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Lee P, Kim J, Oh H, Kim CU, Jeong AY, Lee MS, Jang MS, Hong JJ, Park JE, Kim DJ. Coronavirus Nucleocapsid-based Vaccine Provides Partial Protection against Hetero-species Coronavirus in Murine Models. Antiviral Res 2024:105991. [PMID: 39181216 DOI: 10.1016/j.antiviral.2024.105991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/06/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
Most coronavirus vaccines focus on the spike (S) antigen, but the frequent mutations in S raise concerns about the vaccine efficacy against new variants. Although additional antigens with conserved sequences are have been tested, the extent to which these vaccines can provide immunity against different coronavirus species remains unclear. In this study, we assessed the potential of nucleocapsid (N) as a coronavirus vaccine antigen. Immunization with MERS-CoV N induced robust immune responses, providing significant protection against MERS-CoV. Notably, MERS-CoV N elicited cross-reactive T cell responses to SARS-CoV-2 N and significantly reduced lung inflammation following a SARS-CoV-2 challenge in the transient hACE2 mouse model. However, in K18-hACE transgenic mice, the vaccine showed limited protection. Collectively, our findings suggest that coronavirus N can be an effective vaccine antigen against homologous viruses, but its efficacy may vary across different coronaviruses, highlighting the need for further research on pan-coronavirus vaccines using conserved antigens.
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Affiliation(s)
- Pureum Lee
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea; University of Science and Technology (UST), Daejeon, South Korea
| | - Jihee Kim
- Chungnam National University College of Veterinary Medicine, Daejeon, South Korea
| | - Hanseul Oh
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea; Chungbuk National University College of Veterinary Medicine, Cheongju, South Korea
| | - Chang-Ung Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | | | - Moo-Seung Lee
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea; University of Science and Technology (UST), Daejeon, South Korea
| | | | - Jung Joo Hong
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.
| | - Jung-Eun Park
- Chungnam National University College of Veterinary Medicine, Daejeon, South Korea.
| | - Doo-Jin Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea; Chungbuk National University College of Medicine, Cheongju, South Korea.
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2
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Bolaji AJ, Duggan AT. In silico analyses identify sequence contamination thresholds for Nanopore-generated SARS-CoV-2 sequences. PLoS Comput Biol 2024; 20:e1011539. [PMID: 39159257 DOI: 10.1371/journal.pcbi.1011539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 07/14/2024] [Indexed: 08/21/2024] Open
Abstract
The SARS-CoV-2 pandemic has brought molecular biology and genomic sequencing into the public consciousness and lexicon. With an emphasis on rapid turnaround, genomic data informed both diagnostic and surveillance decisions for the current pandemic at a previously unheard-of scale. The surge in the submission of genomic data to publicly available databases proved essential as comparing different genome sequences offers a wealth of knowledge, including phylogenetic links, modes of transmission, rates of evolution, and the impact of mutations on infection and disease severity. However, the scale of the pandemic has meant that sequencing runs are rarely repeated due to limited sample material and/or the availability of sequencing resources, resulting in the upload of some imperfect runs to public repositories. As a result, it is crucial to investigate the data obtained from these imperfect runs to determine whether the results are reliable prior to depositing them in a public database. Numerous studies have identified a variety of sources of contamination in public next-generation sequencing (NGS) data as the number of NGS studies increases along with the diversity of sequencing technologies and procedures. For this study, we conducted an in silico experiment with known SARS-CoV-2 sequences produced from Oxford Nanopore Technologies sequencing to investigate the effect of contamination on lineage calls and single nucleotide variants (SNVs). A contamination threshold below which runs are expected to generate accurate lineage calls and maintain genome-relatedness and integrity was identified. Together, these findings provide a benchmark below which imperfect runs may be considered robust for reporting results to both stakeholders and public repositories and reduce the need for repeat or wasted runs.
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Affiliation(s)
- Ayooluwa J Bolaji
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
- Cadham Provincial Laboratory, Winnipeg, Canada
| | - Ana T Duggan
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
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3
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Wang YC, Tsai CH, Wang YC, Yen LC, Chang YW, Sun JR, Lin TY, Chiu CH, Chao YC, Chang FY. SARS-CoV-2 nucleocapsid protein, rather than spike protein, triggers a cytokine storm originating from lung epithelial cells in patients with COVID-19. Infection 2024; 52:955-983. [PMID: 38133713 PMCID: PMC11143065 DOI: 10.1007/s15010-023-02142-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023]
Abstract
PURPOSE The aim of this study was to elucidate the factors associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that may initiate cytokine cascades and correlate the clinical characteristics of patients with coronavirus disease 2019 (COVID-19) with their serum cytokine profiles. METHODS Recombinant baculoviruses displaying SARS-CoV-2 spike or nucleocapsid protein were constructed and transfected into A549 cells and THP-1-derived macrophages, to determine which protein initiate cytokine release. SARS-CoV-2-specific antibody titers and cytokine profiles of patients with COVID-19 were determined, and the results were associated with their clinical characteristics, such as development of pneumonia or length of hospital stay. RESULTS The SARS-CoV-2 nucleocapsid protein, rather than the spike protein, triggers lung epithelial A549 cells to express IP-10, RANTES, IL-16, MIP-1α, basic FGF, eotaxin, IL-15, PDGF-BB, TRAIL, VEGF-A, and IL-5. Additionally, serum CTACK, basic FGF, GRO-α, IL-1α, IL-1RA, IL-2Rα, IL-9, IL-15, IL-16, IL-18, IP-10, M-CSF, MIF, MIG, RANTES, SCGF-β, SDF-1α, TNF-α, TNF-β, VEGF, PDGF-BB, TRAIL, β-NGF, eotaxin, GM-CSF, IFN-α2, INF-γ, and MCP-1 levels were considerably increased in patients with COVID-19. Among them, patients with pneumonia had higher serum IP-10 and M-CSF levels than patients without. Patients requiring less than 3 weeks to show negative COVID-19 tests after contracting COVID-19 had higher serum IP-10 levels than the remaining patients. CONCLUSION Our study revealed that nucleocapsid protein, lung epithelial cells, and IP-10 may be potential targets for the development of new strategies to prevent, or control, severe COVID-19.
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Affiliation(s)
- Ying-Chuan Wang
- Department of Family Medicine, Tri-Service General Hospital, National Defense Medical Center, No. 161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 11499, Taiwan, ROC
| | - Chih-Hsuan Tsai
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Yung-Chih Wang
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, No. 161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 11499, Taiwan, ROC
| | - Li-Chen Yen
- Department of Microbiology and Immunology, National Defense Medical Center, No. 161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 11499, Taiwan, ROC
| | - Yao-Wen Chang
- Taoyuan Armed Forces General Hospital, Taoyuan, 32551, Taiwan, ROC
| | - Jun-Ren Sun
- Institute of Preventive Medicine, National Defense Medical Center, No. 161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 11499, Taiwan, ROC
| | - Te-Yu Lin
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, No. 161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 11499, Taiwan, ROC
| | - Chun-Hsiang Chiu
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, No. 161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 11499, Taiwan, ROC.
| | - Yu-Chan Chao
- Department of Entomology, College of Agriculture and Nature Resources, National Chung Hsing University, Taichung, 40227, Taiwan, ROC
| | - Feng-Yee Chang
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, No. 161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 11499, Taiwan, ROC
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4
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Yu T, Zhang C, Xing J, Zhang T, Xu Z, Di Y, Yang S, Jiang R, Tang J, Zhuang X, Jin N, Tian M. Ferritin-binding and ubiquitination-modified mRNA vaccines induce potent immune responses and protective efficacy against SARS-CoV-2. Int Immunopharmacol 2024; 129:111630. [PMID: 38320355 DOI: 10.1016/j.intimp.2024.111630] [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: 12/14/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/08/2024]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) incessantly engenders mutating strains via immune escape mechanisms, substantially escalating the risk of severe acute respiratory syndrome. In this context, the urgent development of innovative and efficacious mRNA vaccines is imperative. In our study, we synthesized six unique mRNA vaccine formulations: the Receptor Binding Domain (RBD) monomer vaccine, RBD dimer (2RBD) vaccine, RBD-Ferritin (RBD-Fe) vaccine, ubiquitin-modified wild-type Nucleocapsid gene (WT-N) vaccine, rearranged Nucleocapsid gene (Re-N) vaccine, and an epitope-based (COVID-19 epitope) vaccine, all encapsulated within the lipid nanoparticle SM102. Immunization studies conducted on C57BL/6 mice with these vaccines revealed that the RBD monomer, RBD dimer (2RBD), and RBD-Fe vaccines elicited robust titers of specific antibodies, including neutralizing antibodies. In contrast, the wild-type N gene (WT-N), rearrange N gene (Re-N), and COVID-19 epitope vaccines predominantly induced potent cellular immune responses. Protective efficacy assays in golden hamsters demonstrated that vaccinated cohorts showed significant reduction in lung pathology, markedly lower viral loads in the lungs, nasal turbinates, and trachea, and substantially reduced transcriptional and expression levels of pro-inflammatory cytokines. Overall, our vaccine candidates pave the way for novel strategies in vaccine development against various infectious agents and establish a critical foundation for the formulation of advanced vaccines targeting emerging pathogens.
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Affiliation(s)
- Tong Yu
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - ChenChao Zhang
- College of Agriculture, Yanbian University, Yanji, China
| | - JunHong Xing
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
| | - Tong Zhang
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - ZhiQiang Xu
- College of Agriculture, Yanbian University, Yanji, China
| | - YaXin Di
- College of Veterinary Medicine, Northeast Agricultural University, Nanning, China
| | - SongHui Yang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - RenYue Jiang
- College of Agriculture, Yanbian University, Yanji, China
| | - JiaFeng Tang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - XinYu Zhuang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.
| | - NingYi Jin
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.
| | - MingYao Tian
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.
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5
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Rahmasari R, Raekiansyah M, Aliyah SH, Yodi P, Baihaqy F, Irhamsyah M, Sari KCDP, Suryadi H, Moi ML, Sauriasari R. Development and validation of cost-effective SYBR Green-based RT-qPCR and its evaluation in a sample pooling strategy for detecting SARS-CoV-2 infection in the Indonesian setting. Sci Rep 2024; 14:1817. [PMID: 38245603 PMCID: PMC10799953 DOI: 10.1038/s41598-024-52250-w] [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: 04/27/2023] [Accepted: 01/16/2024] [Indexed: 01/22/2024] Open
Abstract
A low-cost SYBR Green-based RT-qPCR method to detect SARS-CoV-2 were developed and validated. Primers targeting a conserved and vital region of the N genes of SARS-CoV-2 were designed. In-silico study was performed to analyse the compatibility of the selected primer pair with Indonesian SARS-CoV-2 genome sequences available from the GISAID database. We determined the linearity of our new assay using serial dilution of SARS-CoV-2 RNA from clinical samples with known virus concentration. The assay was then evaluated using clinically relevant samples in comparison to a commercial TaqMan-based test kit. Finally, we applied the assay in sample pooling strategies for SARS-CoV-2 detection. The SYBR Green-based RT-qPCR method was successfully developed with sufficient sensitivity. There is a very low prevalence of genome variation in the selected N primer binding regions, indicating their high conservation. The validation of the assay using clinical samples demonstrated similar performance to the TaqMan method suggesting the SYBR methods is reliable. The pooling strategy by combining 5 RNA samples for SARS-CoV-2 detection using the SYBR RT-qPCR methods is feasible and provides a high diagnostic yield. However, when dealing with samples having a very low viral load, it may increase the risk of missing positive cases.
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Affiliation(s)
- Ratika Rahmasari
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia.
| | | | - Siti Hana Aliyah
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Priska Yodi
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Fathan Baihaqy
- Helix Laboratory & Clinic, Depok, West Java, Indonesia
- Department of Microbiology, School of Life Sciences & Technology, Institut Teknologi Bandung, Bandung, West Java, Indonesia
| | | | | | - Herman Suryadi
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Meng Ling Moi
- School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Rani Sauriasari
- Clinical Pharmacy and Social Pharmacy Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
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Yang G, Yue Z, Pan P, Li Y. In Memory of the Virologist Jianguo Wu, 1957-2022. Viruses 2023; 15:1754. [PMID: 37632095 PMCID: PMC10457867 DOI: 10.3390/v15081754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
It is with deep sorrow that we mourn the passing of the virologist Professor Jianguo Wu [...].
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Affiliation(s)
- Ge Yang
- Foshan Institute of Medical Microbiology, Foshan 528315, China
| | - Zhaoyang Yue
- Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China
- Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou 510632, China
| | - Pan Pan
- Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou 510632, China
- The First Affiliated Hospital of Jinan University, Guangzhou 510632, China
| | - Yongkui Li
- Foshan Institute of Medical Microbiology, Foshan 528315, China
- Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China
- Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou 510632, China
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7
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Song W, Fang Z, Ma F, Li J, Huang Z, Zhang Y, Li J, Chen K. The role of SARS-CoV-2 N protein in diagnosis and vaccination in the context of emerging variants: present status and prospects. Front Microbiol 2023; 14:1217567. [PMID: 37675423 PMCID: PMC10478715 DOI: 10.3389/fmicb.2023.1217567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023] Open
Abstract
Despite many countries rapidly revising their strategies to prevent contagions, the number of people infected with Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to surge. The emergent variants that can evade the immune response significantly affect the effectiveness of mainstream vaccines and diagnostic products based on the original spike protein. Therefore, it is essential to focus on the highly conserved nature of the nucleocapsid protein as a potential target in the field of vaccines and diagnostics. In this regard, our review initially discusses the structure, function, and mechanism of action of N protein. Based on this discussion, we summarize the relevant research on the in-depth development and application of diagnostic methods and vaccines based on N protein, such as serology and nucleic acid detection. Such valuable information can aid in designing more efficient diagnostic and vaccine tools that could help end the SARS-CoV-2 pandemic.
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Affiliation(s)
- Wanchen Song
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhongbiao Fang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Feike Ma
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jiaxuan Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Zhiwei Huang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yanjun Zhang
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jianhua Li
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
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8
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Employing T-Cell Memory to Effectively Target SARS-CoV-2. Pathogens 2023; 12:pathogens12020301. [PMID: 36839573 PMCID: PMC9967959 DOI: 10.3390/pathogens12020301] [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: 01/04/2023] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
Well-trained T-cell immunity is needed for early viral containment, especially with the help of an ideal vaccine. Although most severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected convalescent cases have recovered with the generation of virus-specific memory T cells, some cases have encountered T-cell abnormalities. The emergence of several mutant strains has even threatened the effectiveness of the T-cell immunity that was established with the first-generation vaccines. Currently, the development of next-generation vaccines involves trying several approaches to educate T-cell memory to trigger a broad and fast response that targets several viral proteins. As the shaping of T-cell immunity in its fast and efficient form becomes important, this review discusses several interesting vaccine approaches to effectively employ T-cell memory for efficient viral containment. In addition, some essential facts and future possible consequences of using current vaccines are also highlighted.
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9
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Cerracchio C, Serra F, Amoroso MG, Fiorito F. Canine Coronavirus Activates Aryl Hydrocarbon Receptor during In Vitro Infection. Viruses 2022; 14:v14112437. [PMID: 36366535 PMCID: PMC9692492 DOI: 10.3390/v14112437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/20/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that interacts with substrates, including microbial metabolites. Recent advances reveal that AhR is involved in the host response to coronaviruses (CoVs) infection. Particularly, AhR antagonists decrease the expression of angiotensin-converting enzyme 2 (ACE2) via AhR up-regulation, resulting in suppression of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in mammalian cells. Herein, we report that AhR is expressed in canine fibrosarcoma (A72) cells, where it is considerably activated by infection with genotype II of canine coronavirus (CCoV-II). The pharmacological inhibition of AhR, by CH223191, suppressed cell death signs and increased cell viability. Furthermore, the AhR antagonist induced a meaningful decline in virus yield, accompanied by the inhibition of the expression of viral nuclear protein (NP). Fascinatingly, during CCoV infection, a novel co-expression of NP and AhR expression was found. Taken together, our preliminary findings show that infection with CCoV activates AhR, and pharmacologic AhR inhibition reduces CCoV replication, identifying AhR as a possible candidate target for CCoV antiviral therapy.
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Affiliation(s)
- Claudia Cerracchio
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy
| | - Francesco Serra
- Department of Animal Health, Unit of Virology, Istituto Zooprofilattico del Mezzogiorno, 80055 Portici, Naples, Italy
| | - Maria Grazia Amoroso
- Department of Animal Health, Unit of Virology, Istituto Zooprofilattico del Mezzogiorno, 80055 Portici, Naples, Italy
| | - Filomena Fiorito
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy
- Correspondence: (F.F.); Tel.: +39-0812536180
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10
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Lima K, Fontoura JC, de Souza PO, Fazolo T, Hilario G, Zorzetto R, Rodrigues Junior LC, Coimbra LD, Borin A, Bispo-dos-Santos K, Granja F, Marques RE, Zavaglia GO, Fernandes IR, Varela FH, Polese-Bonatto M, Tonini ML, Ikeda do Carmo GM, de Almeida WAF, Borges TJ, Nakaya HI, Proenca-Modena JL, Callegari-Jacques SM, Scotta MC, Stein RT, Bonorino C. SARS-CoV-2 infected children form early immune memory responses dominated by nucleocapsid-specific CD8+ T cells and antibodies. Front Immunol 2022; 13:1033364. [PMID: 36405692 PMCID: PMC9667737 DOI: 10.3389/fimmu.2022.1033364] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/03/2022] [Indexed: 08/13/2023] Open
Abstract
This is the third year of the SARS-CoV-2 pandemic, and yet most children remain unvaccinated. COVID-19 in children manifests as mostly mild or asymptomatic, however high viral titers and strong cellular and humoral responses are observed upon acute infection. It is still unclear how long these responses persist, and if they can protect from re-infection and/or disease severity. Here, we analyzed immune memory responses in a cohort of children and adults with COVID-19. Important differences between children and adults are evident in kinetics and profile of memory responses. Children develop early N-specific cytotoxic T cell responses, that rapidly expand and dominate their immune memory to the virus. Children's anti-N, but not anti-S, antibody titers increase over time. Neutralization titers correlate with N-specific antibodies and CD8+T cells. However, antibodies generated by infection do not efficiently cross-neutralize variants Gamma or Delta. Our results indicate that mechanisms that protect from disease severity are possibly different from those that protect from reinfection, bringing novel insights for pediatric vaccine design. They also underline the importance of vaccination in children, who remain at risk for COVID-19 despite having been previously infected.
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Affiliation(s)
- Karina Lima
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA, Porto Alegre, Brazil
| | - Julia C. Fontoura
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA, Porto Alegre, Brazil
| | - Priscila Oliveira de Souza
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA, Porto Alegre, Brazil
| | - Tiago Fazolo
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA, Porto Alegre, Brazil
| | - Gabriel Hilario
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA, Porto Alegre, Brazil
| | - Renata Zorzetto
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA, Porto Alegre, Brazil
| | - Luiz C Rodrigues Junior
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA, Porto Alegre, Brazil
| | - Lais D. Coimbra
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Alexandre Borin
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Karina Bispo-dos-Santos
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (Unicamp), Campinas, Brazil
| | - Fabiana Granja
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (Unicamp), Campinas, Brazil
- Biodiversity Research Centre, Federal University of Roraima (UFRR), Boa Vista, Brazil
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Gabriela Oliveira Zavaglia
- Social Responsibility – Programa de Apoio ao Desenvolvimento Institucional do Sistema Único de Saúde (PROADI-SUS ), Hospital Moinhos de Vento, Porto Alegre, Brazil
| | - Ingrid Rodrigues Fernandes
- Social Responsibility – Programa de Apoio ao Desenvolvimento Institucional do Sistema Único de Saúde (PROADI-SUS ), Hospital Moinhos de Vento, Porto Alegre, Brazil
| | - Fernanda Hammes Varela
- Social Responsibility – Programa de Apoio ao Desenvolvimento Institucional do Sistema Único de Saúde (PROADI-SUS ), Hospital Moinhos de Vento, Porto Alegre, Brazil
| | - Marcia Polese-Bonatto
- Social Responsibility – Programa de Apoio ao Desenvolvimento Institucional do Sistema Único de Saúde (PROADI-SUS ), Hospital Moinhos de Vento, Porto Alegre, Brazil
| | - Maiko Luís Tonini
- Coordenação-Geral de Vigilância das Doenças de Transmissão Respiratória de Condições Crônicas, Departamento de Doenças de Condições Crônicas e IST, Secretaria de Vigilância em Saúde – Ministério da Saúde (CGDR/DCCI/SVS/MS)., Brasília, Brazil
| | - Greice Madeleine Ikeda do Carmo
- Departamento de Imunizações e doenças transmissíveis, Secretaria de Vigilância em Saúde - Ministério da Saúde (DEIDT/SVS/MS), Brasília, Brazil
| | | | - Thiago J. Borges
- Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Helder I. Nakaya
- Computational System Biology Laboratory (CSBL), Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - José Luiz Proenca-Modena
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (Unicamp), Campinas, Brazil
- Hub of Global Health (HGH), University of Campinas (Unicamp), Campinas, Brazil
| | | | - Marcelo Comerlato Scotta
- Social Responsibility – Programa de Apoio ao Desenvolvimento Institucional do Sistema Único de Saúde (PROADI-SUS ), Hospital Moinhos de Vento, Porto Alegre, Brazil
- Escola de Medicina, Pontifícia Universidade Católica do Rio Grande do Sul – PUCRS, Porto Alegre, Brazil
| | - Renato T. Stein
- Social Responsibility – Programa de Apoio ao Desenvolvimento Institucional do Sistema Único de Saúde (PROADI-SUS ), Hospital Moinhos de Vento, Porto Alegre, Brazil
- Escola de Medicina, Pontifícia Universidade Católica do Rio Grande do Sul – PUCRS, Porto Alegre, Brazil
| | - Cristina Bonorino
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA, Porto Alegre, Brazil
- Department of Surgery, University of California at San Diego – UCSD, La Jolla, CA, United States
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11
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O’Donnell KL, Gourdine T, Fletcher P, Clancy CS, Marzi A. Protection from COVID-19 with a VSV-based vaccine expressing the spike and nucleocapsid proteins. Front Immunol 2022; 13:1025500. [PMID: 36353642 PMCID: PMC9638159 DOI: 10.3389/fimmu.2022.1025500] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/04/2022] [Indexed: 11/24/2022] Open
Abstract
Successful vaccine efforts countering the COVID-19 pandemic are centralized around the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein as viral antigen and have greatly reduced the morbidity and mortality associated with COVID-19. Since the start of this pandemic, SARS-CoV-2 has evolved resulting in new variants of concern (VOC) challenging the vaccine-established immunologic memory. We show that vaccination with a vesicular stomatitis virus (VSV)-based vaccine expressing the SARS-CoV-2 S plus the conserved nucleocapsid (N) protein was protective in a hamster challenge model when a single dose was administered 28 or 10 days prior to challenge, respectively. In this study, only intranasal vaccination resulted in protection against challenge with multiple VOC highlighting that the addition of the N protein indeed improved protective efficacy. This data demonstrates the ability of a VSV-based dual-antigen vaccine to reduce viral shedding and protect from disease caused by SARS-CoV-2 VOC.
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Affiliation(s)
- Kyle L. O’Donnell
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Tylisha Gourdine
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Paige Fletcher
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Chad S. Clancy
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
- *Correspondence: Andrea Marzi,
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12
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Rigo MM, Fasoulis R, Conev A, Hall-Swan S, Antunes DA, Kavraki LE. SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development. Front Immunol 2022; 13:931155. [PMID: 35903104 PMCID: PMC9315150 DOI: 10.3389/fimmu.2022.931155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/10/2022] [Indexed: 02/01/2023] Open
Abstract
The pandemic caused by the SARS-CoV-2 virus, the agent responsible for the COVID-19 disease, has affected millions of people worldwide. There is constant search for new therapies to either prevent or mitigate the disease. Fortunately, we have observed the successful development of multiple vaccines. Most of them are focused on one viral envelope protein, the spike protein. However, such focused approaches may contribute for the rise of new variants, fueled by the constant selection pressure on envelope proteins, and the widespread dispersion of coronaviruses in nature. Therefore, it is important to examine other proteins, preferentially those that are less susceptible to selection pressure, such as the nucleocapsid (N) protein. Even though the N protein is less accessible to humoral response, peptides from its conserved regions can be presented by class I Human Leukocyte Antigen (HLA) molecules, eliciting an immune response mediated by T-cells. Given the increased number of protein sequences deposited in biological databases daily and the N protein conservation among viral strains, computational methods can be leveraged to discover potential new targets for SARS-CoV-2 and SARS-CoV-related viruses. Here we developed SARS-Arena, a user-friendly computational pipeline that can be used by practitioners of different levels of expertise for novel vaccine development. SARS-Arena combines sequence-based methods and structure-based analyses to (i) perform multiple sequence alignment (MSA) of SARS-CoV-related N protein sequences, (ii) recover candidate peptides of different lengths from conserved protein regions, and (iii) model the 3D structure of the conserved peptides in the context of different HLAs. We present two main Jupyter Notebook workflows that can help in the identification of new T-cell targets against SARS-CoV viruses. In fact, in a cross-reactive case study, our workflows identified a conserved N protein peptide (SPRWYFYYL) recognized by CD8+ T-cells in the context of HLA-B7+. SARS-Arena is available at https://github.com/KavrakiLab/SARS-Arena.
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Affiliation(s)
| | - Romanos Fasoulis
- Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States
| | - Anja Conev
- Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States
| | - Sarah Hall-Swan
- Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States
| | - Dinler Amaral Antunes
- Antunes Lab, Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, United States,*Correspondence: Lydia E. Kavraki, ; Dinler Amaral Antunes,
| | - Lydia E. Kavraki
- Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States,*Correspondence: Lydia E. Kavraki, ; Dinler Amaral Antunes,
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13
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Feng W, Xiang Y, Wu L, Chen Z, Li Q, Chen J, Guo Y, Xia D, Chen N, Zhang L, Zhu S, Zhao K. Nucleocapsid protein of SARS-CoV-2 is a potential target for developing new generation of vaccine. J Clin Lab Anal 2022; 36:e24479. [PMID: 35527696 PMCID: PMC9169192 DOI: 10.1002/jcla.24479] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/28/2022] [Accepted: 04/23/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND SARS-CoV-2 has spread worldwide causing more than 400 million people with virus infections since early 2020. Currently, the existing vaccines targeting the spike glycoprotein (S protein) of SARS-CoV-2 are facing great challenge from the infection of SARS-CoV-2 virus and its multiple S protein variants. Thus, we need to develop a new generation of vaccines to prevent infection of the SARS-CoV-2 variants. Compared with the S protein, the nucleocapsid protein (N protein) of SARS-CoV-2 is more conservative and less mutations, which also plays a vital role in viral infection. Therefore, the N protein may have the great potential for developing new vaccines. METHODS The N protein of SARS-CoV-2 was recombinantly expressed and purified in Escherichia coli. Western Blot and ELISA assays were used to demonstrate the immunoreactivity of the recombinant N protein with the serum of 22 COVID-19 patients. We investigated further the response of the specific serum antibodies and cytokine production in BALB/c mice immunized with recombinant N protein by Western Blot and ELISA. RESULTS The N protein had good immunoreactivity and the production of IgG antibody against N protein in COVID-19 patients was tightly correlated with disease severity. Furthermore, the N protein was used to immunize BALB/c mice to have elicited strong immune responses. Not only high levels of IgG antibody, but also cytokine-IFN-γ were produced in the N protein-immunized mice. Importantly, the N protein immunization induced a high level of IgM antibody produced in the mice. CONCLUSION SARS-CoV-2 N protein shows a great big bundle of potentiality for developing a new generation of vaccines in fighting infection of SARS-CoV-2 and its variants.
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Affiliation(s)
- Weixu Feng
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Yunru Xiang
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Lianpeng Wu
- Department of Laboratory MedicineThe Sixth People Hospital of WenzhouWenzhouChina
| | - Zhuo Chen
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Qingfeng Li
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Jun Chen
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Yanru Guo
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Dandan Xia
- Department of Laboratory MedicineThe Sixth People Hospital of WenzhouWenzhouChina
| | - Na Chen
- Department of Laboratory MedicineThe Sixth People Hospital of WenzhouWenzhouChina
| | - Lifang Zhang
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Shanli Zhu
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Kong‐Nan Zhao
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
- Department of Obstetrics and GynaecologyThe Second Affiliated Hospital and Yuyin Children Hospital of Wenzhou Medical UniversityWenzhouChina
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQueenslandAustralia
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14
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Yoo KH, Thapa N, Kim BJ, Lee JO, Jang YN, Chwae YJ, Kim J. Possibility of exosome‑based coronavirus disease 2019 vaccine (Review). Mol Med Rep 2022; 25:26. [PMID: 34821373 PMCID: PMC8630821 DOI: 10.3892/mmr.2021.12542] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/16/2021] [Indexed: 12/29/2022] Open
Abstract
Coronavirus disease 2019 (COVID‑19) is a global pandemic that can have a long‑lasting impact on public health if not properly managed. Ongoing vaccine development trials involve classical molecular strategies based on inactivated or attenuated viruses, single peptides or viral vectors. However, there are multiple issues, such as the risk of reversion to virulence, inability to provide long‑lasting protection and limited protective immunity. To overcome the aforementioned drawbacks of currently available COVID‑19 vaccines, an alternative strategy is required to produce safe and efficacious vaccines that impart long‑term immunity. Exosomes (key intercellular communicators characterized by low immunogenicity, high biocompatibility and innate cargo‑loading capacity) offer a novel approach for effective COVID‑19 vaccine development. An engineered exosome‑based vaccine displaying the four primary structural proteins of SARS‑CoV‑2 (spike, membrane, nucleocapside and envelope proteins) induces humoral and cell mediated immunity and triggers long‑lasting immunity. The present review investigated the prospective use of exosomes in the development of COVID‑19 vaccines; moreover, exosome‑based vaccines may be key to control the COVID‑19 pandemic by providing enhanced protection compared with existing vaccines.
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Affiliation(s)
- Kwang Ho Yoo
- Department of Dermatology, Chung-Ang University College of Medicine, Seoul 06973, Republic of Korea
| | - Nikita Thapa
- CK-Exogene, Inc., Seongnam, Gyeonggi-do 13201, Republic of Korea
| | - Beom Joon Kim
- Department of Dermatology, Chung-Ang University College of Medicine, Seoul 06973, Republic of Korea
| | - Jung Ok Lee
- Department of Dermatology, Chung-Ang University College of Medicine, Seoul 06973, Republic of Korea
| | - You Na Jang
- Department of Dermatology, Chung-Ang University College of Medicine, Seoul 06973, Republic of Korea
| | - Yong Joon Chwae
- Department of Microbiology, Ajou University School of Medicine, Suwon, Gyeonggi-do 16499, Republic of Korea
| | - Jaeyoung Kim
- CK-Exogene, Inc., Seongnam, Gyeonggi-do 13201, Republic of Korea
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15
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Genomic, proteomic and metabolomic profiling of severe acute respiratory syndrome-Coronavirus-2. COMPUTATIONAL APPROACHES FOR NOVEL THERAPEUTIC AND DIAGNOSTIC DESIGNING TO MITIGATE SARS-COV-2 INFECTION 2022. [PMCID: PMC9300679 DOI: 10.1016/b978-0-323-91172-6.00019-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2) is one of the worst human health problems faced by humanity in recent centuries. An end to this health crisis relies on our ability to monitor viral transmission dynamics to check spread, develop therapeutics and preventatives for treatment of SARS-CoV-2 infection and understand the pathophysiology of the disease for better management of the patients. Omics technologies have played a crucial part in understanding the different aspects of COVID-19 disease. While whole-genome sequencing of SARS-CoV-2 isolates from across the globe has aided in the development of molecular diagnostic assays and informed about the viral evolution, knowledge of structure and function of viral proteome fueled the development of small molecule and biologicals therapeutics as well as vaccines. Concurrently, metabolomic profiling of samples from COVID-19 patients experiencing a varying level of disease severity has provided a snapshot of the pathophysiology of the disease helping device effective treatment regimen. This chapter deals with genomic, proteomic, and metabolomic profiling of SRAS-CoV-2.
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16
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De Vos J, Pereira Aguilar P, Köppl C, Fischer A, Grünwald-Gruber C, Dürkop M, Klausberger M, Mairhofer J, Striedner G, Cserjan-Puschmann M, Jungbauer A, Lingg N. Production of full-length SARS-CoV-2 nucleocapsid protein from Escherichia coli optimized by native hydrophobic interaction chromatography hyphenated to multi-angle light scattering detection. Talanta 2021; 235:122691. [PMID: 34517577 PMCID: PMC8284068 DOI: 10.1016/j.talanta.2021.122691] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 11/22/2022]
Abstract
The nucleocapsid protein (NP) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for several steps of the viral life cycle, and is abundantly expressed during infection, making it an ideal diagnostic target protein. This protein has a strong tendency for dimerization and interaction with nucleic acids. For the first time, high titers of NP were expressed in E. coli with a CASPON tag, using a growth-decoupled protein expression system. Purification was accomplished by nuclease treatment of the cell homogenate and a sequence of downstream processing (DSP) steps. An analytical method consisting of native hydrophobic interaction chromatography hyphenated to multi-angle light scattering detection (HIC-MALS) was established for in-process control, in particular, to monitor product fragmentation and multimerization throughout the purification process. 730 mg purified NP per liter of fermentation could be produced by the optimized process, corresponding to a yield of 77% after cell lysis. The HIC-MALS method was used to demonstrate that the NP product can be produced with a purity of 95%. The molecular mass of the main NP fraction is consistent with dimerized protein as was verified by a complementary native size-exclusion separation (SEC)-MALS analysis. Peptide mapping mass spectrometry and host cell specific enzyme-linked immunosorbent assay confirmed the high product purity, and the presence of a minor endogenous chaperone explained the residual impurities. The optimized HIC-MALS method enables monitoring of the product purity, and simultaneously access its molecular mass, providing orthogonal information complementary to established SEC-MALS methods. Enhanced resolving power can be achieved over SEC, attributed to the extended variables to tune selectivity in HIC mode.
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Affiliation(s)
- Jelle De Vos
- Vrije Universiteit Brussel, Department of Chemical Engineering, 1050, Brussels, Belgium; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria
| | - Patricia Pereira Aguilar
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria.
| | - Christoph Köppl
- acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria
| | - Andreas Fischer
- acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria
| | - Clemens Grünwald-Gruber
- BOKU Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
| | - Mark Dürkop
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; Novasign GmbH, 1190, Vienna, Austria
| | - Miriam Klausberger
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria
| | | | - Gerald Striedner
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria; enGenes Biotech GmbH, 1190, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria
| | - Alois Jungbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria
| | - Nico Lingg
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria
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17
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Thura M, Sng J, Ang K, Li J, Gupta A, Hong J, Hong C, Zeng Q. Targeting intra-viral conserved nucleocapsid (N) proteins as novel vaccines against SARS-CoVs. Biosci Rep 2021; 41:BSR20211491. [PMID: 34519332 PMCID: PMC8463655 DOI: 10.1042/bsr20211491] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/30/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the global pandemic of the Coronavirus disease in late 2019 (COVID-19). Vaccine development efforts have predominantly been aimed at 'Extra-viral' Spike (S) protein as vaccine vehicles, but there are concerns regarding 'viral immune escape' since multiple mutations may enable the mutated virus strains to escape from immunity against S protein. The 'Intra-viral' Nucleocapsid (N-protein) is relatively conserved among mutant strains of coronaviruses during spread and evolution. Herein, we demonstrate novel vaccine candidates against SARS-CoV-2 by using the whole conserved N-protein or its fragment/peptides. Using ELISA assay, we showed that high titers of specific anti-N antibodies (IgG, IgG1, IgG2a, IgM) were maintained for a reasonably long duration (> 5 months), suggesting that N-protein is an excellent immunogen to stimulate host immune system and robust B-cell activation. We synthesized three peptides located at the conserved regions of N-protein among CoVs. One peptide showed as a good immunogen for vaccination as well. Cytokine arrays on post-vaccination mouse sera showed progressive up-regulation of various cytokines such as IFN-γ and CCL5, suggesting that TH1 associated responses are also stimulated. Furthermore, vaccinated mice exhibited an elevated memory T cells population. Here, we propose an unconventional vaccine strategy targeting the conserved N-protein as an alternative vaccine target for coronaviruses. Moreover, we generated a mouse monoclonal antibody specifically against an epitope shared between SARS-CoV and SARS-CoV-2, and we are currently developing the First-in-Class humanized anti-N-protein antibody to potentially treat patients infected by various CoVs in the future.
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MESH Headings
- Animals
- Antibodies, Monoclonal, Murine-Derived
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- COVID-19/immunology
- COVID-19/prevention & control
- COVID-19/virology
- COVID-19 Vaccines/administration & dosage
- COVID-19 Vaccines/genetics
- COVID-19 Vaccines/immunology
- Coronavirus Nucleocapsid Proteins/genetics
- Coronavirus Nucleocapsid Proteins/immunology
- Epitopes/immunology
- Humans
- Immune Evasion
- Immunogenicity, Vaccine
- Mice
- Models, Animal
- Pandemics/prevention & control
- Severe acute respiratory syndrome-related coronavirus/genetics
- Severe acute respiratory syndrome-related coronavirus/immunology
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Sequence Homology, Amino Acid
- Spike Glycoprotein, Coronavirus/immunology
- Th1 Cells/immunology
- Vaccines, Subunit/administration & dosage
- Vaccines, Subunit/genetics
- Vaccines, Subunit/immunology
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Affiliation(s)
- Min Thura
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673
| | - Joel Xuan En Sng
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673
| | - Koon Hwee Ang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673
| | - Jie Li
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673
| | - Abhishek Gupta
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673
| | | | - Cheng William Hong
- Department of Radiology, University of California San Diego, San Diego, CA 92103, USA
| | - Qi Zeng
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119260
- INTRA-ImmuSG Private Limited, Singapore 079903
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18
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Wollschläger P, Todt D, Gerlitz N, Pfaender S, Bollinger T, Sing A, Dangel A, Ackermann N, Korn K, Ensser A, Steinmann E, Buhl M, Steinmann J. SARS-CoV-2 N gene dropout and N gene Ct value shift as indicator for the presence of B.1.1.7 lineage in a commercial multiplex PCR assay. Clin Microbiol Infect 2021; 27:1353.e1-1353.e5. [PMID: 34044153 PMCID: PMC8142743 DOI: 10.1016/j.cmi.2021.05.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Detection and surveillance of SARS-CoV-2 is of eminent importance, particularly due to the rapid emergence of variants of concern (VOCs). In this study we evaluated if a commercially available quantitative real-time PCR (qRT-PCR) assay can identify SARS-CoV-2 B.1.1.7 lineage samples by a specific N gene dropout or Ct value shift compared with the S or RdRp gene. METHODS VOC B.1.1.7 and non-B.1.1.7 SARS-CoV-2-positive patient samples were identified via whole-genome sequencing and variant-specific PCR. Confirmed B.1.1.7 (n = 48) and non-B.1.1.7 samples (n = 58) were analysed using the Allplex™ SARS-CoV-2/FluA/FluB/RSV™ PCR assay for presence of SARS-CoV-2 S, RdRp and N genes. The N gene coding sequence of SARS-CoV-2 with and without the D3L mutation (specific for B.1.1.7) was cloned into pCR™II-TOPO™ vectors to validate polymorphism-dependent N gene dropout with the Allplex™ SARS-CoV-2/FluA/FluB/RSV™ PCR assay. RESULTS All studied B.1.1.7-positive patient samples showed significantly higher Ct values in qRT-PCR (Δ6-10, N gene dropout on Ct values > 29) of N gene than the corresponding values of S (p ≤ 0.0001) and RdRp (p ≤ 0.0001) genes. The assay reliably discriminated B.1.1.7 and non-B.1.1.7 positive samples (area under the curve = 1) in a receiver operating characteristic curve analysis. Identical Ct value shifts (Δ7-10) were detected in reverse genetic experiments, using isolated plasmids containing N gene coding sequences corresponding to D3 or 3L variants. DISCUSSION An N gene dropout or Ct value shift is shown for B.1.1.7-positive samples in the Allplex™ SARS-CoV-2/FluA/FluB/RSV™ PCR assay. This approach can be used as a rapid tool for B.1.1.7 detection in single assay high throughput diagnostics.
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Affiliation(s)
- Paul Wollschläger
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Nuremberg, Germany
| | - Daniel Todt
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany; European Virus Bioinformatics Center (EVBC), Jena, Germany
| | - Nadja Gerlitz
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Nuremberg, Germany
| | - Stephanie Pfaender
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Thomas Bollinger
- Microbiology, Laboratory Medicine, Klinikum Bayreuth GmbH, Bayreuth, Germany
| | - Andreas Sing
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| | - Alexandra Dangel
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| | | | - Klaus Korn
- Institute of Clinical and Molecular Virology, University Hospital of Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Armin Ensser
- Institute of Clinical and Molecular Virology, University Hospital of Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Eike Steinmann
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Michael Buhl
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Nuremberg, Germany
| | - Joerg Steinmann
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Nuremberg, Germany.
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19
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Bappy SS, Shibly AZ, Sultana S, Mohiuddin AKM, Kabir Y. Designing potential siRNA molecule for the nucleocapsid(N) gene silencing of different SARS-CoV-2 strains of Bangladesh: Computational approach. Comput Biol Chem 2021; 92:107486. [PMID: 33984653 PMCID: PMC8099544 DOI: 10.1016/j.compbiolchem.2021.107486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 03/18/2021] [Accepted: 04/08/2021] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2 is a single-stranded RNA (+) virus first identified in China and then became an ongoing global outbreak. In most cases, it is fatal in humans due to respiratory malfunction. Extensive researches are going to find an effective therapeutic technique for the treatment of SARS-CoV-2 infected individuals. In this study, we attempted to design a siRNA molecule to silence the most suitable nucleocapsid(N) gene of SARS-CoV-2, which play a major role during viral pathogenesis, replication, encapsidation and RNA packaging. At first, 270 complete N gene sequences of different strains in Bangladesh of these viruses were retrieved from the NCBI database. Different computational methods were used to design siRNA molecules. A siRNA molecule was built against these strains using the SiDirect 2.0 server. Using Mfold and the OligoCalc server, the siRNA molecule was tested for its secondary structure and GC material. The Clustal Omega tool was employed to evaluate any off-target harmony of the planned siRNA molecule. Herein, we proposed a duplex siRNA molecule that does not fit any off-target sequences for the gene silencing of SARS-CoV-2. To treat SARS-CoV-2 infections, currently, any effective therapy is not available. Our engineered siRNA molecule could give an alternative therapeutic approach against various sequenced SARS-CoV-2 strains in Bangladesh.
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Affiliation(s)
- Syed Shahariar Bappy
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh; Research and Development, Incepta Vaccine Ltd, Zirabo, Savar, Dhaka, 1341, Bangladesh
| | - Abu Zaffar Shibly
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - Sorna Sultana
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - A K M Mohiuddin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - Yearul Kabir
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh.
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Pushparajah D, Jimenez S, Wong S, Alattas H, Nafissi N, Slavcev RA. Advances in gene-based vaccine platforms to address the COVID-19 pandemic. Adv Drug Deliv Rev 2021; 170:113-141. [PMID: 33422546 PMCID: PMC7789827 DOI: 10.1016/j.addr.2021.01.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/23/2020] [Accepted: 01/01/2021] [Indexed: 01/07/2023]
Abstract
The novel betacoronavirus, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), has spread across the globe at an unprecedented rate since its first emergence in Wuhan City, China in December 2019. Scientific communities around the world have been rigorously working to develop a potent vaccine to combat COVID-19 (coronavirus disease 2019), employing conventional and novel vaccine strategies. Gene-based vaccine platforms based on viral vectors, DNA, and RNA, have shown promising results encompassing both humoral and cell-mediated immune responses in previous studies, supporting their implementation for COVID-19 vaccine development. In fact, the U.S. Food and Drug Administration (FDA) recently authorized the emergency use of two RNA-based COVID-19 vaccines. We review current gene-based vaccine candidates proceeding through clinical trials, including their antigenic targets, delivery vehicles, and route of administration. Important features of previous gene-based vaccine developments against other infectious diseases are discussed in guiding the design and development of effective vaccines against COVID-19 and future derivatives.
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Affiliation(s)
- Deborah Pushparajah
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada
| | - Salma Jimenez
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada; Theraphage, 151 Charles St W Suite # 199, Kitchener, ON, N2G 1H6, Canada
| | - Shirley Wong
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada
| | - Hibah Alattas
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada
| | - Nafiseh Nafissi
- Mediphage Bioceuticals, 661 University Avenue, Suite 1300, Toronto, ON, M5G 0B7, Canada
| | - Roderick A Slavcev
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada; Mediphage Bioceuticals, 661 University Avenue, Suite 1300, Toronto, ON, M5G 0B7, Canada; Theraphage, 151 Charles St W Suite # 199, Kitchener, ON, N2G 1H6, Canada.
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21
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Tseng YY, Liao GR, Lien A, Hsu WL. Current concepts in the development of therapeutics against human and animal coronavirus diseases by targeting NP. Comput Struct Biotechnol J 2021; 19:1072-1080. [PMID: 33552444 PMCID: PMC7847285 DOI: 10.1016/j.csbj.2021.01.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 11/15/2022] Open
Abstract
The coronavirus (CoV) infects a broad range of hosts including humans as well as a variety of animals. It has gained overwhelming concerns since the emergence of deadly human coronaviruses (HCoVs), severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003, followed by Middle East respiratory syndrome coronavirus (MERS-CoV) in 2015. Very recently, special attention has been paid to the novel coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 due to its high mobility and mortality. As the COVID-19 pandemic continues, despite vast research efforts, the effective pharmaceutical interventions are still not available for clinical uses. Both expanded knowledge on structure insights and the essential function of viral nucleocapsid (N) protein are key basis for the development of novel, and potentially, a broad-spectrum inhibitor against coronavirus diseases. This review aimed to delineate the current research from the perspective of biochemical and structural study in cell-based assays as well as virtual screen approaches to identify N protein antagonists targeting not only HCoVs but also animal CoVs.
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Key Words
- AMP, UMP, GMP and CMP, ribonucleoside 5′-monophosphates
- Antagonists
- BCoV, bovine coronavirus
- CCoV, canine coronavirus
- COVID-19
- COVID-19, coronavirus disease 2019
- CTD, C-terminus dimerization domain
- CoV, coronavirus
- Coronavirus
- E, envelope protein
- ECoV, equine coronavirus
- FECV, feline enteric coronavirus
- FIPV, feline infectious peritonitis virus
- HCoVs, human coronaviruses
- HIV, human immunodeficiency virus
- IBV, infectious bronchitis virus
- IFN, interferon
- Inhibitors
- MERS-CoV, Middle East respiratory syndrome coronavirus
- MHV, mouse hepatitis virus
- MP, membrane protein
- N protein
- NTD, N-terminus RNA-binding domain
- PDCoV, porcine deltacoronavirus
- PEDV, Porcine epidemic diarrhea virus
- PRCV, porcine respiratory coronavirus
- RBD, RNA-binding domain
- RNP, ribonucleoproteins
- SARS-CoV, severe acute respiratory syndrome coronavirus
- SARS-CoV-2
- SP, spike protein
- SeCoV, swine enteric coronavirus
- TCoV, turkey coronavirus
- TGEV, transmissible gastroenteritis virus
- nsp3, the nonstructural protein 3
- shRNAs, short hairpin RNAs
- siRNA, small interfering RNA
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Affiliation(s)
- Yeu-Yang Tseng
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Guan-Ru Liao
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taiwan
| | - Abigail Lien
- Department of Biochemistry, University of Washington, Seattle, USA
| | - Wei-Li Hsu
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taiwan
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22
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Hodge CD, Rosenberg DJ, Wilamowski M, Joachimiak A, Hura GL, Hammel M. Rigid monoclonal antibodies improve detection of SARS-CoV-2 nucleocapsid protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.13.426597. [PMID: 33469584 PMCID: PMC7814821 DOI: 10.1101/2021.01.13.426597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Monoclonal antibodies (mAbs) are the basis of treatments and diagnostics for pathogens and other biological phenomena. We conducted a structural characterization of mAbs against the N-terminal domain of nucleocapsid protein (NP NTD ) from SARS-CoV-2 using small angle X-ray scattering (SAXS). Our solution-based results distinguished the mAbs' flexibility and how this flexibility impacts the assembly of multiple mAbs on an antigen. By pairing two mAbs that bind different epitopes on the NP NTD , we show that flexible mAbs form a closed sandwich-like complex. With rigid mAbs, a juxtaposition of the Fabs is prevented, enforcing a linear arrangement of the mAb pair, which facilitates further mAb polymerization. In a modified sandwich ELISA, we show the rigid mAb-pairings with linear polymerization led to increased NP NTD detection sensitivity. These enhancements can expedite the development of more sensitive and selective antigen-detecting point-of-care lateral flow devices (LFA), key for early diagnosis and epidemiological studies of SARS-CoV-2 and other pathogens.
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Affiliation(s)
- Curtis D Hodge
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Daniel J Rosenberg
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mateusz Wilamowski
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Hodge CD, Rosenberg DJ, Grob P, Wilamowski M, Joachimiak A, Hura GL, Hammel M. Rigid monoclonal antibodies improve detection of SARS-CoV-2 nucleocapsid protein. MAbs 2021; 13:1905978. [PMID: 33843452 PMCID: PMC8043170 DOI: 10.1080/19420862.2021.1905978] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Monoclonal antibodies (mAbs) are the basis of treatments and diagnostics for pathogens and other biological phenomena. We conducted a structural characterization of mAbs against the N-terminal domain of nucleocapsid protein (NPNTD) from SARS-CoV-2 using small-angle X-ray scattering and transmission electron microscopy. Our solution-based results distinguished the mAbs' flexibility and how this flexibility affects the assembly of multiple mAbs on an antigen. By pairing two mAbs that bind different epitopes on the NPNTD, we show that flexible mAbs form a closed sandwich-like complex. With rigid mAbs, a juxtaposition of the antigen-binding fragments is prevented, enforcing a linear arrangement of the mAb pair, which facilitates further mAb polymerization. In a modified sandwich enzyme-linked immunosorbent assay, we show that rigid mAb-pairings with linear polymerization led to increased NPNTD detection sensitivity. These enhancements can expedite the development of more sensitive and selective antigen-detecting point-of-care lateral flow devices, which are critical for early diagnosis and epidemiological studies of SARS-CoV-2 and other pathogens.
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Affiliation(s)
- Curtis D. Hodge
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Daniel. J. Rosenberg
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Graduate Group in Biophysics, University of California, Berkeley, CA, USA
| | - Patricia Grob
- Howard Hughes Medical Institute, UC Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Mateusz Wilamowski
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Greg L. Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Chemistry and Biochemistry Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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24
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Oliveira SC, de Magalhães MTQ, Homan EJ. Immunoinformatic Analysis of SARS-CoV-2 Nucleocapsid Protein and Identification of COVID-19 Vaccine Targets. Front Immunol 2020; 11:587615. [PMID: 33193414 PMCID: PMC7655779 DOI: 10.3389/fimmu.2020.587615] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 10/02/2020] [Indexed: 12/23/2022] Open
Abstract
COVID-19 is a worldwide emergency; therefore, there is a critical need for foundational knowledge about B and T cell responses to SARS-CoV-2 essential for vaccine development. However, little information is available defining which determinants of SARS-CoV-2 other than the spike glycoprotein are recognized by the host immune system. In this study, we focus on the SARS-CoV-2 nucleocapsid protein as a suitable candidate target for vaccine formulations. Major B and T cell epitopes of the SARS-CoV-2 N protein are predicted and resulting sequences compared with the homolog immunological domains of other coronaviruses that infect human beings. The most dominant of B cell epitope is located between 176–206 amino acids in the SRGGSQASSRSSSRSRNSSRNSTPGSSRGTS sequence. Further, we identify sequences which are predicted to bind multiple common MHC I and MHC II alleles. Most notably there is a region of potential T cell cross-reactivity within the SARS-CoV-2 N protein position 102–110 amino acids that traverses multiple human alpha and betacoronaviruses. Vaccination strategies designed to target these conserved epitope regions could generate immune responses that are cross-reactive across human coronaviruses, with potential to protect or modulate disease. Finally, these predictions can facilitate effective vaccine design against this high priority virus.
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Affiliation(s)
- Sergio C Oliveira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais (INCT-DT), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq), Ministerio de Ciencia e Tecnologia (MCT), Salvador, Brazil
| | - Mariana T Q de Magalhães
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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26
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Small interfering RNA effectively inhibits the expression of SARS coronavirus membrane gene at two novel targeting sites. Molecules 2010; 15:7197-207. [PMID: 20956884 PMCID: PMC6259191 DOI: 10.3390/molecules15107197] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 09/15/2010] [Indexed: 01/07/2023] Open
Abstract
Small interfering RNA (siRNA) is a class of duplex RNA molecules of 21-25 nt nucleotides in length functioning post-transcriptionally to downregulate targeted gene expression. The membrane (M) protein of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is highly abundant during viral infections and is a critical element for viral assembly. Nucleotide substitution in the viral genome occurs frequently during SARS-CoV infection. In the current study, we analyzed the M gene sequences derived from 15 SARS-CoV isolates and uncovered six nucleotide substitutions among these isolates. Interestingly, these nucleotide substitutions are all located at the 5’ half of the M gene. Based on this information and previous reports, we created two novel siRNAs targeting two unexplored and well conserved regions in the M gene. The effects of these two siRNAs were tested by semi-quantitative RT-PCR and EGFP-M fusion gene expression. The results demonstrated that both siRNAs effectively and specifically blocked the targeted gene expression. Real time quantitative RT-PCR (qRT-PCR) revealed that siRNA targeting the 3’ half of the M gene (si-M2) induced more potent inhibition than that targeting the 5’ half (si-M1). Both si-M1 and si-M2 significantly downregulated M gene mediated upregulation of interferon β expression. Thus, our results indicate that SARS-CoV M gene specific siRNA might function in a sequence-dependent manner.
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27
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Yang Y, Hussain S, Wang H, Ke M, Guo D. Translational control of the subgenomic RNAs of severe acute respiratory syndrome coronavirus. Virus Genes 2009; 39:10-8. [PMID: 19363699 PMCID: PMC7089290 DOI: 10.1007/s11262-009-0357-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Accepted: 03/30/2009] [Indexed: 12/15/2022]
Abstract
The 3′-one-third of the severe acute respiratory syndrome coronavirus (SARS-CoV) genome contains genes for four essential structural proteins and eight virus-specific genes. The expression of this genomic information of SARS-CoV involves synthesis of a nested set of subgenomic RNAs (sgRNAs). In this study, we showed that the translational levels of 10 SARS-CoV sgRNAs including the two low-abundance sgRNAs 2-1 and 3-1 varied considerably in translation reporter assays. We also demonstrated that the initiator AUG codon of sgRNA-8 was silent and the repressive control was most likely positioned in the upstream untranslated region (UTR) of sgRNA-8. The initiator AUG codons of most sgRNAs are in poor Kozak contexts and the translation of truncated proteins from downstream AUG codons by leaky scanning was common in our experimental settings. No significant correlation was found between complexity of 5′-UTR and the sequence context of AUG codon with the level of translation of SARS-CoV sgRNAs. These results will be helpful for further studies to reveal the biological functions and translation regulatory mechanisms of sgRNAs in the coronavirus life cycle and pathogenesis.
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Affiliation(s)
- Yaling Yang
- State Key Laboratory of Virology and the Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China
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28
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Pan J, Peng X, Gao Y, Li Z, Lu X, Chen Y, Ishaq M, Liu D, DeDiego ML, Enjuanes L, Guo D. Genome-wide analysis of protein-protein interactions and involvement of viral proteins in SARS-CoV replication. PLoS One 2008; 3:e3299. [PMID: 18827877 PMCID: PMC2553179 DOI: 10.1371/journal.pone.0003299] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Accepted: 09/09/2008] [Indexed: 02/05/2023] Open
Abstract
Analyses of viral protein-protein interactions are an important step to understand viral protein functions and their underlying molecular mechanisms. In this study, we adopted a mammalian two-hybrid system to screen the genome-wide intraviral protein-protein interactions of SARS coronavirus (SARS-CoV) and therefrom revealed a number of novel interactions which could be partly confirmed by in vitro biochemical assays. Three pairs of the interactions identified were detected in both directions: non-structural protein (nsp) 10 and nsp14, nsp10 and nsp16, and nsp7 and nsp8. The interactions between the multifunctional nsp10 and nsp14 or nsp16, which are the unique proteins found in the members of Nidovirales with large RNA genomes including coronaviruses and toroviruses, may have important implication for the mechanisms of replication/transcription complex assembly and functions of these viruses. Using a SARS-CoV replicon expressing a luciferase reporter under the control of a transcription regulating sequence, it has been shown that several viral proteins (N, X and SUD domains of nsp3, and nsp12) provided in trans stimulated the replicon reporter activity, indicating that these proteins may regulate coronavirus replication and transcription. Collectively, our findings provide a basis and platform for further characterization of the functions and mechanisms of coronavirus proteins.
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Affiliation(s)
- Ji'An Pan
- State Key Laboratory of Virology and Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Xiaoxue Peng
- State Key Laboratory of Virology and Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yajing Gao
- State Key Laboratory of Virology and Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Zhilin Li
- State Key Laboratory of Virology and Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Xiaolu Lu
- State Key Laboratory of Virology and Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yingzhao Chen
- State Key Laboratory of Virology and Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Musarat Ishaq
- State Key Laboratory of Virology and Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Dan Liu
- State Key Laboratory of Virology and Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Marta L. DeDiego
- Centro Nacional de Biotecnología, CSIC, Department of Molecular and Cell Biology, Campus Universidad Autónoma, Madrid, Spain
| | - Luis Enjuanes
- Centro Nacional de Biotecnología, CSIC, Department of Molecular and Cell Biology, Campus Universidad Autónoma, Madrid, Spain
| | - Deyin Guo
- State Key Laboratory of Virology and Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
- * E-mail:
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Wu S, Xu J, Liu J, Yan X, Zhu X, Xiao G, Sun L, Tien P. An efficient RNA-cleaving DNA enzyme can specifically target the 5'-untranslated region of severe acute respiratory syndrome associated coronavirus (SARS-CoV). J Gene Med 2008; 9:1080-6. [PMID: 17966113 PMCID: PMC7166399 DOI: 10.1002/jgm.1111] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background The worldwide epidemic of severe acute respiratory syndrome (SARS) in 2003 was caused by a novel coronavirus called SARS‐CoV. We report the use of DNAzyme (catalytic DNA) to target the 5′‐untranslated region (5′UTR) of a highly conserved fragment in the SARS genome as an approach to suppression of SARS‐CoV replication. A mono‐DNA enzyme (Dz‐104) possessing the 10–23 catalytic motif was synthesized and tested both in vitro and in cell culture. Materials and methods SARS‐CoV total RNA was isolated, extracted from the SARS‐CoV‐WHU strain and converted into cDNA. We designed a RNA‐cleaving 10–23 DNAzyme targeting at the loop region of the 5′UTR of SARS‐CoV. The designed DNAzyme, Dz‐104, and its mutant version, Dz‐104 (mut), as a control consist of 9 + 9 arm sequences with a 10–23 catalytic core. In vitro cleavage was performed using an in vitro transcribed 5′UTR RNA substrate. A vector containing a fused 5′UTR and enhanced green fluorescent protein (eGFP) was co‐transfected with the DNAzyme into E6 cells and the cells expressing eGFP were visualized with fluorescence microscopy and analyzed by fluorescence‐activated cell sorting (FACS). Results and conclusions Our results demonstrated that this DNAzyme could efficiently cleave the SARS‐CoV RNA substrate in vitro and inhibit the expression of the SARS‐CoV 5′UTR‐eGFP fusion RNA in mammalian cells. This work presents a model system to rapidly screen effective DNAzymes targeting SARS and provides a basis for potential therapeutic use of DNA enzymes to combat the SARS infection. Copyright © 2007 John Wiley & Sons, Ltd.
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Affiliation(s)
- Shuwen Wu
- Modern Virology Research Center, State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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30
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Luo F, Feng Y, Liu M, Li P, Pan Q, Jeza VT, Xia B, Wu J, Zhang XL. Type IVB pilus operon promoter controlling expression of the severe acute respiratory syndrome-associated coronavirus nucleocapsid gene in Salmonella enterica Serovar Typhi elicits full immune response by intranasal vaccination. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2007; 14:990-7. [PMID: 17596427 PMCID: PMC2044483 DOI: 10.1128/cvi.00076-07] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Attenuated Salmonella enterica serovar Typhi strains have been considered to be attractive as potential live oral delivery vector vaccines because of their ability to elicit the full array of immune responses in humans. In this study, we constructed an attenuated S. enterica serovar Typhi strain stably expressing conserved nucleocapsid (N) protein of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) by integrating the N gene into the pilV gene, which was under the control of the type IVB pilus operon promoter in S. enterica serovar Typhi. BALB/c mice were immunized with this recombinant strain through different routes: intranasally, orogastrically, intraperitoneally, and intravenously. Results showed that the intranasal route caused the highest production of specific immunoglobulin G (IgG), IgG2a, and secretory IgA, where IgG2a was imprinted as a Th1 cell bias. Moreover, this recombinant live vaccine induced significantly high levels of specific cytotoxic T-lymphocyte activities and increased gamma interferon-producing T cells compared with the parental strain. Our work provides insights into how the type IVB pilus operon promoter controlling SARS-CoV N gene expression in Salmonella might be attractive for a live-vector vaccine against SRAS-CoV infection, for it could induce mucosal, humoral, and cellular immune responses. Our work also indicates that the type IVB pilus operon promoter controlling foreign gene expression in Salmonella can elicit full immune responses by intranasal vaccination.
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Affiliation(s)
- Fengling Luo
- Department of Immunology, Hubei Province Key Laboratory of Allergy and Immune-Related Diseases, The State Key Laboratory of Virology, Wuhan University School of Medicine, Wuhan 430071, People's Republic of China
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31
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Zhang X, Wu K, Wang D, Yue X, Song D, Zhu Y, Wu J. Nucleocapsid protein of SARS-CoV activates interleukin-6 expression through cellular transcription factor NF-kappaB. Virology 2007; 365:324-35. [PMID: 17490702 PMCID: PMC7103332 DOI: 10.1016/j.virol.2007.04.009] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2006] [Revised: 01/20/2007] [Accepted: 04/09/2007] [Indexed: 12/22/2022]
Abstract
High levels of interleukin-6 (IL-6) in the acute stage associated with lung lesions were found in SARS patients. To evaluate the mechanisms behind this event, we investigated the roles of SARS-CoV proteins in the regulation of IL-6. Results showed that the viral nucleocapsid (N) protein activated IL-6 expression in a concentration-dependent manner. Promoter analyses suggested that NF-κB binding element was required for IL-6 expression regulated by N protein. Further studies demonstrated that N protein bound directly to NF-κB element on the promoter. We also showed that N protein activated IL-6 expression through NF-κB by facilitating the translocation of NF-κB from cytosol to nucleus. Mutational analyses revealed that two regions of N protein were essential for its function in the activation of IL-6. These results provided new insights into understanding the mechanism involved in the function of SARS-CoV N protein and pathogenesis of the virus.
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Affiliation(s)
- Xue Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Kailang Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Di Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Xin Yue
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Degui Song
- College of Biological Sciences, Guangxi Normal University, Guilin 541004, P.R. China
| | - Ying Zhu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
- Corresponding authors. J. Wu is to be contacted at fax: +86 27 68754592.
| | - Jianguo Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
- Corresponding authors. J. Wu is to be contacted at fax: +86 27 68754592.
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Liu M, Yang Y, Gu C, Yue Y, Wu KK, Wu J, Zhu Y. Spike protein of SARS-CoV stimulates cyclooxygenase-2 expression via both calcium-dependent and calcium-independent protein kinase C pathways. FASEB J 2007; 21:1586-96. [PMID: 17267381 DOI: 10.1096/fj.06-6589com] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have previously shown that the nucleocapsid protein of SARS-associated coronavirus (SARS-CoV) activated cyclooxygenase-2 (COX-2) expression. In this study, we identified another viral protein, the spike of SARS-CoV, which played an important role in virus-stimulated COX-2 expression after screening all genes from the SARS-CoV genome. We found that an upstream calcium-dependent PKC isozyme PKC alpha that modulates the downstream ERK/NF-kappaB pathway through an influx of extracellular Ca2+ is induced by the spike protein of SARS-CoV. The ERK/NF-kappaB was identified to be involved in the activation of COX-2 promoter and production of COX-2 protein in HEK293T cells. We also demonstrated that another unusual pathway, the calcium-independent PI3K/PKC epsilon/JNK/CREB pathway, functioned in cooperation with the calcium-dependent pathway to induce COX-2 expression upon stimulation by spike protein. This pathway can be blocked by PKC epsilon-specific, small interfering RNA, PI3K/JNK kinase-specific inhibitors as well as dominant negative JNK. PKC epsilon-specific siRNA also attenuated the phosphorylation of JNK. Our results provide evidence that helps us understand the function of SRAS-CoV spike protein in SARS pathogenesis.
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Affiliation(s)
- Mo Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
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Liu M, Gu C, Wu J, Zhu Y. Amino acids 1 to 422 of the spike protein of SARS associated coronavirus are required for induction of cyclooxygenase-2. Virus Genes 2006; 33:309-17. [PMID: 16991002 PMCID: PMC7088811 DOI: 10.1007/s11262-005-0070-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Accepted: 12/12/2005] [Indexed: 02/07/2023]
Abstract
The causative agent of severe acute respiratory syndrome (SARS) has been identified as SARS-associated coronavirus (SARS-CoV). To evaluate the molecular mechanisms involved in the viral infection, in this study, we investigated the role of SARS-CoV Spike (S) protein in the regulation of cyclooxygenase-2 (COX-2). Expression of COX-2 stimulated by the S protein was verified by RT-PCR and western blot assay. To explore the relationship between S and COX-2, we constructed a series of plasmids containing truncated N-terminal fragments of the SARS-CoV S gene (designated from Sa to Si), which encoded truncated S proteins, and investigated whether these truncated proteins could induce effective expression of COX-2 in 293T cells. Our results showed that S(d) that encoded a truncated S protein with 422 amino acid residues (from 1 to 422 aa), a part of 672 amino-acid S1 subunit is crucial for the induction of COX-2 expression. Immunofluorescence examinations also give the evidence that these N terminal 422 amino acids of the S protein were also required for the correct localization of the protein. We also compared S protein sequences of SARS-CoV isolated during the SARS break with that from palm civets, a possible source of SARS-CoV found in humans. S protein residues (344, 360), which mutated in the epitome from palm civet to human being were characterized in 3D modeling of 252-375 amino acid fragment. Collectively, these results indicate that S protein of SARS-CoV induces the expression of COX-2 and an N-terminal fragment of the Spike protein is crucial for the induction. Our finding may provide clue for the induction of inflammation by SARS-CoV and cast insight into the severity of the SARS epidemic.
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Affiliation(s)
- Mo Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072 P. R. China
| | - Chunfang Gu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072 P. R. China
| | - Jianguo Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072 P. R. China
| | - Ying Zhu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072 P. R. China
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Yan X, Hao Q, Mu Y, Timani KA, Ye L, Zhu Y, Wu J. Nucleocapsid protein of SARS-CoV activates the expression of cyclooxygenase-2 by binding directly to regulatory elements for nuclear factor-kappa B and CCAAT/enhancer binding protein. Int J Biochem Cell Biol 2006; 38:1417-28. [PMID: 16546436 PMCID: PMC7108415 DOI: 10.1016/j.biocel.2006.02.003] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2005] [Revised: 01/17/2006] [Accepted: 02/07/2006] [Indexed: 02/02/2023]
Abstract
SARS-associated coronavirus (SARS-CoV) causes inflammation and damage to the lungs resulting in severe acute respiratory syndrome. To evaluate the molecular mechanisms behind this event, we investigated the roles of SARS-CoV proteins in regulation of the proinflammatory factor, cyclooxygenase-2 (COX-2). Individual viral proteins were tested for their abilities to regulate COX-2 gene expression. Results showed that the COX-2 promoter was activated by the nucleocapsid (N) protein in a concentration-dependent manner. Western blot analysis indicated that N protein was sufficient to stimulate the production of COX-2 protein in mammalian cells. COX-2 promoter mutations suggested that activation of COX-2 transcription depended on two regulatory elements, a nuclear factor-kappa B (NF-κB) binding site, and a CCAAT/enhancer binding protein (C/EBP) binding site. Electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) demonstrated that SARS-CoV N protein bound directly to these regulatory sequences. Protein mutation analysis revealed that a Lys-rich motif of N protein acted as a nuclear localization signal and was essential for the activation of COX-2. In addition, a Leu-rich motif was found to be required for the N protein function. A sequence of 68 residuals was identified as a potential DNA-binding domain essential for activating COX-2 expression. We propose that SARS-CoV N protein causes inflammation of the lungs by activating COX-2 gene expression by binding directly to the promoter resulting in inflammation through multiple COX-2 signaling cascades.
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Affiliation(s)
| | | | | | | | | | | | - Jianguo Wu
- Corresponding author. Tel.: +86 27 68754979; fax: +86 27 68754592.
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Kong WP, Xu L, Stadler K, Ulmer JB, Abrignani S, Rappuoli R, Nabel GJ. Modulation of the immune response to the severe acute respiratory syndrome spike glycoprotein by gene-based and inactivated virus immunization. J Virol 2006; 79:13915-23. [PMID: 16254327 PMCID: PMC1280202 DOI: 10.1128/jvi.79.22.13915-13923.2005] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although the initial isolates of the severe acute respiratory syndrome (SARS) coronavirus (CoV) are sensitive to neutralization by antibodies through their spike (S) glycoprotein, variants of S have since been identified that are resistant to such inhibition. Optimal vaccine strategies would therefore make use of additional determinants of immune recognition, either through cellular or expanded, cross-reactive humoral immunity. Here, the cellular and humoral immune responses elicited by different combinations of gene-based and inactivated viral particles with various adjuvants have been assessed. The T-cell response was altered by different prime-boost immunizations, with the optimal CD8 immunity induced by DNA priming and replication-defective adenoviral vector boosting. The humoral immune response was enhanced most effectively through the use of inactivated virus with adjuvants, either MF59 or alum, and was associated with stimulation of the CD4 but not the CD8 response. The use of inactivated SARS virus with MF59 enhanced the CD4 and antibody response even after gene-based vaccination. Because both cellular and humoral immune responses are generated by gene-based vaccination and inactivated viral boosting, this strategy may prove useful in the generation of SARS-CoV vaccines.
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Affiliation(s)
- Wing-pui Kong
- Vaccine Research Center, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bldg. 40, Room 4502, MSC-3005, 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
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Tan THP, Barkham T, Fielding BC, Chou CF, Shen S, Lim SG, Hong W, Tan YJ. Genetic lesions within the 3a gene of SARS-CoV. Virol J 2005; 2:51. [PMID: 15963240 PMCID: PMC1183252 DOI: 10.1186/1743-422x-2-51] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2005] [Accepted: 06/20/2005] [Indexed: 11/10/2022] Open
Abstract
A series of frameshift mutations within the 3a gene has been observed in culture-derived severe acute respiratory syndrome coronavirus (SARS-CoV). We report here that viral RNA from clinical samples obtained from SARS-CoV infected patients also contains a heterogeneous population of wild-type and mutant 3a transcripts.
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Affiliation(s)
- Timothy HP Tan
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673 Singapore
| | - Timothy Barkham
- Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, 308433 Singapore
| | - Burtram C Fielding
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673 Singapore
| | - Chih-Fong Chou
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673 Singapore
| | - Shuo Shen
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673 Singapore
| | - Seng Gee Lim
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673 Singapore
| | - Wanjin Hong
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673 Singapore
| | - Yee-Joo Tan
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673 Singapore
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Hussain S, Pan J, Chen Y, Yang Y, Xu J, Peng Y, Wu Y, Li Z, Zhu Y, Tien P, Guo D. Identification of novel subgenomic RNAs and noncanonical transcription initiation signals of severe acute respiratory syndrome coronavirus. J Virol 2005; 79:5288-95. [PMID: 15827143 PMCID: PMC1082772 DOI: 10.1128/jvi.79.9.5288-5295.2005] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2004] [Accepted: 12/14/2004] [Indexed: 11/20/2022] Open
Abstract
The expression of the genomic information of severe acute respiratory syndrome coronavirus (SARS CoV) involves synthesis of a nested set of subgenomic RNAs (sgRNAs) by discontinuous transcription. In SARS CoV-infected cells, 10 sgRNAs, including 2 novel ones, were identified, which were predicted to be functional in the expression of 12 open reading frames located in the 3' one-third of the genome. Surprisingly, one new sgRNA could lead to production of a truncated spike protein. Sequence analysis of the leader-body fusion sites of each sgRNA showed that the junction sequences and the corresponding transcription-regulatory sequence (TRS) are unique for each species of sgRNA and are consistent after virus passages. For the two novel sgRNAs, each used a variant of the TRS that has one nucleotide mismatch in the conserved hexanucleotide core (ACGAAC) in the TRS. Coexistence of both plus and minus strands of SARS CoV sgRNAs and evidence for derivation of the sgRNA core sequence from the body core sequence favor the model of discontinuous transcription during minus-strand synthesis. Moreover, one rare species of sgRNA has the junction sequence AAA, indicating that its transcription could result from a noncanonical transcription signal. Taken together, these results provide more insight into the molecular mechanisms of genome expression and subgenomic transcription of SARS CoV.
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Affiliation(s)
- Snawar Hussain
- Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China
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