains have been adapted to grow in avian passage cells. Previously, we reported that a highly pathogenic IBV strain GD17/04 has adaptability in an avian cell line, providing a material basis for further study on the interaction mechanism. In the present work, we describe the suppression of IBV to IFN-I and the potential role of IBV-encoded nucleocapsid (N) protein. We show that IBV significantly inhibits the poly I: C-induced IFN-I production, accordingly the nuclear translocation of STAT1, and the expression of IFN-stimulated genes (ISGs). A detailed analysis revealed that N protein, acting as an IFN-I antagonist, significantly impedes the activation of the IFN-β promoter stimulated by MDA5 and LGP2 but does not counteract its activation by MAVS, TBK1, and IRF7. Further results showed that IBV N protein, verified to be an RNA-binding protein, interferes with MDA5 recognizing double-stranded RNA (dsRNA). Moreover, we found that the N protein targets LGP2, which is required in the chicken IFN-I signaling pathway. Taken together, this study provides a comprehensive analysis of the mechanism by which IBV evades avian innate immune responses.
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Affiliation(s)
- Mengjiao Huang
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Yuan Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yongbo Xia
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jingjing Wang
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Xuewei Zheng
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Yongchang Cao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, China.
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13
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Pereira PDC, Diniz DG, da Costa ER, Magalhães NGDM, da Silva ADJF, Leite JGS, Almeida NIP, Cunha KDN, de Melo MAD, Vasconcelos PFDC, Diniz JAP, Brites D, Anthony DC, Diniz CWP, Guerreiro-Diniz C. Genes, inflammatory response, tolerance, and resistance to virus infections in migratory birds, bats, and rodents. Front Immunol 2023; 14:1239572. [PMID: 37711609 PMCID: PMC10497949 DOI: 10.3389/fimmu.2023.1239572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023] Open
Abstract
Normally, the host immunological response to viral infection is coordinated to restore homeostasis and protect the individual from possible tissue damage. The two major approaches are adopted by the host to deal with the pathogen: resistance or tolerance. The nature of the responses often differs between species and between individuals of the same species. Resistance includes innate and adaptive immune responses to control virus replication. Disease tolerance relies on the immune response allowing the coexistence of infections in the host with minimal or no clinical signs, while maintaining sufficient viral replication for transmission. Here, we compared the virome of bats, rodents and migratory birds and the molecular mechanisms underlying symptomatic and asymptomatic disease progression. We also explore the influence of the host physiology and environmental influences on RNA virus expression and how it impacts on the whole brain transcriptome of seemingly healthy semipalmated sandpiper (Calidris pusilla) and spotted sandpiper (Actitis macularius). Three time points throughout the year were selected to understand the importance of longitudinal surveys in the characterization of the virome. We finally revisited evidence that upstream and downstream regulation of the inflammatory response is, respectively, associated with resistance and tolerance to viral infections.
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Affiliation(s)
- Patrick Douglas Corrêa Pereira
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Daniel Guerreiro Diniz
- Seção de Hepatologia, Laboratório de Microscopia Eletrônica, Instituto Evandro Chagas, Belém, Pará, Brazil
- Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Laboratório de Investigações em Neurodegeneração e Infecção, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Emanuel Ramos da Costa
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
- Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Laboratório de Investigações em Neurodegeneração e Infecção, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Nara Gyzely de Morais Magalhães
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Anderson de Jesus Falcão da Silva
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Jéssica Gizele Sousa Leite
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Natan Ibraim Pires Almeida
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Kelle de Nazaré Cunha
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Mauro André Damasceno de Melo
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Pedro Fernando da Costa Vasconcelos
- Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará, Belém, Pará, Brazil
- Seção de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
| | - José Antonio Picanço Diniz
- Seção de Hepatologia, Laboratório de Microscopia Eletrônica, Instituto Evandro Chagas, Belém, Pará, Brazil
| | - Dora Brites
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Daniel Clive Anthony
- Department of Pharmacology, Laboratory of Experimental Neuropathology, University of Oxford, Oxford, United Kingdom
| | - Cristovam Wanderley Picanço Diniz
- Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Laboratório de Investigações em Neurodegeneração e Infecção, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Cristovam Guerreiro-Diniz
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
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14
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Intragenomic rearrangements involving 5'-untranslated region segments in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses. Virol J 2023; 20:36. [PMID: 36829234 PMCID: PMC9957694 DOI: 10.1186/s12985-023-01998-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Variation of the betacoronavirus SARS-CoV-2 has been the bane of COVID-19 control. Documented variation includes point mutations, deletions, insertions, and recombination among closely or distantly related coronaviruses. Here, we describe yet another aspect of genome variation by beta- and alphacoronaviruses that was first documented in an infectious isolate of the betacoronavirus SARS-CoV-2, obtained from 3 patients in Hong Kong that had a 5'-untranslated region segment at the end of the ORF6 gene that in its new location translated into an ORF6 protein with a predicted modified carboxyl terminus. While comparing the amino acid sequences of translated ORF8 genes in the GenBank database, we found a subsegment of the same 5'-UTR-derived amino acid sequence modifying the distal end of ORF8 of an isolate from the United States and decided to carry out a systematic search. METHODS Using the nucleotide and in the case of SARS-CoV-2 also the translated amino acid sequence in three reading frames of the genomic termini of coronaviruses as query sequences, we searched for 5'-UTR sequences in regions other than the 5'-UTR in SARS-CoV-2 and reference strains of alpha-, beta-, gamma-, and delta-coronaviruses. RESULTS We here report numerous genomic insertions of 5'-untranslated region sequences into coding regions of SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses, but not delta- or gammacoronaviruses. To our knowledge this is the first systematic description of such insertions. In many cases, these insertions would change viral protein sequences and further foster genomic flexibility and viral adaptability through insertion of transcription regulatory sequences in novel positions within the genome. Among human Embecorivus betacoronaviruses, for instance, from 65% to all of the surveyed sequences in publicly available databases contain inserted 5'-UTR sequences. CONCLUSION The intragenomic rearrangements involving 5'-untranslated region sequences described here, which in several cases affect highly conserved genes with a low propensity for recombination, may underlie the generation of variants homotypic with those of concern or interest and with potentially differing pathogenic profiles. Intragenomic rearrangements thus add to our appreciation of how variants of SARS-CoV-2 and other beta- and alphacoronaviruses may arise.
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15
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Hurtado-Tamayo J, Requena-Platek R, Enjuanes L, Bello-Perez M, Sola I. Contribution to pathogenesis of accessory proteins of deadly human coronaviruses. Front Cell Infect Microbiol 2023; 13:1166839. [PMID: 37197199 PMCID: PMC10183600 DOI: 10.3389/fcimb.2023.1166839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/11/2023] [Indexed: 05/19/2023] Open
Abstract
Coronaviruses (CoVs) are enveloped and positive-stranded RNA viruses with a large genome (∼ 30kb). CoVs include essential genes, such as the replicase and four genes coding for structural proteins (S, M, N and E), and genes encoding accessory proteins, which are variable in number, sequence and function among different CoVs. Accessory proteins are non-essential for virus replication, but are frequently involved in virus-host interactions associated with virulence. The scientific literature on CoV accessory proteins includes information analyzing the effect of deleting or mutating accessory genes in the context of viral infection, which requires the engineering of CoV genomes using reverse genetics systems. However, a considerable number of publications analyze gene function by overexpressing the protein in the absence of other viral proteins. This ectopic expression provides relevant information, although does not acknowledge the complex interplay of proteins during virus infection. A critical review of the literature may be helpful to interpret apparent discrepancies in the conclusions obtained by different experimental approaches. This review summarizes the current knowledge on human CoV accessory proteins, with an emphasis on their contribution to virus-host interactions and pathogenesis. This knowledge may help the search for antiviral drugs and vaccine development, still needed for some highly pathogenic human CoVs.
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Affiliation(s)
| | | | | | | | - Isabel Sola
- *Correspondence: Melissa Bello-Perez, ; Isabel Sola,
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16
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Coronaviruses exploit a host cysteine-aspartic protease for replication. Nature 2022; 609:785-792. [PMID: 35922005 DOI: 10.1038/s41586-022-05148-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 07/26/2022] [Indexed: 11/08/2022]
Abstract
Highly pathogenic coronaviruses, including severe acute respiratory syndrome coronavirus 2 (refs. 1,2) (SARS-CoV-2), Middle East respiratory syndrome coronavirus3 (MERS-CoV) and SARS-CoV-1 (ref. 4), vary in their transmissibility and pathogenicity. However, infection by all three viruses results in substantial apoptosis in cell culture5-7 and in patient tissues8-10, suggesting a potential link between apoptosis and pathogenesis of coronaviruses. Here we show that caspase-6, a cysteine-aspartic protease of the apoptosis cascade, serves as an important host factor for efficient coronavirus replication. We demonstrate that caspase-6 cleaves coronavirus nucleocapsid proteins, generating fragments that serve as interferon antagonists, thus facilitating virus replication. Inhibition of caspase-6 substantially attenuates lung pathology and body weight loss in golden Syrian hamsters infected with SARS-CoV-2 and improves the survival of mice expressing human DPP4 that are infected with mouse-adapted MERS-CoV. Our study reveals how coronaviruses exploit a component of the host apoptosis cascade to facilitate virus replication.
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17
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Kitagawa Y, Tsukamoto T, Itoh M, Gotoh B. Middle East respiratory syndrome coronavirus
ORF4b
protein inhibits
TLR7
‐ and
TLR9
‐dependent alpha interferon induction. FEBS Lett 2022; 596:2538-2554. [DOI: 10.1002/1873-3468.14486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/14/2022] [Accepted: 08/18/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Yoshinori Kitagawa
- Division of Microbiology and Infectious Diseases, Department of Pathology Shiga University of Medical Science, Seta, Otsu Shiga 520‐2192 Japan
| | - Takumi Tsukamoto
- Department of Microbiology, Faculty of Bio‐Science Nagahama institute of Bio‐Science and Technology Nagahama Shiga 526‐0829 Japan
| | - Masae Itoh
- Department of Microbiology, Faculty of Bio‐Science Nagahama institute of Bio‐Science and Technology Nagahama Shiga 526‐0829 Japan
| | - Bin Gotoh
- Division of Microbiology and Infectious Diseases, Department of Pathology Shiga University of Medical Science, Seta, Otsu Shiga 520‐2192 Japan
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18
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Li W, Wang H, Zheng SJ. Roles of RNA Sensors in Host Innate Response to Influenza Virus and Coronavirus Infections. Int J Mol Sci 2022; 23:ijms23158285. [PMID: 35955436 PMCID: PMC9368391 DOI: 10.3390/ijms23158285] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022] Open
Abstract
Influenza virus and coronavirus are two important respiratory viruses, which often cause serious respiratory diseases in humans and animals after infection. In recent years, highly pathogenic avian influenza virus (HPAIV) and SARS-CoV-2 have become major pathogens causing respiratory diseases in humans. Thus, an in-depth understanding of the relationship between viral infection and host innate immunity is particularly important to the stipulation of effective control strategies. As the first line of defense against pathogens infection, innate immunity not only acts as a natural physiological barrier, but also eliminates pathogens through the production of interferon (IFN), the formation of inflammasomes, and the production of pro-inflammatory cytokines. In this process, the recognition of viral pathogen-associated molecular patterns (PAMPs) by host pattern recognition receptors (PRRs) is the initiation and the most important part of the innate immune response. In this review, we summarize the roles of RNA sensors in the host innate immune response to influenza virus and coronavirus infections in different species, with a particular focus on innate immune recognition of viral nucleic acids in host cells, which will help to develop an effective strategy for the control of respiratory infectious diseases.
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Affiliation(s)
- Wei Li
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (W.L.); (H.W.)
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Hongnuan Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (W.L.); (H.W.)
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Shijun J. Zheng
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (W.L.); (H.W.)
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Correspondence: ; Tel./Fax: +86-10-62834681
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Comar CE, Otter CJ, Pfannenstiel J, Doerger E, Renner DM, Tan LH, Perlman S, Cohen NA, Fehr AR, Weiss SR. MERS-CoV endoribonuclease and accessory proteins jointly evade host innate immunity during infection of lung and nasal epithelial cells. Proc Natl Acad Sci U S A 2022; 119:e2123208119. [PMID: 35594398 PMCID: PMC9173776 DOI: 10.1073/pnas.2123208119] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/13/2022] [Indexed: 12/25/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into humans in 2012, causing highly lethal respiratory disease. The severity of disease may be, in part, because MERS-CoV is adept at antagonizing early innate immune pathways—interferon (IFN) production and signaling, protein kinase R (PKR), and oligoadenylate synthetase/ribonuclease L (OAS/RNase L)—activated in response to viral double-stranded RNA (dsRNA) generated during genome replication. This is in contrast to severe acute respiratory syndrome CoV-2 (SARS-CoV-2), which we recently reported to activate PKR and RNase L and, to some extent, IFN signaling. We previously found that MERS-CoV accessory proteins NS4a (dsRNA binding protein) and NS4b (phosphodiesterase) could weakly suppress these pathways, but ablation of each had minimal effect on virus replication. Here we investigated the antagonist effects of the conserved coronavirus endoribonuclease (EndoU), in combination with NS4a or NS4b. Inactivation of EndoU catalytic activity alone in a recombinant MERS-CoV caused little if any effect on activation of the innate immune pathways during infection. However, infection with recombinant viruses containing combined mutations with inactivation of EndoU and deletion of NS4a or inactivation of the NS4b phosphodiesterase promoted robust activation of dsRNA-induced innate immune pathways. This resulted in at least tenfold attenuation of replication in human lung–derived A549 and primary nasal cells. Furthermore, replication of these recombinant viruses could be rescued to the level of wild-type MERS-CoV by knockout of host immune mediators MAVS, PKR, or RNase L. Thus, EndoU and accessory proteins NS4a and NS4b together suppress dsRNA-induced innate immunity during MERS-CoV infection in order to optimize viral replication.
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Affiliation(s)
- Courtney E. Comar
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Clayton J. Otter
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Ethan Doerger
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045
| | - David M. Renner
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Li Hui Tan
- Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA 19104
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242
| | - Noam A. Cohen
- Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA 19104
- Department of Surgery, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA 19104
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242
| | - Susan R. Weiss
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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DYT-PRKRA Mutation P222L Enhances PACT’s Stimulatory Activity on Type I Interferon Induction. Biomolecules 2022; 12:biom12050713. [PMID: 35625640 PMCID: PMC9138762 DOI: 10.3390/biom12050713] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 12/10/2022] Open
Abstract
DYT-PRKRA (dystonia 16 or DYT-PRKRA) is caused by mutations in the PRKRA gene that encodes PACT, the protein activator of interferon (IFN)-induced double-stranded (ds) RNA-activated protein kinase (PKR). PACT participates in several cellular pathways, of which its role as a PKR activator protein during integrated stress response (ISR) is the best characterized. Previously, we have established that the DYT-PRKRA mutations cause enhanced activation of PKR during ISR to sensitize DYT-PRKRA cells to apoptosis. In this study, we evaluate if the most prevalent substitution mutation reported in DYT-PRKRA patients alters PACT’s functional role in induction of type I IFNs via the retinoic acid-inducible gene I (RIG-I) signaling. Our results indicate that the P222L mutation augments PACT’s ability to induce IFN β in response to dsRNA and the basal expression of IFN β and IFN-stimulated genes (ISGs) is higher in DYT-PRKRA patient cells compared to cells from the unaffected controls. Additionally, IFN β and ISGs are also induced at higher levels in DYT-PRKRA cells in response to dsRNA. These results offer a new avenue for investigations directed towards understanding the underlying molecular pathomechanisms in DYT-PRKRA.
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Khazaneha M, Tajedini O, Esmaeili O, Abdi M, Khasseh AA, Sadatmoosavi A. Thematic evolution of coronavirus disease: a longitudinal co-word analysis. LIBRARY HI TECH 2022. [DOI: 10.1108/lht-10-2021-0370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PurposeUsing science mapping analysis approach and co-word analysis, the present study explores and visualizes research fields and thematic evolution of the coronavirus. Based on this method, one can get a picture of the real content of the themes in the mentioned thematic area and identify the main minor and emerging themes.Design/methodology/approachThis study was conducted based on co-word science mapping analysis under a longitudinal study (from 1988 to 2020). The collection of documents in this study was further divided into three subperiods: 1988–1998, 1999–2009 and 2010–2020. In order to perform science mapping analysis based on co-word bibliographic networks, SciMAT was utilized as a bibliometric tool. Moreover, WoS, PubMed and Scopus bibliographic databases were used to download all records.FindingsIn this study, strategic diagrams were demonstrated for the coronavirus research for a chronological period to assess the most relevant themes. Each diagram depended on the sum of documents linked to each research topic. In the first period (1988–1998), the most centralizations were on virology and evaluation of coronavirus structure and its structural and nonstructural proteins. In the second period (1999–2009), with due attention to high population density in eastern Asia and the increasing number of people affected with the new generation of coronavirus (named severe acute respiratory syndrome virus or SARS virus), publications have been concentrated on “antiviral activity.” In the third period (2010–2020), there was a tendency to investigate clinical syndromes, and most of the publications and citations were about hot topics like “severe acute respiratory syndrome,” “coronavirus” and “respiratory tract disease.” Scientometric analysis of the field of coronavirus can be regarded as a roadmap for future research and policymaking in this important area.Originality/valueThe originality of this research can be considered in two ways. First, the strategic diagrams of coronavirus are drawn in four thematic areas including motor cluster, basic and transversal cluster, highly developed cluster and emerging and declining cluster. Second, COVID-19 is mentioned as a hot topic of research.
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22
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Chan CP, Jin DY. Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations. RNA (NEW YORK, N.Y.) 2022; 28:449-477. [PMID: 35031583 PMCID: PMC8925969 DOI: 10.1261/rna.079016.121] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Sensing of pathogen-associated molecular patterns including viral RNA by innate immunity represents the first line of defense against viral infection. In addition to RIG-I-like receptors and NOD-like receptors, several other RNA sensors are known to mediate innate antiviral response in the cytoplasm. Double-stranded RNA-binding protein PACT interacts with prototypic RNA sensor RIG-I to facilitate its recognition of viral RNA and induction of host interferon response, but variations of this theme are seen when the functions of RNA sensors are modulated by other RNA-binding proteins to impinge on antiviral defense, proinflammatory cytokine production and cell death programs. Their discrete and coordinated actions are crucial to protect the host from infection. In this review, we will focus on cytoplasmic RNA sensors with an emphasis on their interplay with RNA-binding partners. Classical sensors such as RIG-I will be briefly reviewed. More attention will be brought to new insights on how RNA-binding partners of RNA sensors modulate innate RNA sensing and how viruses perturb the functions of RNA-binding partners.
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Affiliation(s)
- Chi-Ping Chan
- School of Biomedical Sciences and State Key Laboratory of Liver Research, Faculty of Medicine Building, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences and State Key Laboratory of Liver Research, Faculty of Medicine Building, Pokfulam, Hong Kong
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23
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Inhibition of the IFN-α JAK/STAT Pathway by MERS-CoV and SARS-CoV-1 Proteins in Human Epithelial Cells. Viruses 2022; 14:v14040667. [PMID: 35458397 PMCID: PMC9032603 DOI: 10.3390/v14040667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/04/2022] [Accepted: 03/17/2022] [Indexed: 12/10/2022] Open
Abstract
Coronaviruses (CoVs) have caused several global outbreaks with relatively high mortality rates, including Middle East Respiratory Syndrome coronavirus (MERS)-CoV, which emerged in 2012, and Severe Acute Respiratory Syndrome (SARS)-CoV-1, which appeared in 2002. The recent emergence of SARS-CoV-2 highlights the need for immediate and greater understanding of the immune evasion mechanisms used by CoVs. Interferon (IFN)-α is the body's natural antiviral agent, but its Janus kinase/signal transducer and activators of transcription (JAK/STAT) signalling pathway is often antagonized by viruses, thereby preventing the upregulation of essential IFN stimulated genes (ISGs). Therapeutic IFN-α has disappointingly weak clinical responses in MERS-CoV and SARS-CoV-1 infected patients, indicating that these CoVs inhibit the IFN-α JAK/STAT pathway. Here we show that in lung alveolar A549 epithelial cells expression of MERS-CoV-nsp2 and SARS-CoV-1-nsp14, but not MERS-CoV-nsp5, increased basal levels of total and phosphorylated STAT1 & STAT2 protein, but reduced IFN-α-mediated phosphorylation of STAT1-3 and induction of MxA. While MERS-CoV-nsp2 and SARS-CoV-1-nsp14 similarly increased basal levels of STAT1 and STAT2 in bronchial BEAS-2B epithelial cells, unlike in A549 cells, they did not enhance basal pSTAT1 nor pSTAT2. However, both viral proteins reduced IFN-α-mediated induction of pSTAT1-3 and ISGs (MxA, ISG15 and PKR) in BEAS-2B cells. Furthermore, even though IFN-α-mediated induction of pSTAT1-3 was not affected by MERS-CoV-nsp5 expression in BEAS-2B cells, downstream ISG induction was reduced, revealing that MERS-CoV-nsp5 may use an alternative mechanism to reduce antiviral ISG induction in this cell line. Indeed, we subsequently discovered that all three viral proteins inhibited STAT1 nuclear translocation in BEAS-2B cells, unveiling another layer of inhibition by which these viral proteins suppress responses to Type 1 IFNs. While these observations highlight cell line-specific differences in the immune evasion effects of MERS-CoV and SARS-CoV-1 proteins, they also demonstrate the broad spectrum of immune evasion strategies these deadly coronaviruses use to stunt antiviral responses to Type IFN.
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24
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Xue W, Ding C, Qian K, Liao Y. The Interplay Between Coronavirus and Type I IFN Response. Front Microbiol 2022; 12:805472. [PMID: 35317429 PMCID: PMC8934427 DOI: 10.3389/fmicb.2021.805472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/24/2021] [Indexed: 12/14/2022] Open
Abstract
In the past few decades, newly evolved coronaviruses have posed a global threat to public health and animal breeding. To control and prevent the coronavirus-related diseases, understanding the interaction of the coronavirus and the host immune system is the top priority. Coronaviruses have evolved multiple mechanisms to evade or antagonize the host immune response to ensure their replication. As the first line and main component of innate immune response, type I IFN response is able to restrict virus in the initial infection stage; it is thus not surprising that the primary aim of the virus is to evade or antagonize the IFN response. Gaining a profound understanding of the interaction between coronaviruses and type I IFN response will shed light on vaccine development and therapeutics. In this review, we provide an update on the current knowledge on strategies employed by coronaviruses to evade type I IFN response.
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Affiliation(s)
- Wenxiang Xue
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Kun Qian
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Ying Liao,
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25
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Qin Y, Feng T, Shi H, Zhang J, Zhang L, Feng S, Chen J, He Y, Zhang X, Chen Z, Liu J, Liu D, Shi D, Feng L. Identification and epitope mapping of swine acute diarrhea syndrome coronavirus accessory protein NS7a via monoclonal antibodies. Virus Res 2022; 313:198742. [PMID: 35283248 PMCID: PMC8912973 DOI: 10.1016/j.virusres.2022.198742] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 11/16/2022]
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is an emerging swine enteric coronavirus that causes vomiting, severe diarrhea, dehydration and death in suckling piglets. NS7a is putative accessory protein that is predicted to be encoded by SADS-CoV, but still to be confirmed experimentally. In the present study, recombinant NS7a protein was expressed in a prokaryotic expression system and used as an antigen to prepare monoclonal antibodies (mAbs) specific to NS7a protein. We obtained two anti-NS7a mAbs, termed AH5 and EH3, that were shown by western blotting to react with the natural NS7a protein in Vero E6 cells infected with SADS-CoV. Using the produced mAbs, we observed by confocal microscopy that NS7a protein was expressed in the cytoplasm. Further studies revealed that the motif 31VNTWQEFA38 was the minimal unit of the linear B-cell epitope recognized by mAb AH5, and the motif 82FDLFERF88 was the minimal unit of the linear B-cell epitope recognized by mAb EH3. Alignment of amino acids showed that these two epitopes were highly conserved among different SADS-CoV strains and SADS-related coronaviruses from bats, but with one substitution in these two motifs in bat coronavirus HKU2. In summary, we generated and characterized two mAbs against SADS-CoV NS7a protein, and demonstrated NS7a expression in SADS-CoV-infected cells for the first time.
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Affiliation(s)
- Yibin Qin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China; Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Xixiangtang District, Youai North Road 51, Nanning, 530001, China
| | - Tingshuai Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Hongyan Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Jiyu Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Liaoyuan Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Shufeng Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Jianfei Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Ying He
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Xixiangtang District, Youai North Road 51, Nanning, 530001, China
| | - Xin Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Zhongwei Chen
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Xixiangtang District, Youai North Road 51, Nanning, 530001, China
| | - Jianbo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Dakai Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Da Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China.
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China.
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Nature of viruses and pandemics: Coronaviruses. CURRENT RESEARCH IN IMMUNOLOGY 2022; 3:151-158. [PMID: 35966177 PMCID: PMC9359481 DOI: 10.1016/j.crimmu.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022] Open
Abstract
Coronaviruses (CoVs) have the largest genome among RNA viruses and store large amounts of information without genome integration as they replicate in the cell cytoplasm. The replication of the virus is a continuous process, whereas the transcription of the subgenomic mRNAs is a discontinuous one, involving a template switch, which resembles a high frequency recombination mechanism that may favor virus genome variability. The origin of the three deadly human CoVs SARS-CoV, MERS-CoV and SARS-CoV-2 are zoonotic events. SARS-CoV-2 has incorporated in its spike protein a furine proteolytic site that facilitates the activation of the virus in any tissue, making this CoV strain highly polytropic and pathogenic. Using MERS-CoV as a model, a propagation-deficient RNA replicon was generated by removing E protein gene (essential for viral morphogenesis and involved in virulence), and accessory genes 3, 4a, 4b and 5 (responsible for antagonism of the innate immune response) to attenuate the virus: MERS-CoV-Δ[3,4a,4b,5,E]. This RNA replicon is strongly attenuated and elicits sterilizing protection after a single immunization in transgenic mice with the receptor for MERS-CoV, making it a promising vaccine candidate for this virus and an interesting platform for vector-based vaccine development. A strategy could be developed for the design of RNA replicon vaccines for other human pathogenic coronaviruses. CoV RNA transcription is a discontinuous high-frequency recombination process. Human CoVs have a zoonotic origin. Replication-competent propagation-defective CoVs are the bases for vaccines. Single immunization with CoV RNA replicon vaccines elicits sterilizing immunity.
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27
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Comar CE, Otter CJ, Pfannenstiel J, Doerger E, Renner DM, Tan LH, Perlman S, Cohen NA, Fehr AR, Weiss SR. MERS-CoV endoribonuclease and accessory proteins jointly evade host innate immunity during infection of lung and nasal epithelial cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34981054 DOI: 10.1101/2021.12.20.473564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into humans in 2012, causing highly lethal respiratory disease. The severity of disease may be in part because MERS-CoV is adept at antagonizing early innate immune pathways - interferon (IFN) production and signaling, protein kinase R (PKR), and oligoadenylate synthetase ribonuclease L (OAS/RNase L) - generated in response to viral double-stranded (ds)RNA generated during genome replication. This is in contrast to SARS-CoV-2, which we recently reported activates PKR and RNase L and to some extent, IFN signaling. We previously found that MERS-CoV accessory proteins NS4a (dsRNA binding protein) and NS4b (phosphodiesterase) could weakly suppress these pathways, but ablation of each had minimal effect on virus replication. Here we investigated the antagonist effects of the conserved coronavirus endoribonuclease (EndoU), in combination with NS4a or NS4b. Inactivation of EndoU catalytic activity alone in a recombinant MERS-CoV caused little if any effect on activation of the innate immune pathways during infection. However, infection with recombinant viruses containing combined mutations with inactivation of EndoU and deletion of NS4a or inactivation of the NS4b phosphodiesterase promoted robust activation of the dsRNA-induced innate immune pathways. This resulted in ten-fold attenuation of replication in human lung derived A549 and primary nasal cells. Furthermore, replication of these recombinant viruses could be rescued to the level of WT MERS-CoV by knockout of host immune mediators MAVS, PKR, or RNase L. Thus, EndoU and accessory proteins NS4a and NS4b together suppress dsRNA-induced innate immunity during MERS-CoV infection in order to optimize viral replication. IMPORTANCE Middle East Respiratory Syndrome Coronavirus (MERS-CoV) causes highly lethal respiratory disease. MERS-CoV encodes several innate immune antagonists, accessory proteins NS4a and NS4b unique to the merbeco lineage and the nsp15 protein endoribonuclease (EndoU), conserved among all coronaviruses. While mutation of each antagonist protein alone has little effect on innate immunity, infections with recombinant MERS-CoVs with mutations of EndoU in combination with either NS4a or NS4b, activate innate signaling pathways and are attenuated for replication. Our data indicate that EndoU and accessory proteins NS4a and NS4b together suppress innate immunity during MERS-CoV infection, to optimize viral replication. This is in contrast to SARS-CoV-2 which activates these pathways and consistent with greater mortality observed during MERS-CoV infection compared to SARS-CoV-2.
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Te N, Rodon J, Pérez M, Segalés J, Vergara-Alert J, Bensaid A. Enhanced replication fitness of MERS-CoV clade B over clade A strains in camelids explains the dominance of clade B strains in the Arabian Peninsula. Emerg Microbes Infect 2021; 11:260-274. [PMID: 34918620 PMCID: PMC8812806 DOI: 10.1080/22221751.2021.2019559] [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] [Indexed: 01/17/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) continues infecting humans and dromedary camels. While MERS-CoV strains from the Middle East region are subdivided into two clades (A and B), all the contemporary epidemic viruses belong to clade B. Thus, MERS-CoV clade B strains may display adaptive advantages over clade A in humans and/or reservoir hosts. To test this hypothesis in vivo, we compared an early epidemic clade A strain (EMC/2012) with a clade B strain (Jordan-1/2015) in an alpaca model monitoring virological and immunological parameters. Further, the Jordan-1/2015 strain has a partial amino acid (aa) deletion in the double-stranded (ds) RNA binding motif of the open reading frame ORF4a protein. Animals inoculated with the Jordan-1/2015 variant had higher MERS-CoV replicative capabilities in the respiratory tract and larger nasal viral shedding. In the nasal mucosa, the Jordan-1/2015 strain caused an early IFN response, suggesting a role for ORF4a as a moderate IFN antagonist in vivo. However, both strains elicited maximal transcription of antiviral interferon-stimulated genes (ISGs) at the peak of infection on 2 days post inoculation, correlating with subsequent decreases in tissular viral loads. Genome alignment analysis revealed several clade B-specific amino acid substitutions occurring in the replicase and the S proteins, which could explain a better adaptation of clade B strains in camelid hosts. Differences in replication and shedding reported herein indicate a better fitness and transmission capability of MERS-CoV clade B strains than their clade A counterparts.
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Affiliation(s)
- Nigeer Te
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Bellaterra (Cerdanyola del Vallès), Spain
| | - Jordi Rodon
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Bellaterra (Cerdanyola del Vallès), Spain
| | - Mónica Pérez
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Bellaterra (Cerdanyola del Vallès), Spain
| | - Joaquim Segalés
- UAB, CReSA (IRTA-UAB), Campus de la UAB, 08193 Bellaterra (Cerdanyola del Vallès), Spain.,Departament de Sanitat i Anatomia Animals, Facultat de Veterinaria, UAB, 08193 Bellaterra (Cerdanyola del Vallès), Spain
| | - Júlia Vergara-Alert
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Bellaterra (Cerdanyola del Vallès), Spain
| | - Albert Bensaid
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Bellaterra (Cerdanyola del Vallès), Spain
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29
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Alathari MJA, Al Mashhadany Y, Mokhtar MHH, Burham N, Bin Zan MSD, A Bakar AA, Arsad N. Human Body Performance with COVID-19 Affectation According to Virus Specification Based on Biosensor Techniques. SENSORS (BASEL, SWITZERLAND) 2021; 21:8362. [PMID: 34960456 PMCID: PMC8704003 DOI: 10.3390/s21248362] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022]
Abstract
Life was once normal before the first announcement of COVID-19's first case in Wuhan, China, and what was slowly spreading became an overnight worldwide pandemic. Ever since the virus spread at the end of 2019, it has been morphing and rapidly adapting to human nature changes which cause difficult conundrums in the efforts of fighting it. Thus, researchers were steered to investigate the virus in order to contain the outbreak considering its novelty and there being no known cure. In contribution to that, this paper extensively reviewed, compared, and analyzed two main points; SARS-CoV-2 virus transmission in humans and detection methods of COVID-19 in the human body. SARS-CoV-2 human exchange transmission methods reviewed four modes of transmission which are Respiratory Transmission, Fecal-Oral Transmission, Ocular transmission, and Vertical Transmission. The latter point particularly sheds light on the latest discoveries and advancements in the aim of COVID-19 diagnosis and detection of SARS-CoV-2 virus associated with this disease in the human body. The methods in this review paper were classified into two categories which are RNA-based detection including RT-PCR, LAMP, CRISPR, and NGS and secondly, biosensors detection including, electrochemical biosensors, electronic biosensors, piezoelectric biosensors, and optical biosensors.
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Affiliation(s)
- Mohammed Jawad Ahmed Alathari
- Department of Electrical, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia; (M.J.A.A.); (M.H.H.M.); (N.B.); (M.S.D.B.Z.); (A.A.A.B.)
| | - Yousif Al Mashhadany
- Department of Electrical Engineering, College of Engineering, University of Anbar, Anbar 00964, Iraq;
| | - Mohd Hadri Hafiz Mokhtar
- Department of Electrical, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia; (M.J.A.A.); (M.H.H.M.); (N.B.); (M.S.D.B.Z.); (A.A.A.B.)
| | - Norhafizah Burham
- Department of Electrical, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia; (M.J.A.A.); (M.H.H.M.); (N.B.); (M.S.D.B.Z.); (A.A.A.B.)
- School of Electrical Engineering, College of Engineering, Universiti Teknologi MARA, Shah Alam 40450, Malaysia
| | - Mohd Saiful Dzulkefly Bin Zan
- Department of Electrical, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia; (M.J.A.A.); (M.H.H.M.); (N.B.); (M.S.D.B.Z.); (A.A.A.B.)
| | - Ahmad Ashrif A Bakar
- Department of Electrical, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia; (M.J.A.A.); (M.H.H.M.); (N.B.); (M.S.D.B.Z.); (A.A.A.B.)
| | - Norhana Arsad
- Department of Electrical, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia; (M.J.A.A.); (M.H.H.M.); (N.B.); (M.S.D.B.Z.); (A.A.A.B.)
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30
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Locke M, Lythe G, López-García M, Muñoz-Fontela C, Carroll M, Molina-París C. Quantification of Type I Interferon Inhibition by Viral Proteins: Ebola Virus as a Case Study. Viruses 2021; 13:v13122441. [PMID: 34960709 PMCID: PMC8705787 DOI: 10.3390/v13122441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 11/16/2022] Open
Abstract
Type I interferons (IFNs) are cytokines with both antiviral properties and protective roles in innate immune responses to viral infection. They induce an antiviral cellular state and link innate and adaptive immune responses. Yet, viruses have evolved different strategies to inhibit such host responses. One of them is the existence of viral proteins which subvert type I IFN responses to allow quick and successful viral replication, thus, sustaining the infection within a host. We propose mathematical models to characterise the intra-cellular mechanisms involved in viral protein antagonism of type I IFN responses, and compare three different molecular inhibition strategies. We study the Ebola viral protein, VP35, with this mathematical approach. Approximate Bayesian computation sequential Monte Carlo, together with experimental data and the mathematical models proposed, are used to perform model calibration, as well as model selection of the different hypotheses considered. Finally, we assess if model parameters are identifiable and discuss how such identifiability can be improved with new experimental data.
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Affiliation(s)
- Macauley Locke
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK; (M.L.); (G.L.); (M.L.-G.)
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK; (M.L.); (G.L.); (M.L.-G.)
| | - Martín López-García
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK; (M.L.); (G.L.); (M.L.-G.)
| | - César Muñoz-Fontela
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Straße 74, 20359 Hamburg, Germany;
- German Center for Infection Research (DZIF), Partner Site Hamburg, Bernhard Nocht Straße 74, 20359 Hamburg, Germany
| | - Miles Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK;
| | - Carmen Molina-París
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK; (M.L.); (G.L.); (M.L.-G.)
- T-6, Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Correspondence:
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31
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The N-terminal Region of Middle East Respiratory Syndrome Coronavirus Accessory Protein 8b is Essential for Enhanced Virulence of an Attenuated Murine Coronavirus. J Virol 2021; 96:e0184221. [PMID: 34817197 PMCID: PMC8826903 DOI: 10.1128/jvi.01842-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a beta coronavirus that emerged in 2012, causing severe pneumonia and renal failure. MERS-CoV encodes five accessory proteins. Some of them have been shown to interfere with host antiviral immune response. However, the roles of protein 8b in innate immunity and viral virulence was rarely studied. Here, we introduced individual MERS-CoV accessory protein genes into the genome of an attenuated murine coronavirus (Mouse hepatitis virus, MHV), respectively, and found accessory protein 8b could enhance viral replication in vivo and in vitro and increase the lethality of infected mice. RNA-seq analysis revealed that protein 8b could significantly inhibit type I interferon production (IFN-I) and innate immune response in mice infected with MHV expressing protein 8b. We also found that MERS-CoV protein 8b could initiate from multiple internal methionine sites and at least three protein variants were identified. Residues 1-23 of protein 8b was demonstrated to be responsible for increased virulence in vivo. In addition, the inhibitory effect on IFN-I of protein 8b might not contribute to its virulence enhancement as aa1-23 deletion did not affect IFN-I production in vitro and in vivo. Next, we also found that protein 8b was localized to the endoplasmic reticulum (ER)/Golgi membrane in infected cells, which was disrupted by C-terminal region aa 88-112 deletion. This study will provide new insight into the pathogenesis of MERS-CoV infection. IMPORTANCE Multiple coronaviruses (CoV) cause severe respiratory infections and become global public health threats such as SARS-CoV, MERS-CoV, and SARS-CoV-2. Each coronavirus contains different numbers of accessory proteins which show high variability among different CoVs. Accessory proteins are demonstrated to play essential roles in pathogenesis of CoVs. MERS-CoV contains 5 accessory proteins (protein 3, 4a, 4b, 5, 8b), and deletion of all four accessory proteins (protein 3, 4a, 4b, 5), significantly affects MERS-CoV replication and pathogenesis. However, whether ORF8b also regulates MERS-CoV infection is unknown. Here, we constructed mouse hepatitis virus (MHV) recombinant virus expressing MERS-CoV protein 8b and demonstrated protein 8b could significantly enhance the virulence of MHV, which is mediated by N-terminal domain of protein 8b. This study will shed light on the understanding of pathogenesis of MERS-CoV infection.
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32
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Chukwurah E, Farabaugh KT, Guan BJ, Ramakrishnan P, Hatzoglou M. A tale of two proteins: PACT and PKR and their roles in inflammation. FEBS J 2021; 288:6365-6391. [PMID: 33387379 PMCID: PMC9248962 DOI: 10.1111/febs.15691] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/14/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022]
Abstract
Inflammation is a pathological hallmark associated with bacterial and viral infections, autoimmune diseases, genetic disorders, obesity and diabetes, as well as environmental stresses including physical and chemical trauma. Among numerous proteins regulating proinflammatory signaling, very few such as Protein kinase R (PKR), have been shown to play an all-pervading role in inflammation induced by varied stimuli. PKR was initially characterized as an interferon-inducible gene activated by viral double-stranded RNA with a role in protein translation inhibition. However, it has become increasingly clear that PKR is involved in multiple pathways that promote inflammation in response to stress activation, both dependent on and independent of its cellular protein activator of PKR (PACT). In this review, we discuss the signaling pathways that contribute to the initiation of inflammation, including Toll-like receptor, interferon, and RIG-I-like receptor signaling, as well as inflammasome activation. We go on to discuss the specific roles that PKR and PACT play in such proinflammatory signaling, as well as in metabolic syndrome- and environmental stress-induced inflammation.
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Affiliation(s)
- Evelyn Chukwurah
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106
| | - Kenneth T. Farabaugh
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106
| | - Bo-Jhih Guan
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106
| | | | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106
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33
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Li JY, Zhou ZJ, Wang Q, He QN, Zhao MY, Qiu Y, Ge XY. Innate Immunity Evasion Strategies of Highly Pathogenic Coronaviruses: SARS-CoV, MERS-CoV, and SARS-CoV-2. Front Microbiol 2021; 12:770656. [PMID: 34777324 PMCID: PMC8586461 DOI: 10.3389/fmicb.2021.770656] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022] Open
Abstract
In the past two decades, coronavirus (CoV) has emerged frequently in the population. Three CoVs (SARS-CoV, MERS-CoV, SARS-CoV-2) have been identified as highly pathogenic human coronaviruses (HP-hCoVs). Particularly, the ongoing COVID-19 pandemic caused by SARS-CoV-2 warns that HP-hCoVs present a high risk to human health. Like other viruses, HP-hCoVs interact with their host cells in sophisticated manners for infection and pathogenesis. Here, we reviewed the current knowledge about the interference of HP-hCoVs in multiple cellular processes and their impacts on viral infection. HP-hCoVs employed various strategies to suppress and evade from immune response, including shielding viral RNA from recognition by pattern recognition receptors (PRRs), impairing IFN-I production, blocking the downstream pathways of IFN-I, and other evasion strategies. This summary provides a comprehensive view of the interplay between HP-hCoVs and the host cells, which is helpful to understand the mechanism of viral pathogenesis and develop antiviral therapies.
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Affiliation(s)
- Jin-Yan Li
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, China
| | - Zhi-Jian Zhou
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, China
| | - Qiong Wang
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, China
| | - Qing-Nan He
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ming-Yi Zhao
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, China
| | - Xing-Yi Ge
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, China
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34
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Interspecies Jumping of Bat Coronaviruses. Viruses 2021; 13:v13112188. [PMID: 34834994 PMCID: PMC8620431 DOI: 10.3390/v13112188] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
In the last two decades, several coronavirus (CoV) interspecies jumping events have occurred between bats and other animals/humans, leading to major epidemics/pandemics and high fatalities. The SARS epidemic in 2002/2003 had a ~10% fatality. The discovery of SARS-related CoVs in horseshoe bats and civets and genomic studies have confirmed bat-to-civet-to-human transmission. The MERS epidemic that emerged in 2012 had a ~35% mortality, with dromedaries as the reservoir. Although CoVs with the same genome organization (e.g., Tylonycteris BatCoV HKU4 and Pipistrellus BatCoV HKU5) were also detected in bats, there is still a phylogenetic gap between these bat CoVs and MERS-CoV. In 2016, 10 years after the discovery of Rhinolophus BatCoV HKU2 in Chinese horseshoe bats, fatal swine disease outbreaks caused by this virus were reported in southern China. In late 2019, an outbreak of pneumonia emerged in Wuhan, China, and rapidly spread globally, leading to >4,000,000 fatalities so far. Although the genome of SARS-CoV-2 is highly similar to that of SARS-CoV, patient zero and the original source of the pandemic are still unknown. To protect humans from future public health threats, measures should be taken to monitor and reduce the chance of interspecies jumping events, either occurring naturally or through recombineering experiments.
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35
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Gutiérrez-Álvarez J, Honrubia JM, Sanz-Bravo A, González-Miranda E, Fernández-Delgado R, Rejas MT, Zúñiga S, Sola I, Enjuanes L. Middle East respiratory syndrome coronavirus vaccine based on a propagation-defective RNA replicon elicited sterilizing immunity in mice. Proc Natl Acad Sci U S A 2021; 118:e2111075118. [PMID: 34686605 PMCID: PMC8639359 DOI: 10.1073/pnas.2111075118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2021] [Indexed: 12/11/2022] Open
Abstract
Self-amplifying RNA replicons are promising platforms for vaccine generation. Their defects in one or more essential functions for viral replication, particle assembly, or dissemination make them highly safe as vaccines. We previously showed that the deletion of the envelope (E) gene from the Middle East respiratory syndrome coronavirus (MERS-CoV) produces a replication-competent propagation-defective RNA replicon (MERS-CoV-ΔE). Evaluation of this replicon in mice expressing human dipeptidyl peptidase 4, the virus receptor, showed that the single deletion of the E gene generated an attenuated mutant. The combined deletion of the E gene with accessory open reading frames (ORFs) 3, 4a, 4b, and 5 resulted in a highly attenuated propagation-defective RNA replicon (MERS-CoV-Δ[3,4a,4b,5,E]). This RNA replicon induced sterilizing immunity in mice after challenge with a lethal dose of a virulent MERS-CoV, as no histopathological damage or infectious virus was detected in the lungs of challenged mice. The four mutants lacking the E gene were genetically stable, did not recombine with the E gene provided in trans during their passage in cell culture, and showed a propagation-defective phenotype in vivo. In addition, immunization with MERS-CoV-Δ[3,4a,4b,5,E] induced significant levels of neutralizing antibodies, indicating that MERS-CoV RNA replicons are highly safe and promising vaccine candidates.
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MESH Headings
- Animals
- Antibodies, Neutralizing/biosynthesis
- Antibodies, Viral/biosynthesis
- Coronavirus Infections/genetics
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/virology
- Defective Viruses/genetics
- Defective Viruses/immunology
- Female
- Gene Deletion
- Genes, env
- Humans
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Middle East Respiratory Syndrome Coronavirus/genetics
- Middle East Respiratory Syndrome Coronavirus/immunology
- Middle East Respiratory Syndrome Coronavirus/pathogenicity
- RNA, Viral/administration & dosage
- RNA, Viral/genetics
- RNA, Viral/immunology
- Replicon
- Vaccines, DNA
- Vaccines, Virus-Like Particle/administration & dosage
- Vaccines, Virus-Like Particle/genetics
- Vaccines, Virus-Like Particle/immunology
- Viral Vaccines/administration & dosage
- Viral Vaccines/genetics
- Viral Vaccines/immunology
- Virulence/genetics
- Virulence/immunology
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Affiliation(s)
- J Gutiérrez-Álvarez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid 28049 Madrid, Spain
| | - J M Honrubia
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid 28049 Madrid, Spain
| | - A Sanz-Bravo
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid 28049 Madrid, Spain
| | - E González-Miranda
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid 28049 Madrid, Spain
| | - R Fernández-Delgado
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid 28049 Madrid, Spain
| | - M T Rejas
- Electron Microscopy Service, Centro de Biología Molecular "Severo Ochoa" (CBMSO-CSIC-UAM), Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - S Zúñiga
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid 28049 Madrid, Spain
| | - I Sola
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid 28049 Madrid, Spain
| | - L Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid 28049 Madrid, Spain;
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36
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Kumar S, Saurabh MK, Narasimha VL, Maharshi V. Efficacy of Interferon-β in Moderate-to-Severe Hospitalised Cases of COVID-19: A Systematic Review and Meta-analysis. Clin Drug Investig 2021; 41:1037-1046. [PMID: 34687413 PMCID: PMC8540871 DOI: 10.1007/s40261-021-01092-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2021] [Indexed: 11/30/2022]
Abstract
Background and Objective Interferon-β, as with several other anti-viral agents, has been investigated as a treatment option for COVID-19 as a repurposed drug. The present study is a systematic review and meta-analysis of interferon-β to determine its efficacy among moderate-to-severe COVID-19 patients. Methods A systematic literature search was done using relevant terms for ‘COVID-19’ and ‘interferon-β’. Randomised controlled trials (RCT) evaluating the efficacy of interferon-β in COVID-19 were included. Data were extracted for outcome measures, namely mortality, time to clinical improvement and length of hospital stay. Random effects meta-analysis was performed using RevMan V.5.4.1 to calculate overall effect estimate as odds ratio/hazard ratio for categorical variables and mean difference for continuous variable. Result Eight RCTs were eligible for qualitative synthesis and seven for meta-analysis. The overall effect estimate (odds ratio [OR] 0.59; 95 % CI 0.91, 1.12) and (mean difference [MD] − 1.41; 95 % CI − 2.84, 0.02) indicated no statistically significant difference between effect of IFN-β and that of control on mortality and length of hospital stay, respectively. However, the overall effect estimate (hazard ratio [HR] 1.95; 95 % CI 1.36, 2.79) denoted a favourable effect of INF-β on reducing the time to clinical improvement in moderate-to-severe COVID-19 patients. Conclusion Addition of interferon-β to standard of care resulted in significant reduction in time to clinical improvement but no significant benefit in terms of reduction in mortality and length of hospital stay in moderate-to-severe cases of COVID-19.
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Affiliation(s)
- Subodh Kumar
- All India Institute of Medical Sciences, Deoghar, India
| | | | | | - Vikas Maharshi
- All India Institute of Medical Sciences, Deoghar, India.
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37
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Schroeder S, Mache C, Kleine-Weber H, Corman VM, Muth D, Richter A, Fatykhova D, Memish ZA, Stanifer ML, Boulant S, Gultom M, Dijkman R, Eggeling S, Hocke A, Hippenstiel S, Thiel V, Pöhlmann S, Wolff T, Müller MA, Drosten C. Functional comparison of MERS-coronavirus lineages reveals increased replicative fitness of the recombinant lineage 5. Nat Commun 2021; 12:5324. [PMID: 34493730 PMCID: PMC8423819 DOI: 10.1038/s41467-021-25519-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/05/2021] [Indexed: 01/20/2023] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is enzootic in dromedary camels across the Middle East and Africa. Virus-induced pneumonia in humans results from animal contact, with a potential for limited onward transmission. Phenotypic changes have been suspected after a novel recombinant clade (lineage 5) caused large nosocomial outbreaks in Saudi Arabia and South Korea in 2016. However, there has been no functional assessment. Here we perform a comprehensive in vitro and ex vivo comparison of viruses from parental and recombinant virus lineages (lineage 3, n = 7; lineage 4, n = 8; lineage 5, n = 9 viruses) from Saudi Arabia, isolated immediately before and after the shift toward lineage 5. Replication of lineage 5 viruses is significantly increased. Transcriptional profiling finds reduced induction of immune genes IFNB1, CCL5, and IFNL1 in lung cells infected with lineage 5 strains. Phenotypic differences may be determined by IFN antagonism based on experiments using IFN receptor knock out and signaling inhibition. Additionally, lineage 5 is more resilient against IFN pre-treatment of Calu-3 cells (ca. 10-fold difference in replication). This phenotypic change associated with lineage 5 has remained undiscovered by viral sequence surveillance, but may be a relevant indicator of pandemic potential. MERS-CoV is enzootic in dromedary camels, can spread to humans but undergoes limited onward transmission. Here, Schroeder et al. compare clinical isolates of MERS-CoV in vitro and show that the predominantly circulating recombinant lineage 5 possess a fitness advantage over parental lineage 3 and 4 due to reduced activation of innate immune signaling.
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Affiliation(s)
- Simon Schroeder
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christin Mache
- Unit 17, Influenza and other Respiratory Viruses, Robert Koch Institut, Berlin, Germany
| | - Hannah Kleine-Weber
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Centre for Infection Research (DZIF), Berlin, Germany
| | - Doreen Muth
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Anja Richter
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Diana Fatykhova
- Dept. of Infectious and Respiratory Diseases, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ziad A Memish
- Research and Innovation Department, King Saud Medical City, Ministry of Health, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Kingdom of Saudi Arabia.,Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Megan L Stanifer
- Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Steeve Boulant
- Research Group "Cellular polarity and viral infection", German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Mitra Gultom
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Ronald Dijkman
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Stephan Eggeling
- Department of Thoracic Surgery, Vivantes Clinics Neukölln, Berlin, Germany
| | - Andreas Hocke
- Dept. of Infectious and Respiratory Diseases, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Stefan Hippenstiel
- Dept. of Infectious and Respiratory Diseases, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Thorsten Wolff
- Unit 17, Influenza and other Respiratory Viruses, Robert Koch Institut, Berlin, Germany
| | - Marcel A Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Centre for Infection Research (DZIF), Berlin, Germany.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany. .,German Centre for Infection Research (DZIF), Berlin, Germany.
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38
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Ayatollahi SA, Sharifi-Rad J, Tsouh Fokou PV, Mahady GB, Ansar Rasul Suleria H, Krishna Kapuganti S, Gadhave K, Giri R, Garg N, Sharma R, Ribeiro D, Rodrigues CF, Reiner Ž, Taheri Y, Cruz-Martins N. Naturally Occurring Bioactives as Antivirals: Emphasis on Coronavirus Infection. Front Pharmacol 2021; 12:575877. [PMID: 34267652 PMCID: PMC8277242 DOI: 10.3389/fphar.2021.575877] [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: 06/24/2020] [Accepted: 02/23/2021] [Indexed: 12/24/2022] Open
Abstract
The current coronavirus disease (COVID-19) outbreak is a significant threat to human health and the worldwide economy. Coronaviruses cause a variety of diseases, such as pneumonia-like upper respiratory tract illnesses, gastroenteritis, encephalitis, multiple organ failure involving lungs and kidneys which might cause death. Since the pandemic started there have been more than 107 million COVID-19 infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and ∼2.4 million deaths globally. SARS-CoV-2 is easily transmitted from person-to-person and has spread quickly across all continents. With the continued increase in morbidity and mortality caused by COVID-19, and the damage to the global economy, there is an urgent need for effective prevention and treatment strategies. The advent of safe and effective vaccines has been a significant step forward in the battle against COVID-19, however treatment of the symptoms associated with the disease still requires new anti-viral and anti-inflammatory drug therapies. To this end, scientists have been investigating available natural products that may be effective against SARS-CoV-2, with some products showing promise in fighting several viral infections. Since many natural products are dietary components or are prepared as dietary supplements people tend to consider them safer than synthetic drugs. For example, Traditional Chinese Medicines have been effectively utilized to treat SARS-CoV-2 infected patients with promising results. In this review, we summarize the current knowledge of COVID-19 therapies and the therapeutic potential of medicinal plant extracts and natural compounds for the treatment of several viral infections, with special emphasis on SARS-CoV-2 infection. Realistic strategies that can be employed for the effective use of bioactive compounds for anti-SARS-CoV-2 research are also provided.
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Affiliation(s)
- Seyed Abdulmajid Ayatollahi
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Pharmacognosy and Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Javad Sharifi-Rad
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Gail B. Mahady
- Department of Pharmacy Practice, PAHO/WHO Collaborating Centre for Traditional Medicine, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| | | | | | - Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Neha Garg
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Daniel Ribeiro
- Northern Superior Health School of the Portuguese Red Cross, Oliveira de Azeméis, Portugal
- Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Rua Central de Gandra, Gandra, Portugal
| | - Célia F. Rodrigues
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Željko Reiner
- Department of Internal Medicine, University Hospital Centre Zagreb, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Yasaman Taheri
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Natália Cruz-Martins
- Laboratory of Neuropsychophysiology, Faculty of Psychology and Education Sciences, University of Porto, Porto, Portugal
- Department of Biomedicine/Medicine, Faculty of Medicine, University of Porto, Porto, Portugal
- Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
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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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Awogbindin IO, Ben-Azu B, Olusola BA, Akinluyi ET, Adeniyi PA, Di Paolo T, Tremblay MÈ. Microglial Implications in SARS-CoV-2 Infection and COVID-19: Lessons From Viral RNA Neurotropism and Possible Relevance to Parkinson's Disease. Front Cell Neurosci 2021; 15:670298. [PMID: 34211370 PMCID: PMC8240959 DOI: 10.3389/fncel.2021.670298] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 05/05/2021] [Indexed: 12/24/2022] Open
Abstract
Since December 2019, humankind has been experiencing a ravaging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak, the second coronavirus pandemic in a decade after the Middle East respiratory syndrome coronavirus (MERS-CoV) disease in 2012. Infection with SARS-CoV-2 results in Coronavirus disease 2019 (COVID-19), which is responsible for over 3.1 million deaths worldwide. With the emergence of a second and a third wave of infection across the globe, and the rising record of multiple reinfections and relapses, SARS-CoV-2 infection shows no sign of abating. In addition, it is now evident that SARS-CoV-2 infection presents with neurological symptoms that include early hyposmia, ischemic stroke, meningitis, delirium and falls, even after viral clearance. This may suggest chronic or permanent changes to the neurons, glial cells, and/or brain vasculature in response to SARS-CoV-2 infection or COVID-19. Within the central nervous system (CNS), microglia act as the central housekeepers against altered homeostatic states, including during viral neurotropic infections. In this review, we highlight microglial responses to viral neuroinfections, especially those with a similar genetic composition and route of entry as SARS-CoV-2. As the primary sensor of viral infection in the CNS, we describe the pathogenic and neuroinvasive mechanisms of RNA viruses and SARS-CoV-2 vis-à-vis the microglial means of viral recognition. Responses of microglia which may culminate in viral clearance or immunopathology are also covered. Lastly, we further discuss the implication of SARS-CoV-2 CNS invasion on microglial plasticity and associated long-term neurodegeneration. As such, this review provides insight into some of the mechanisms by which microglia could contribute to the pathophysiology of post-COVID-19 neurological sequelae and disorders, including Parkinson's disease, which could be pervasive in the coming years given the growing numbers of infected and re-infected individuals globally.
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Affiliation(s)
- Ifeoluwa O. Awogbindin
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Neuroimmunology Group, Molecular Drug Metabolism and Toxicology Laboratory, Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Benneth Ben-Azu
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Neuropharmacology Unit, Department of Pharmacology and Therapeutics, Faculty of Basic Medical Sciences, College of Health Sciences, Delta State University, Abraka, Nigeria
| | - Babatunde A. Olusola
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Elizabeth T. Akinluyi
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, Afe Babalola University, Ado-Ekiti, Nigeria
| | - Philip A. Adeniyi
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Therese Di Paolo
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Faculté de Pharmacie, Université Laval, Québec, QC, Canada
| | - Marie-Ève Tremblay
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Neurology and Neurosurgery Department, McGill University, Montréal, QC, Canada
- Department of Molecular Medicine, Université Laval, Québec, QC, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
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Fang P, Fang L, Zhang H, Xia S, Xiao S. Functions of Coronavirus Accessory Proteins: Overview of the State of the Art. Viruses 2021; 13:1139. [PMID: 34199223 PMCID: PMC8231932 DOI: 10.3390/v13061139] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus accessory proteins are a unique set of proteins whose genes are interspersed among or within the genes encoding structural proteins. Different coronavirus genera, or even different species within the same coronavirus genus, encode varying amounts of accessory proteins, leading to genus- or species-specificity. Though accessory proteins are dispensable for the replication of coronavirus in vitro, they play important roles in regulating innate immunity, viral proliferation, and pathogenicity. The function of accessory proteins on virus infection and pathogenesis is an area of particular interest. In this review, we summarize the current knowledge on accessory proteins of several representative coronaviruses that infect humans or animals, including the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with an emphasis on their roles in interaction between virus and host, mainly involving stress response, innate immunity, autophagy, and apoptosis. The cross-talking among these pathways is also discussed.
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Affiliation(s)
- Puxian Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (P.F.); (L.F.); (H.Z.); (S.X.)
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (P.F.); (L.F.); (H.Z.); (S.X.)
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Huichang Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (P.F.); (L.F.); (H.Z.); (S.X.)
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Sijin Xia
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (P.F.); (L.F.); (H.Z.); (S.X.)
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (P.F.); (L.F.); (H.Z.); (S.X.)
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, 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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43
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Blalock WL. Opposing forces fight over the same ground to regulate interferon signaling. Biochem J 2021; 478:1853-1859. [PMID: 34003254 DOI: 10.1042/bcj20210110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 11/17/2022]
Abstract
The current SARS-CoV-2 pandemic has spurred new interest in interferon signaling in response to viral pathogens. Much of what we know about the signaling molecules and associated signal transduction induced during the host cellular response to viral pathogens has been gained from research conducted from the 1990's to the present day, but certain intricacies of the mechanisms involved, still remain unclear. In a recent study by Vaughn et al. the authors examine one of the main mechanisms regulating interferon induction following viral infection, the RIG-I/MAVS/IRF3 pathway, and find that similar to PKR both DICER interacting proteins, PACT and TRBP, regulate RIG-I signaling in an opposing manner. More specifically, the reported findings demonstrate, like others, that PACT stimulates RIG-I-mediated signaling in a manner independent of PACT dsRNA-binding ability or phosphorylation at sites known to be important for PACT-dependent PKR activation. In contrast, they show for the first time that TRBP inhibits RIG-I-mediated signaling. RIG-I inhibition by TRBP did not require phosphorylation of sites shown to be important for inhibiting PKR, nor did it involve PACT or PKR, but it did require the dsRNA-binding ability of TRBP. These findings open the door to a complex co-regulation of RIG-I, PKR, MDA5, miRNA processing, and interferon induction.
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Affiliation(s)
- William L Blalock
- 'Luigi Luca Cavalli-Sforza' Istituto di Genetica Molecolare-Consiglio Nazionale delle Ricerche (IGM-CNR), Bologna, Italy
- IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
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Mubarak A, Alrfaei B, Aljurayyan A, Alqafil MM, Farrag MA, Hamed ME, Alosaimi B, Almajhdi F, Alturaiki W. In vivo and in vitro Evaluation of Cytokine Expression Profiles During Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Infection. J Inflamm Res 2021; 14:2121-2131. [PMID: 34045884 PMCID: PMC8149276 DOI: 10.2147/jir.s312337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/10/2021] [Indexed: 01/12/2023] Open
Abstract
Background Middle East respiratory syndrome coronavirus (MERS-CoV) first emerged in the Kingdom of Saudi Arabia, is associated with a high mortality rate. Aim To determine the effect of MERS-CoV on the immune response in infected patients and investigate cytokine production in the A549 epithelial cell line in response to a recombinant MERS-CoV spike protein (rSP) in the presence or absence of anti-dipeptidyl peptidase 4 (DPP4) antibody (3 independent experiments). Cytokine levels were measured using a cytokine ELISA array. Methods A Bio-Plex multiplex assay and cytokine ELISA were used in our study to measure the cytokine levels. Results Comparative analysis of MERS-CoV-infected patients (4 samples) and noninfected healthy controls (HCs) (5 samples) showed that serum levels of the following cytokines and chemokines were significantly higher in MERS-CoV patients than in the HCs (*p < 0.05): interferon (IFN)-α2 (43.4 vs 5.4), IFN-β (17.7 vs 6.2), IFN-γ (43.4 vs 9.7), interleukin (IL)-8 (13.7 vs 0), IL-2 (11.2 vs 3), IL-27p28 (57.8 vs 13.8), and IL-35 (167.5 vs 87.5). Discussion Our results revealed that MERS-CoV infection induced a slight increase in IFN levels but triggered a more pronounced increase in expression of the regulatory cytokines IL-27 and IL-35. A recombinant version of the full-length MERS-CoV spike protein increased the expression of IL-8 (160 pg/mL), IL-2 (100 pg/mL) and IL-12 (65 pg/mL) in A549 lung epithelial cells compared to that in the unstimulated control cells. The presence of anti-DPP4 antibody did not affect cytokine suppression or induction in A549 cells in vitro but decreased the level of IL-8 from 160 pg/mL to 65 pg/mL. Conclusion MERS-CoV can decrease IFN levels to interfere with the IFN pathway and enhance the production of regulatory cytokines. Inhibition of the increases in IL-27 and IL-35 may contribute to halting MERS-CoV in the early stage of infection.
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Affiliation(s)
- Ayman Mubarak
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Bahauddeen Alrfaei
- Stem Cells Unit, Department of Cellular Therapy, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Science, MNGHA, Riyadh, Saudi Arabia
| | - Abdullah Aljurayyan
- Immunology and HLA Department, Pathology and Laboratory Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Mahfoudh M Alqafil
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed A Farrag
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Maaweya E Hamed
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Bandar Alosaimi
- Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Fahad Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Wael Alturaiki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, 11952, Saudi Arabia
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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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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: 118] [Impact Index Per Article: 39.3] [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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Banerjee A, El-Sayes N, Budylowski P, Jacob RA, Richard D, Maan H, Aguiar JA, Demian WL, Baid K, D'Agostino MR, Ang JC, Murdza T, Tremblay BJM, Afkhami S, Karimzadeh M, Irving AT, Yip L, Ostrowski M, Hirota JA, Kozak R, Capellini TD, Miller MS, Wang B, Mubareka S, McGeer AJ, McArthur AG, Doxey AC, Mossman K. Experimental and natural evidence of SARS-CoV-2-infection-induced activation of type I interferon responses. iScience 2021; 24:102477. [PMID: 33937724 PMCID: PMC8074517 DOI: 10.1016/j.isci.2021.102477] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/26/2021] [Accepted: 04/23/2021] [Indexed: 12/22/2022] Open
Abstract
Type I interferons (IFNs) are our first line of defense against virus infection. Recent studies have suggested the ability of SARS-CoV-2 proteins to inhibit IFN responses. Emerging data also suggest that timing and extent of IFN production is associated with manifestation of COVID-19 severity. In spite of progress in understanding how SARS-CoV-2 activates antiviral responses, mechanistic studies into wild-type SARS-CoV-2-mediated induction and inhibition of human type I IFN responses are scarce. Here we demonstrate that SARS-CoV-2 infection induces a type I IFN response in vitro and in moderate cases of COVID-19. In vitro stimulation of type I IFN expression and signaling in human airway epithelial cells is associated with activation of canonical transcriptions factors, and SARS-CoV-2 is unable to inhibit exogenous induction of these responses. Furthermore, we show that physiological levels of IFNα detected in patients with moderate COVID-19 is sufficient to suppress SARS-CoV-2 replication in human airway cells.
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Affiliation(s)
- Arinjay Banerjee
- Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
- Corresponding author
| | - Nader El-Sayes
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Patrick Budylowski
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Rajesh Abraham Jacob
- Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Daniel Richard
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hassaan Maan
- Vector Institute for Artificial Intelligence, Toronto, ON M5G 1M1, Canada
- Peter Munk Cardiac Centre, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Jennifer A. Aguiar
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Wael L. Demian
- Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Kaushal Baid
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Michael R. D'Agostino
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Jann Catherine Ang
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Tetyana Murdza
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | | | - Sam Afkhami
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Mehran Karimzadeh
- Vector Institute for Artificial Intelligence, Toronto, ON M5G 1M1, Canada
| | - Aaron T. Irving
- Zhejiang University – University of Edinburgh Institute, Haining, Zhejiang 314400, China
- Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310027, China
| | - Lily Yip
- Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
| | - Mario Ostrowski
- Department of Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
- Keenan Research Centre for Biomedical Science of St. Michael's Hospital, UnityHealth, Toronto, ON M5B 1W8, Canada
| | - Jeremy A. Hirota
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- Division of Respirology, Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
- Division of Respiratory Medicine, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Robert Kozak
- Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Terence D. Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Matthew S. Miller
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Bo Wang
- Vector Institute for Artificial Intelligence, Toronto, ON M5G 1M1, Canada
- Peter Munk Cardiac Centre, University Health Network, Toronto, ON M5G 2C4, Canada
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Samira Mubareka
- Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Allison J. McGeer
- Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Andrew G. McArthur
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Andrew C. Doxey
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Karen Mossman
- Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
- Corresponding author
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48
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Barik S. Systematizing the genomic order and relatedness in the open reading frames (ORFs) of the coronaviruses. INFECTION GENETICS AND EVOLUTION 2021; 92:104858. [PMID: 33848683 PMCID: PMC8053407 DOI: 10.1016/j.meegid.2021.104858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 11/16/2022]
Abstract
The coronaviruses (CoVs), including SARS-CoV-2, the agent of the ongoing deadly CoVID-19 pandemic (Coronavirus disease-2019), represent a highly complex and diverse class of RNA viruses with large genomes, complex gene repertoire, and intricate transcriptional and translational mechanisms. The 3′-terminal one-third of the genome encodes four structural proteins, namely spike, envelope, membrane, and nucleocapsid, interspersed with genes for accessory proteins that are largely nonstructural and called ‘open reading frame’ (ORF) proteins with alphanumerical designations, but not in a consistent or sequential order. Here, I report a comparative study of these ORF proteins, mainly encoded in two gene clusters, i.e. between the Spike and the Envelope genes, and between the Membrane and the Nucleocapsid genes. For brevity and focus, a greater emphasis was placed on the first cluster, collectively designated as the ‘orf3 region’ for ease of referral. Overall, an apparently diverse set of ORFs, such as ORF3a, ORF3b, ORF3c, ORF3d, ORF4 and ORF5, but not necessarily numbered in that order on all CoV genomes, were analyzed along with other ORFs. Unexpectedly, the gene order or naming of the ORFs were never fully conserved even within the members of one Genus. These studies also unraveled hitherto unrecognized orf genes in alternative translational frames, encoding potentially novel polypeptides as well as some that are highly similar to known ORFs. Finally, several options of an inclusive and systematic numbering are proposed not only for the orf3 region but also for the other orf genes in the viral genome in an effort to regularize the apparently confusing names and orders. Regardless of the ultimate acceptability of one system over the others, this treatise is hoped to initiate an informed discourse in this area.
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Zhang Y, Gargan S, Lu Y, Stevenson NJ. An Overview of Current Knowledge of Deadly CoVs and Their Interface with Innate Immunity. Viruses 2021; 13:560. [PMID: 33810391 PMCID: PMC8066579 DOI: 10.3390/v13040560] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Coronaviruses are a large family of zoonotic RNA viruses, whose infection can lead to mild or lethal respiratory tract disease. Severe Acute Respiratory Syndrome-Coronavirus-1 (SARS-CoV-1) first emerged in Guangdong, China in 2002 and spread to 29 countries, infecting 8089 individuals and causing 774 deaths. In 2012, Middle East Respiratory Syndrome-Coronavirus (MERS-CoV) emerged in Saudi Arabia and has spread to 27 countries, with a mortality rate of ~34%. In 2019, SARS-CoV-2 emerged and has spread to 220 countries, infecting over 100,000,000 people and causing more than 2,000,000 deaths to date. These three human coronaviruses cause diseases of varying severity. Most people develop mild, common cold-like symptoms, while some develop acute respiratory distress syndrome (ARDS). The success of all viruses, including coronaviruses, relies on their evolved abilities to evade and modulate the host anti-viral and pro-inflammatory immune responses. However, we still do not fully understand the transmission, phylogeny, epidemiology, and pathogenesis of MERS-CoV and SARS-CoV-1 and -2. Despite the rapid application of a range of therapies for SARS-CoV-2, such as convalescent plasma, remdesivir, hydroxychloroquine and type I interferon, no fully effective treatment has been determined. Remarkably, COVID-19 vaccine research and development have produced several offerings that are now been administered worldwide. Here, we summarise an up-to-date understanding of epidemiology, immunomodulation and ongoing anti-viral and immunosuppressive treatment strategies. Indeed, understanding the interplay between coronaviruses and the anti-viral immune response is crucial to identifying novel targets for therapeutic intervention, which may even prove invaluable for the control of future emerging coronavirus.
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Affiliation(s)
- Yamei Zhang
- Viral Immunology Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland; (Y.Z.); (S.G.)
| | - Siobhan Gargan
- Viral Immunology Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland; (Y.Z.); (S.G.)
| | - Yongxu Lu
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK;
| | - Nigel J. Stevenson
- Viral Immunology Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland; (Y.Z.); (S.G.)
- Viral Immunology Group, Royal College of Surgeons in Ireland—Medical University of Bahrain, Adliya 15503, Bahrain
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50
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Dabbish AM, Yonis N, Salama M, Essa MM, Qoronfleh MW. Inflammatory pathways and potential therapies for COVID-19: A mini review. EUR J INFLAMM 2021. [DOI: 10.1177/20587392211002986] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The public health crisis of the novel coronavirus disease (COVID-19) is alarming since January 2020. COVID-19 genome (SARS-CoV-2) is related to other highly pathogenic coronaviruses SARS-CoV (severe acute respiratory syndrome coronavirus) and MERS-CoV (Middle East respiratory syndrome coronavirus). Amino acid substitutions in some of SARS-CoV-2 proteins resulted in mutations proposing more virulent and contagious properties for this novel virus. Coronavirus penetrates the host cell via endocytosis and once infected, immune responses are triggered to fight against the pathogen. Innate immune response activates major transcription factors to secrete proinflammatory cytokines and type 1 interferon response (T1INF) to induce antiviral immunity. While adaptive immunity initiates cascade of B-cells antibody mediated and T-cells cellular mediate immunities, several mechanisms are raised by SARS-CoV-2 to evade host immune response. Consequently, a surge of proinflammatory cytokines, known as cytokine storm (CS) are released. Failure to manage CS results in several pathological complications as acute respiratory distress syndrome (ARDS). Although researches have not discovered an effective treatment against SARS-CoV-2, recent therapeutic approaches recommending the use of anti-inflammatories in combination with antivirals and some repurposed drugs for COVID-19 patients. Future medications should be designed to target essential hallmarks in the CS to improve clinical outcomes.
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Affiliation(s)
- Areeg M Dabbish
- Biotechnology Graduate Program, School of Science and Engineering, The American University in Cairo, New Cairo, Egypt
| | - Nouran Yonis
- Institute of Global Health and Human Ecology (IGHHE) Graduate Program, The American University in Cairo, New Cairo, Egypt
| | - Mohamed Salama
- Institute of Global Health and Human Ecology (IGHHE), The American University in Cairo, New Cairo, Egypt
| | - Musthafa M Essa
- Department of Food Science and Nutrition, CAMS, Sultan Qaboos University, Muscat, Oman
- Ageing and Dementia Research Group, Sultan Qaboos University, Muscat, Oman
| | - M Walid Qoronfleh
- Research & Policy Department, World Innovation Summit for Health (WISH), Qatar Foundation, Doha, Qatar
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