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Jabeen M, Shoukat S, Shireen H, Bao Y, Khan A, Abbasi AA. Unraveling the genetic variations underlying virulence disparities among SARS-CoV-2 strains across global regions: insights from Pakistan. Virol J 2024; 21:55. [PMID: 38449001 PMCID: PMC10916261 DOI: 10.1186/s12985-024-02328-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
Over the course of the COVID-19 pandemic, several SARS-CoV-2 variants have emerged that may exhibit different etiological effects such as enhanced transmissibility and infectivity. However, genetic variations that reduce virulence and deteriorate viral fitness have not yet been thoroughly investigated. The present study sought to evaluate the effects of viral genetic makeup on COVID-19 epidemiology in Pakistan, where the infectivity and mortality rate was comparatively lower than other countries during the first pandemic wave. For this purpose, we focused on the comparative analyses of 7096 amino-acid long polyprotein pp1ab. Comparative sequence analysis of 203 SARS-CoV-2 genomes, sampled from Pakistan during the first wave of the pandemic revealed 179 amino acid substitutions in pp1ab. Within this set, 38 substitutions were identified within the Nsp3 region of the pp1ab polyprotein. Structural and biophysical analysis of proteins revealed that amino acid variations within Nsp3's macrodomains induced conformational changes and modified protein-ligand interactions, consequently diminishing the virulence and fitness of SARS-CoV-2. Additionally, the epistatic effects resulting from evolutionary substitutions in SARS-CoV-2 proteins may have unnoticed implications for reducing disease burden. In light of these findings, further characterization of such deleterious SARS-CoV-2 mutations will not only aid in identifying potential therapeutic targets but will also provide a roadmap for maintaining vigilance against the genetic variability of diverse SARS-CoV-2 strains circulating globally. Furthermore, these insights empower us to more effectively manage and respond to potential viral-based pandemic outbreaks of a similar nature in the future.
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Affiliation(s)
- Momina Jabeen
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad, Pakistan
| | - Shifa Shoukat
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad, Pakistan
| | - Huma Shireen
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad, Pakistan
| | - Yiming Bao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
- School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad, Pakistan.
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2
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Móvio MI, de Almeida GWC, Martines IDGL, Barros de Lima G, Sasaki SD, Kihara AH, Poole E, Nevels M, Carlan da Silva MC. SARS-CoV-2 ORF8 as a Modulator of Cytokine Induction: Evidence and Search for Molecular Mechanisms. Viruses 2024; 16:161. [PMID: 38275971 PMCID: PMC10819295 DOI: 10.3390/v16010161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/11/2024] [Accepted: 01/14/2024] [Indexed: 01/27/2024] Open
Abstract
Severe cases of SARS-CoV-2 infection are characterized by an immune response that leads to the overproduction of pro-inflammatory cytokines, resulting in lung damage, cardiovascular symptoms, hematologic symptoms, acute kidney injury and multiple organ failure that can lead to death. This remarkable increase in cytokines and other inflammatory molecules is primarily caused by viral proteins, and particular interest has been given to ORF8, a unique accessory protein specific to SARS-CoV-2. Despite plenty of research, the precise mechanisms by which ORF8 induces proinflammatory cytokines are not clear. Our investigations demonstrated that ORF8 augments production of IL-6 induced by Poly(I:C) in human embryonic kidney (HEK)-293 and monocyte-derived dendritic cells (mono-DCs). We discuss our findings and the multifaceted roles of ORF8 as a modulator of cytokine response, focusing on type I interferon and IL-6, a key component of the immune response to SARS-CoV-2. In addition, we explore the hypothesis that ORF8 may act through pattern recognition receptors of dsRNA such as TLRs.
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Affiliation(s)
- Marília Inês Móvio
- Laboratório de Neurogenética, Universidade Federal do ABC (UFABC), São Bernardo do Campo, São Paulo 09606-070, Brazil; (M.I.M.)
| | - Giovana Waner Carneiro de Almeida
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do UFABC (UFABC), São Bernardo do Campo, São Paulo 09606-070, Brazil; (G.W.C.d.A.); (G.B.d.L.); (S.D.S.)
| | - Isabella das Graças Lopes Martines
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do UFABC (UFABC), São Bernardo do Campo, São Paulo 09606-070, Brazil; (G.W.C.d.A.); (G.B.d.L.); (S.D.S.)
| | - Gilmara Barros de Lima
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do UFABC (UFABC), São Bernardo do Campo, São Paulo 09606-070, Brazil; (G.W.C.d.A.); (G.B.d.L.); (S.D.S.)
| | - Sergio Daishi Sasaki
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do UFABC (UFABC), São Bernardo do Campo, São Paulo 09606-070, Brazil; (G.W.C.d.A.); (G.B.d.L.); (S.D.S.)
| | - Alexandre Hiroaki Kihara
- Laboratório de Neurogenética, Universidade Federal do ABC (UFABC), São Bernardo do Campo, São Paulo 09606-070, Brazil; (M.I.M.)
| | - Emma Poole
- Division of Virology, Department of Pathology, Cambridge University, Level 5, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Michael Nevels
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK;
| | - Maria Cristina Carlan da Silva
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do UFABC (UFABC), São Bernardo do Campo, São Paulo 09606-070, Brazil; (G.W.C.d.A.); (G.B.d.L.); (S.D.S.)
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3
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Moriyama M, Lucas C, Monteiro V, Iwasaki A. Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants. Proc Natl Acad Sci U S A 2023; 120:e2221652120. [PMID: 37036977 PMCID: PMC10120007 DOI: 10.1073/pnas.2221652120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/09/2023] [Indexed: 04/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) possess mutations that confer resistance to neutralizing antibodies within the Spike protein and are associated with breakthrough infection and reinfection. By contrast, less is known about the escape from CD8+ T cell-mediated immunity by VOC. Here, we demonstrated that all SARS-CoV-2 VOCs possess the ability to suppress major histocompatibility complex class I (MHC-I) expression. We identified several viral genes that contribute to the suppression of MHC I expression. Notably, MHC-I upregulation was strongly inhibited after SARS-CoV-2 but not influenza virus infection in vivo. While earlier VOCs possess similar capacity as the ancestral strain to suppress MHC-I, the Omicron subvariants exhibited a greater ability to suppress surface MHC-I expression. We identified a common mutation in the E protein of Omicron that further suppressed MHC-I expression. Collectively, our data suggest that in addition to escaping from neutralizing antibodies, the success of Omicron subvariants to cause breakthrough infection and reinfection may in part be due to its optimized evasion from T cell recognition.
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Affiliation(s)
- Miyu Moriyama
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | | | | | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
- Department of Molecular Cellular and Developmental Biology, Yale University, New HavenCT06520
- HHMI, Chevy Chase, MD20815
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4
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Arduini A, Laprise F, Liang C. SARS-CoV-2 ORF8: A Rapidly Evolving Immune and Viral Modulator in COVID-19. Viruses 2023; 15:871. [PMID: 37112851 PMCID: PMC10141009 DOI: 10.3390/v15040871] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
The COVID-19 pandemic has resulted in upwards of 6.8 million deaths over the past three years, and the frequent emergence of variants continues to strain global health. Although vaccines have greatly helped mitigate disease severity, SARS-CoV-2 is likely to remain endemic, making it critical to understand its viral mechanisms contributing to pathogenesis and discover new antiviral therapeutics. To efficiently infect, this virus uses a diverse set of strategies to evade host immunity, accounting for its high pathogenicity and rapid spread throughout the COVID-19 pandemic. Behind some of these critical host evasion strategies is the accessory protein Open Reading Frame 8 (ORF8), which has gained recognition in SARS-CoV-2 pathogenesis due to its hypervariability, secretory property, and unique structure. This review discusses the current knowledge on SARS-CoV-2 ORF8 and proposes actualized functional models describing its pivotal roles in both viral replication and immune evasion. A better understanding of ORF8's interactions with host and viral factors is expected to reveal essential pathogenic strategies utilized by SARS-CoV-2 and inspire the development of novel therapeutics to improve COVID-19 disease outcomes.
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Affiliation(s)
- Ariana Arduini
- Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (A.A.); (F.L.)
- Department of Medicine, McGill University, Montreal, QC H3G 2M1, Canada
| | - Frederique Laprise
- Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (A.A.); (F.L.)
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Chen Liang
- Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (A.A.); (F.L.)
- Department of Medicine, McGill University, Montreal, QC H3G 2M1, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
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5
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Moriyama M, Lucas C, Monteiro VS, Iwasaki A. SARS-CoV-2 Omicron subvariants evolved to promote further escape from MHC-I recognition. bioRxiv 2022:2022.05.04.490614. [PMID: 35547852 PMCID: PMC9094094 DOI: 10.1101/2022.05.04.490614] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
SARS-CoV-2 variants of concern (VOCs) possess mutations that confer resistance to neutralizing antibodies within the Spike protein and are associated with breakthrough infection and reinfection. By contrast, less is known about the escape from CD8+ T cell-mediated immunity by VOC. Here, we demonstrated that all SARS-CoV-2 VOCs possess the ability to suppress MHC I expression. We identified several viral genes that contribute to the suppression of MHC I expression. Notably, MHC-I upregulation was strongly inhibited after SARS-CoV-2 infection in vivo. While earlier VOCs possess similar capacity as the ancestral strain to suppress MHC I, Omicron subvariants exhibit a greater ability to suppress surface MHC-I expressions. Collectively, our data suggest that, in addition to escape from neutralizing antibodies, the success of Omicron subvariants to cause breakthrough infection and reinfection may in part be due to its optimized evasion from T cell recognition.
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6
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Abstract
SARS-CoV-2 is the virus responsible for the COVID-19 pandemic. The genome of SARS-CoV-2 encodes nine accessory proteins that are involved in host-pathogen interaction. ORF8 is unique among these accessory proteins. SARS-CoV-2 ORF8 shares a surprisingly low amino acid sequence similarity with SARS-COV ORF8 (30%), and it is presumed to have originated from bat. Studies have shown that ORF8 exerts multiple different functions that interfere with host immune responses, including the downregulation of MHC class I molecules. These functions may represent strategies of host immune evasion. The x-ray crystal structure of ORF8 revealed an immunoglobulin-like domain with several distinguishing features. To date, there are numerous unanswered questions about SARS-CoV-2 ORF8 protein and its structure-function relationship that we discuss in this mini-review. A better understanding of how ORF8 interacts with components of the immune system is needed for elucidating COVID-19 pathogenesis and to develop new avenues for the treatment of the disease.
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Affiliation(s)
| | | | - Marlene Bouvier
- Department of Microbiology and Immunology, University of Illinois at Chicago, College of Medicine, Chicago, IL, United States
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7
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Kohyama M, Suzuki T, Nakai W, Ono C, Matsuoka S, Iwatani K, Liu Y, Sakai Y, Nakagawa A, Tomii K, Ohmura K, Okada M, Matsuura Y, Ohshima S, Maeda Y, Okamoto T, Arase H. SARS-CoV-2 ORF8 is a viral cytokine regulating immune responses. Int Immunol 2022; 35:43-52. [PMID: 36053553 PMCID: PMC9494306 DOI: 10.1093/intimm/dxac044] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/01/2022] [Indexed: 02/05/2023] Open
Abstract
Many patients with severe COVID-19 suffer from pneumonia and the elucidation of the mechanisms underlying the development of this severe condition is important. The in vivo function of the ORF8 protein secreted by SARS-CoV-2 is not well understood. Here, we analyzed the function of ORF8 protein by generating ORF8-knockout SARS-CoV-2 and found that the lung inflammation observed in wild-type SARS-CoV-2-infected hamsters was decreased in ORF8-knockout SARS-CoV-2-infected hamsters. Administration of recombinant ORF8 protein to hamsters also induced lymphocyte infiltration into the lungs. Similar pro-inflammatory cytokine production was observed in primary human monocytes treated with recombinant ORF8 protein. Furthermore, we demonstrated that the serum ORF8 protein levels are well-correlated with clinical markers of inflammation. These results demonstrated that the ORF8 protein is a SARS-CoV-2 viral cytokine involved in the immune dysregulation observed in COVID-19 patients, and that the ORF8 protein could be a novel therapeutic target in severe COVID-19 patients.
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Affiliation(s)
- Masako Kohyama
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan,Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka, 565-0871, Japan
| | - Tatsuya Suzuki
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan,Center for Infectious Diseases Education and Research, Osaka University, Osaka, 565-0871, Japan
| | - Wataru Nakai
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan,Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka, 565-0871, Japan
| | - Chikako Ono
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Sumiko Matsuoka
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan,Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka, 565-0871, Japan
| | - Koichi Iwatani
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan,Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka, 565-0871, Japan
| | - Yafei Liu
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan,Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka, 565-0871, Japan
| | - Yusuke Sakai
- Department of Veterinary Pathology, Yamaguchi University, Yamaguchi, Japan
| | - Atsushi Nakagawa
- Department of Respiratory Medicine, Kobe City Medical Center General Hospital, Hyogo, 650-0047, Japan
| | - Keisuke Tomii
- Department of Respiratory Medicine, Kobe City Medical Center General Hospital, Hyogo, 650-0047, Japan
| | - Koichiro Ohmura
- Department of Rheumatology, Kobe City Medical Center General Hospital, Hyogo, 650-0047, Japan
| | - Masato Okada
- Center for Infectious Diseases Education and Research, Osaka University, Osaka, 565-0871, Japan,Department of Oncogene Research, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Yoshiharu Matsuura
- Center for Infectious Diseases Education and Research, Osaka University, Osaka, 565-0871, Japan,Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Shiro Ohshima
- Department of Clinical Research, Osaka Minami Medical Center, Osaka, 586-8521, Japan
| | - Yusuke Maeda
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
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8
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Gubarev YA, Lebedeva NS, Yurina ES, Mamardashvili GM, Zaitceva SV, Zdanovich SA, Koifman OI. Prospects for the use of macrocyclic photosensitizers for inactivation of SARS-CoV-2: selection of compounds leaders based on the molecular docking data. J Biomol Struct Dyn 2022:1-10. [DOI: 10.1080/07391102.2022.2079562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Yury A. Gubarev
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russia
| | - Natalia Sh. Lebedeva
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russia
| | - Elena S. Yurina
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russia
| | | | - Svetlana V. Zaitceva
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russia
| | - Sergey A. Zdanovich
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russia
| | - Oskar I. Koifman
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russia
- Ivanovo State University of Chemistry and Technology, Ivanovo, Russia
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Chou JM, Tsai JL, Hung JN, Chen IH, Chen ST, Tsai MH. The ORF8 Protein of SARS-CoV-2 Modulates the Spike Protein and Its Implications in Viral Transmission. Front Microbiol 2022; 13:883597. [PMID: 35663899 PMCID: PMC9161165 DOI: 10.3389/fmicb.2022.883597] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/01/2022] [Indexed: 01/09/2023] Open
Abstract
COVID-19 is currently global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Accompanying the rapid spread of the error-prone RNA-based genome, several dominant SARS-CoV-2 variants have been genetically identified. The mutations in the spike protein, which are essential for receptor binding and fusion, have been intensively investigated for their contributions to viral transmission. Nevertheless, the importance of other viral proteins and their mutations in SARS-CoV-2 lifecycle and transmission remains fairly understood. Here, we report the strong potency of an accessory protein ORF8 in modulating the level and processing of the spike protein. The expression of ORF8 protein does not affect propagation but expression of spike protein, which may lead to pseudovirions with less spike protein on the surface, therefore less infection potential. At the protein level, ORF8 expression led to downregulation and insufficient S1/S2 cleavage of the spike protein in a dose-dependent manner. ORF8 exhibits a strong interaction with the spike protein mainly at S1 domains and mediates its degradation through multiple pathways. The dominant clinical isolated ORF8 variants with the reduced protein stability exhibited the increased capacity of viral transmission without compromising their inhibitory effects on HLA-A2. Although the increase in spike protein level and Spike pseudovirus production observed by using highly transmissible clinical spike variants, there was no significant compromise in ORF8-mediated downregulation. Because ORF8 is important for immune surveillance and might be required for viral fitness in vivo, the alteration of the spike protein might be an optional strategy used by SARS-CoV-2 to promote viral transmission by escaping the inhibitory effects of ORF8. Therefore, our report emphasized the importance of ORF8 in SARS-CoV-2 spike protein production, maturation, and possible evolution.
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Affiliation(s)
- Jen-Mei Chou
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Jo-Ling Tsai
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Jo-Ning Hung
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - I-Hua Chen
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Szu-Ting Chen
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Research Center for Epidemic Prevention, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Ming-Han Tsai
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
- Research Center for Epidemic Prevention, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- *Correspondence: Ming-Han Tsai,
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Wu X, Xia T, Shin WJ, Yu KM, Jung W, Herrmann A, Foo SS, Chen W, Zhang P, Lee JS, Poo H, Comhair SAA, Jehi L, Choi YK, Ensser A, Jung JU. Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. mBio 2022; 13:e0040222. [PMID: 35343786 PMCID: PMC9040823 DOI: 10.1128/mbio.00402-22] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 02/25/2022] [Indexed: 01/04/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection triggers cytokine-mediated inflammation, leading to a myriad of clinical presentations in COVID-19. The SARS-CoV-2 open reading frame 8 (ORF8) is a secreted and rapidly evolving glycoprotein. Patients infected with SARS-CoV-2 variants with ORF8 deleted are associated with mild disease outcomes, but the molecular mechanism behind this is unknown. Here, we report that SARS-CoV-2 ORF8 is a viral cytokine that is similar to but distinct from interleukin 17A (IL-17A) as it induces stronger and broader human IL-17 receptor (hIL-17R) signaling than IL-17A. ORF8 primarily targeted blood monocytes and induced the heterodimerization of hIL-17RA and hIL-17RC, triggering a robust inflammatory response. Transcriptome analysis revealed that besides its activation of the hIL-17R pathway, ORF8 upregulated gene expression for fibrosis signaling and coagulation dysregulation. A naturally occurring ORF8 L84S variant that was highly associated with mild COVID-19 showed reduced hIL-17RA binding and attenuated inflammatory responses. This study reveals how SARS-CoV-2 ORF8 by a viral mimicry of the IL-17 cytokine contributes to COVID-19 severe inflammation. IMPORTANCE Patients infected with SARS-CoV-2 variants lacking open reading frame 8 (ORF8) have been associated with milder infection and disease outcome, but the molecular mechanism behind how this viral accessory protein mediates disease pathogenesis is not yet known. In our study, we revealed that secreted ORF8 protein mimics host IL-17 to activate IL-17 receptors A and C (IL-17RA/C) and induces a significantly stronger inflammatory response than host IL-17A, providing molecular insights into the role of ORF8 in COVID-19 pathogenesis and serving as a potential therapeutic target.
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Affiliation(s)
- Xin Wu
- Cancer Biology Department, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Tian Xia
- Cancer Biology Department, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Woo-Jin Shin
- Cancer Biology Department, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Cleveland Clinic Florida Research & Innovation Center, Port St. Lucie, Florida, USA
| | - Kwang-Min Yu
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Wooram Jung
- Cancer Biology Department, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Alexandra Herrmann
- Institute for Clinical and Molecular Virology, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Suan-Sin Foo
- Cancer Biology Department, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Weiqiang Chen
- Cancer Biology Department, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Pengfei Zhang
- Cancer Biology Department, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jong-Soo Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Haryoung Poo
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Suzy A. A. Comhair
- Respiratory Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Lara Jehi
- Department of Neurology, Epilepsy Center, Cleveland Clinic, Cleveland, Ohio, USA
| | - Young Ki Choi
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Armin Ensser
- Institute for Clinical and Molecular Virology, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Jae U. Jung
- Cancer Biology Department, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
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11
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Hassan SS, Kodakandla V, Redwan EM, Lundstrom K, Pal Choudhury P, Abd El-Aziz TM, Takayama K, Kandimalla R, Lal A, Serrano-Aroca Á, Azad GK, Aljabali AA, Palù G, Chauhan G, Adadi P, Tambuwala M, Brufsky AM, Baetas-da-Cruz W, Barh D, Azevedo V, Bazan NG, Andrade BS, Santana Silva RJ, Uversky VN. An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. PeerJ 2022; 10:e13136. [PMID: 35341060 PMCID: PMC8944340 DOI: 10.7717/peerj.13136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/27/2022] [Indexed: 01/12/2023] Open
Abstract
Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
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Affiliation(s)
- Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, India
| | - Vaishnavi Kodakandla
- Department of Life sciences, Sophia College For Women, University of Mumbai, Mumbai, India
| | - Elrashdy M. Redwan
- Faculty of Science, Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic Rochester, Rochester, NY, United States
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Catolica de Valencia San Vicente Martir, Valencia, Spain
| | | | - Alaa A.A. Aljabali
- Department of Pharmaceutics and Pharmaceutical, Yarmouk University, Irbid, Jordan
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico
| | - Parise Adadi
- Department of Food Science, University of Otago, University of Otago, Dunedin, New Zealand
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, UK
| | - Adam M. Brufsky
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and 46 Applied Biotechnology (IIOAB), Nonakuri, India
| | - Vasco Azevedo
- Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Nikolas G. Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA, United States
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | - Raner José Santana Silva
- Departamento de Ciencias Biologicas (DCB), Programa de Pos-Graduacao em Genetica e Biologia Molecular (PPGGBM), Universidade Estadual de Santa Cruz (UESC), Ilheus, Brazil
| | - Vladimir N. Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
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12
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Narowski TM, Raphel K, Adams LE, Huang J, Vielot NA, Jadi R, de Silva AM, Baric RS, Lafleur JE, Premkumar L. SARS-CoV-2 mRNA vaccine induces robust specific and cross-reactive IgG and unequal neutralizing antibodies in naive and previously infected people. Cell Rep 2022; 38:110336. [PMID: 35090596 PMCID: PMC8769879 DOI: 10.1016/j.celrep.2022.110336] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 12/01/2021] [Accepted: 01/12/2022] [Indexed: 12/02/2022] Open
Abstract
Understanding vaccine-mediated protection against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is critical to overcoming the global coronavirus disease 2019 (COVID-19) pandemic. We investigate mRNA-vaccine-induced antibody responses against the reference strain, seven variants, and seasonal coronaviruses in 168 healthy individuals at three time points: before vaccination, after the first dose, and after the second dose. Following complete vaccination, both naive and previously infected individuals developed comparably robust SARS-CoV-2 spike antibodies and variable levels of cross-reactive antibodies to seasonal coronaviruses. However, the strength and frequency of SARS-CoV-2 neutralizing antibodies in naive individuals were lower than in previously infected individuals. After the first vaccine dose, one-third of previously infected individuals lacked neutralizing antibodies; this was improved to one-fifth after the second dose. In all individuals, neutralizing antibody responses against the Alpha and Delta variants were weaker than against the reference strain. Our findings support future tailored vaccination strategies against emerging SARS-CoV-2 variants as mRNA-vaccine-induced neutralizing antibodies are highly variable among individuals.
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Affiliation(s)
- Tara M Narowski
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Kristin Raphel
- Department Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA
| | - Lily E Adams
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Epidemiology, University of North Carolina at Chapel Hill School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jenny Huang
- Department Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA
| | - Nadja A Vielot
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ramesh Jadi
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Aravinda M de Silva
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Ralph S Baric
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Epidemiology, University of North Carolina at Chapel Hill School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - John E Lafleur
- Department Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA.
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
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13
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Hassan SS, Kodakandla V, Redwan EM, Lundstrom K, Pal Choudhury P, Abd El-Aziz TM, Takayama K, Kandimalla R, Lal A, Serrano-Aroca Á, Azad GK, Aljabali AAA, Palù G, Chauhan G, Adadi P, Tambuwala M, Brufsky AM, Baetas-da-Cruz W, Barh D, Azevedo V, Bazan NG, Andrade BS, Santana Silva RJ, Uversky VN. An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. PeerJ 2022. [PMID: 35341060 DOI: 10.1101/2021.05.25.445557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023] Open
Abstract
Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, India
| | - Vaishnavi Kodakandla
- Department of Life sciences, Sophia College For Women, University of Mumbai, Mumbai, India
| | - Elrashdy M Redwan
- Faculty of Science, Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic Rochester, Rochester, NY, United States
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Catolica de Valencia San Vicente Martir, Valencia, Spain
| | | | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical, Yarmouk University, Irbid, Jordan
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico
| | - Parise Adadi
- Department of Food Science, University of Otago, University of Otago, Dunedin, New Zealand
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, UK
| | - Adam M Brufsky
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and 46 Applied Biotechnology (IIOAB), Nonakuri, India
| | - Vasco Azevedo
- Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Nikolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA, United States
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | - Raner José Santana Silva
- Departamento de Ciencias Biologicas (DCB), Programa de Pos-Graduacao em Genetica e Biologia Molecular (PPGGBM), Universidade Estadual de Santa Cruz (UESC), Ilheus, Brazil
| | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
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14
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Balasco N, Damaggio G, Esposito L, Villani F, Berisio R, Colonna V, Vitagliano L. A global analysis of conservative and non-conservative mutations in SARS-CoV-2 detected in the first year of the COVID-19 world-wide diffusion. Sci Rep 2021; 11:24495. [PMID: 34969951 PMCID: PMC8718531 DOI: 10.1038/s41598-021-04147-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 12/03/2021] [Indexed: 02/08/2023] Open
Abstract
The ability of SARS-CoV-2 to rapidly mutate represents a remarkable complicancy. Quantitative evaluations of the effects that these mutations have on the virus structure/function is of great relevance and the availability of a large number of SARS-CoV-2 sequences since the early phases of the pandemic represents a unique opportunity to follow the adaptation of the virus to humans. Here, we evaluated the SARS-CoV-2 amino acid mutations and their progression by analyzing publicly available viral genomes at three stages of the pandemic (2020 March 15th and October 7th, 2021 February 7th). Mutations were classified in conservative and non-conservative based on the probability to be accepted during the evolution according to the Point Accepted Mutation substitution matrices and on the similarity of the encoding codons. We found that the most frequent substitutions are T > I, L > F, and A > V and we observe accumulation of hydrophobic residues. These findings are consistent among the three stages analyzed. We also found that non-conservative mutations are less frequent than conservative ones. This finding may be ascribed to a progressive adaptation of the virus to the host. In conclusion, the present study provides indications of the early evolution of the virus and tools for the global and genome-specific evaluation of the possible impact of mutations on the structure/function of SARS-CoV-2 variants.
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Affiliation(s)
- Nicole Balasco
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Naples, Italy
| | - Gianluca Damaggio
- Institute of Genetics and Biophysics, National Research Council (CNR), Naples, Italy
| | - Luciana Esposito
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Naples, Italy
| | - Flavia Villani
- Institute of Genetics and Biophysics, National Research Council (CNR), Naples, Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Naples, Italy
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council (CNR), Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Naples, Italy.
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15
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Abstract
Coronaviruses are single-stranded RNA viruses that affect humans and a wide variety of animal species, including livestock, wild animals, birds, and pets. These viruses have an affinity for different tissues, such as those of the respiratory and gastrointestinal tract of most mammals and birds and the hepatic and nervous tissues of rodents and porcine. As coronaviruses target different host cell receptors and show divergence in the sequences and motifs of their structural and accessory proteins, they are classified into groups, which may explain the evolutionary relationship between them. The interspecies transmission, zoonotic potential, and ability to mutate at a higher rate and emerge into variants of concern highlight their importance in the medical and veterinary fields. The contribution of various factors that result in their evolution will provide better insight and may help to understand the complexity of coronaviruses in the face of pandemics. In this review, important aspects of coronaviruses infecting livestock, birds, and pets, in particular, their structure and genome organization having a bearing on evolutionary and zoonotic outcomes, have been discussed.
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Affiliation(s)
| | - Subhash Verma
- Department of Veterinary Microbiology, DGCN College of Veterinary and Animal Sciences, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, India
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16
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Valcarcel A, Bensussen A, Álvarez-Buylla ER, Díaz J. Structural Analysis of SARS-CoV-2 ORF8 Protein: Pathogenic and Therapeutic Implications. Front Genet 2021; 12:693227. [PMID: 34552615 PMCID: PMC8450498 DOI: 10.3389/fgene.2021.693227] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/29/2021] [Indexed: 12/27/2022] Open
Abstract
Current therapeutic strategies and vaccines against SARS-CoV-2 are mainly focused on the Spike protein despite there are other viral proteins with important roles in COVID-19 pathogenicity. For example, ORF8 restructures vesicular trafficking in the host cell, impacts intracellular immunity through the IFN-I signaling, and growth pathways through the mitogen-activated protein kinases (MAPKs). In this mini-review, we analyze the main structural similarities of ORF8 with immunological molecules such as IL-1, contributing to the immunological deregulation observed in COVID-19. We also propose that the blockage of some effector functions of ORF8 with Rapamycin, such as the mTORC1 activation through MAPKs 40 pathway, with Rapamycin, can be a promising approach to reduce COVID-19 mortality.
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Affiliation(s)
- Antonio Valcarcel
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Antonio Bensussen
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Elena R Álvarez-Buylla
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.,Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evoluciónde Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - José Díaz
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
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17
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Chen R, Kan L, Duan F, He L, Wang M, Cui J, Zhang Z, Zhang Z. Surface plasmon resonance aptasensor based on niobium carbide MXene quantum dots for nucleocapsid of SARS-CoV-2 detection. Mikrochim Acta 2021; 188:316. [PMID: 34476615 PMCID: PMC8412382 DOI: 10.1007/s00604-021-04974-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/11/2021] [Indexed: 12/19/2022]
Abstract
A novel label-free surface plasmon resonance (SPR) aptasensor has been constructed for the detection of N-gene of SARS-CoV-2 by using thiol-modified niobium carbide MXene quantum dots (Nb2C-SH QDs) as the bioplatform for anchoring N-gene-targeted aptamer. In the presence of SARS-CoV-2 N-gene, the immobilized aptamer strands changed their conformation to specifically bind with N-gene. It thus increased the contact area or enlarged the distance between aptamer and the SPR chip, resulting in a change of the SPR signal irradiated by the laser (He-Ne) with the wavelength (λ) of 633 nm. Nb2C QDs were derived from Nb2C MXene nanosheets via a solvothermal method, followed by functionalization with octadecanethiol through a self-assembling method. Subsequently, the gold chip for SPR measurements was modified with Nb2C-SH QDs via covalent binding of the Au-S bond also by self-assembling interaction. Nb2C-SH QDs not only resulted in high bioaffinity toward aptamer but also enhanced the SPR response. Thus, the Nb2C-SH QD-based SPR aptasensor had low limit of detection (LOD) of 4.9 pg mL−1 toward N-gene within the concentration range 0.05 to 100 ng mL−1. The sensor also showed excellent selectivity in the presence of various respiratory viruses and proteins in human serum and high stability. Moreover, the Nb2C-SH QD-based SPR aptasensor displayed a vast practical application for the qualitative analysis of N-gene from different samples, including seawater, seafood, and human serum. Thus, this work can provide a deep insight into the construction of the aptasensor for detecting SARS-CoV-2 in complex environments.
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Affiliation(s)
- Rongyuan Chen
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Lun Kan
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Fenghe Duan
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Linghao He
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Minghua Wang
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Jing Cui
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Zhihong Zhang
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China.
| | - Zhonghou Zhang
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China.
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18
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UĞUREL OM, ATA O, TURGUT-BALIK D. Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences. Turk J Biol 2021; 45:425-435. [PMID: 34803444 PMCID: PMC8573839 DOI: 10.3906/biy-2106-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/30/2021] [Indexed: 11/26/2022] Open
Abstract
Use of information technologies to analyse big data on SARS-CoV-2 genome provides an insight for tracking variations and examining the evolution of the virus. Nevertheless, storing, processing, alignment and analyses of these numerous genomes are still a challenge. In this study, over 1 million SARS-CoV-2 genomes have been analysed to show distribution and relationship of variations that could enlighten development and evolution of the virus. In all genomes analysed in this study, a total of over 215M SNVs have been detected and average number of SNV per isolate was found to be 21.83. Single nucleotide variant (SNV) average is observed to reach 31.25 just in March 2021. The average variation number of isolates is increasing and compromising with total case numbers around the world. Remarkably, cytosine deamination, which is one of the most important biochemical processes in the evolutionary development of coronaviruses, accounts for 46% of all SNVs seen in SARS-CoV-2 genomes within 16 months. This study is one of the most comprehensive SARS-CoV-2 genomic analysis study in terms of number of genomes analysed in an academic publication so far, and reported results could be useful in monitoring the development of SARS-CoV-2.
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Affiliation(s)
- Osman Mutluhan UĞUREL
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical University, İstanbulTurkey
- Department of Basic Sciences, School of Engineering and Natural Sciences, Altınbaş University, İstanbulTurkey
| | - Oğuz ATA
- Department of Software Engineering, School of Engineering and Natural Sciences, Altınbaş University, İstanbulTurkey
| | - Dilek TURGUT-BALIK
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical University, İstanbulTurkey
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19
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Jiang Y, Tong K, Yao R, Zhou Y, Lin H, Du L, Jin Y, Cao L, Tan J, Zhang XD, Guo D, Pan JA, Peng X. Genome-wide analysis of protein-protein interactions and involvement of viral proteins in SARS-CoV-2 replication. Cell Biosci 2021; 11:140. [PMID: 34294141 PMCID: PMC8295636 DOI: 10.1186/s13578-021-00644-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/01/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Analysis of viral protein-protein interactions is an essential step to uncover the viral protein functions and the molecular mechanism for the assembly of a viral protein complex. We employed a mammalian two-hybrid system to screen all the viral proteins of SARS-CoV-2 for the protein-protein interactions. RESULTS Our study detected 48 interactions, 14 of which were firstly reported here. Unlike Nsp1 of SARS-CoV, Nsp1 of SARS-CoV-2 has the most interacting partners among all the viral proteins and likely functions as a hub for the viral proteins. Five self-interactions were confirmed, and five interactions, Nsp1/Nsp3.1, Nsp3.1/N, Nsp3.2/Nsp12, Nsp10/Nsp14, and Nsp10/Nsp16, were determined to be positive bidirectionally. Using the replicon reporter system of SARS-CoV-2, we screened all viral Nsps for their impacts on the viral replication and revealed Nsp3.1, the N-terminus of Nsp3, significantly inhibited the replicon reporter gene expression. We found Nsp3 interacted with N through its acidic region at N-terminus, while N interacted with Nsp3 through its NTD, which is rich in the basic amino acids. Furthermore, using purified truncated N and Nsp3 proteins, we determined the direct interactions between Nsp3 and N protein. CONCLUSIONS Our findings provided a basis for understanding the functions of coronavirus proteins and supported the potential of interactions as the target for antiviral drug development.
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Affiliation(s)
- Yiling Jiang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Kuijie Tong
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Roubin Yao
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Yuanze Zhou
- Nanjing CRYCISION Biotechnology Co., Ltd, Nanjing, 211100, China
| | - Hanwen Lin
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Liubing Du
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Yunyun Jin
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Liu Cao
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Jingquan Tan
- Nanjing CRYCISION Biotechnology Co., Ltd, Nanjing, 211100, China
| | - Xing-Ding Zhang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Deyin Guo
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Ji-An Pan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China.
| | - Xiaoxue Peng
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China.
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20
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Ilmjärv S, Abdul F, Acosta-Gutiérrez S, Estarellas C, Galdadas I, Casimir M, Alessandrini M, Gervasio FL, Krause KH. Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Sci Rep 2021; 11:13705. [PMID: 34210996 PMCID: PMC8249556 DOI: 10.1038/s41598-021-91662-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/25/2021] [Indexed: 01/18/2023] Open
Abstract
The D614G mutation in the Spike protein of the SARS-CoV-2 has effectively replaced the early pandemic-causing variant. Using pseudotyped lentivectors, we confirmed that the aspartate replacement by glycine in position 614 is markedly more infectious. Molecular modelling suggests that the G614 mutation facilitates transition towards an open state of the Spike protein. To explain the epidemiological success of D614G, we analysed the evolution of 27,086 high-quality SARS-CoV-2 genome sequences from GISAID. We observed striking coevolution of D614G with the P323L mutation in the viral polymerase. Importantly, the exclusive presence of G614 or L323 did not become epidemiologically relevant. In contrast, the combination of the two mutations gave rise to a viral G/L variant that has all but replaced the initial D/P variant. Our results suggest that the P323L mutation, located in the interface domain of the RNA-dependent RNA polymerase, is a necessary alteration that led to the epidemiological success of the present variant of SARS-CoV-2. However, we did not observe a significant correlation between reported COVID-19 mortality in different countries and the prevalence of the Wuhan versus G/L variant. Nevertheless, when comparing the speed of emergence and the ultimate predominance in individual countries, it is clear that the G/L variant displays major epidemiological supremacy over the original variant.
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Affiliation(s)
- Sten Ilmjärv
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Fabien Abdul
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Silvia Acosta-Gutiérrez
- Department of Chemistry, University College London, London, UK.,Institute for the Physics of Living Systems, University College London, London, UK.,Institute of Structural and Molecular Biology, University College London, London, UK
| | | | | | | | - Marco Alessandrini
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Francesco Luigi Gervasio
- Department of Chemistry, University College London, London, UK.,Institute of Structural and Molecular Biology, University College London, London, UK.,School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland. .,Division of Infectious Disease and Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland.
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21
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Abstract
The SARS-CoV-2 Variant of Concern 202012/01 (VOC-202012/01) is rapidly spreading worldwide owing to its substantial transmission advantage. The variant has changes in critical sites of the spike protein with potential biological significance. Moreover, VOC-202012/01 has a mutation that inactivates the ORF8 protein, whose absence can change the clinical features of the infection. Why VOC-202012/01 is more transmissible remains unclear, but spike mutations and ORF8 inactivation stand out by their known phenotypic effects. Here I show that variants combining relevant spike mutations and the absence of ORF8 occurred in SARS-CoV-2 and related viruses circulating in other host species. A truncated ORF8 (Q23stop) occurred in a SARS-CoV-2-related virus from a pangolin seized in China in 2017, also with several mutations in critical spike sites. Strikingly, I found that variants without ORF8 (E19stop) and with the N501T spike mutation circulated in farmed mink and humans from Denmark. Although with differences to VOC-202012/01, the identification of these variants highlights the danger of having reservoirs of SARS-CoV-2 and related viruses where more transmissible variants may occur and spill over to humans.
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Affiliation(s)
- Filipe Pereira
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal; IDENTIFICA genetic testing, Rua Simão Bolívar 259 3° Dir Tras, Maia 4470-214, Portugal.
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