1
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Bezerra PR, Almeida FCL. Structural basis for the participation of the SARS-CoV-2 nucleocapsid protein in the template switch mechanism and genomic RNA reorganization. J Biol Chem 2024:107834. [PMID: 39343000 DOI: 10.1016/j.jbc.2024.107834] [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: 04/13/2024] [Revised: 09/17/2024] [Accepted: 09/18/2024] [Indexed: 10/01/2024] Open
Abstract
The COVID-19 pandemic has resulted in a significant toll of deaths worldwide, exceeding seven million individuals, prompting intensive research efforts aimed at elucidating the molecular mechanisms underlying the pathogenesis of SARS-CoV-2 infection. Despite the rapid development of effective vaccines and therapeutic interventions, COVID-19 remains a threat to humans due to the emergence of novel variants and largely unknown long-term consequences. Among the viral proteins, the nucleocapsid protein (N) stands out as the most conserved and abundant, playing the primary role in nucleocapsid assembly and genome packaging. The N protein is promiscuous for the recognition of RNA, yet it can perform specific functions. Here, we discuss the structural basis of specificity, which is directly linked to its regulatory role. Notably, the RNA chaperone activity of N is central to its multiple roles throughout the viral life cycle. This activity encompasses double-stranded RNA (dsRNA) annealing and melting and facilitates template switching, enabling discontinuous transcription. N also promotes the formation of membraneless compartments through liquid‒liquid phase separation (LLPS), thereby facilitating the congregation of the replication and transcription complex (RTC). Considering the information available regarding the catalytic activities and binding signatures of the N protein‒RNA interaction, this review focuses on the regulatory role of the SARS-CoV‒2 N protein. We emphasize the participation of the N protein in discontinuous transcription, template switching, and RNA chaperone activity, including double-stranded RNA melting and annealing activities.
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Affiliation(s)
- Peter R Bezerra
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabio C L Almeida
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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2
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El-Maradny YA, Badawy MA, Mohamed KI, Ragab RF, Moharm HM, Abdallah NA, Elgammal EM, Rubio-Casillas A, Uversky VN, Redwan EM. Unraveling the role of the nucleocapsid protein in SARS-CoV-2 pathogenesis: From viral life cycle to vaccine development. Int J Biol Macromol 2024; 279:135201. [PMID: 39216563 DOI: 10.1016/j.ijbiomac.2024.135201] [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: 05/30/2024] [Revised: 08/24/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND The nucleocapsid protein (N protein) is the most abundant protein in SARS-CoV-2. Viral RNA and this protein are bound by electrostatic forces, forming cytoplasmic helical structures known as nucleocapsids. Subsequently, these nucleocapsids interact with the membrane (M) protein, facilitating virus budding into early secretory compartments. SCOPE OF REVIEW Exploring the role of the N protein in the SARS-CoV-2 life cycle, pathogenesis, post-sequelae consequences, and interaction with host immunity has enhanced our understanding of its function and potential strategies for preventing SARS-CoV-2 infection. MAJOR CONCLUSION This review provides an overview of the N protein's involvement in SARS-CoV-2 infectivity, highlighting its crucial role in the virus-host protein interaction and immune system modulation, which in turn influences viral spread. GENERAL SIGNIFICANCE Understanding these aspects identifies the N protein as a promising target for developing effective antiviral treatments and vaccines against SARS-CoV-2.
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Affiliation(s)
- Yousra A El-Maradny
- Pharmaceutical and Fermentation Industries Development Center, City of Scientific Research and Technological Applications (SRTA-City), New Borg EL-Arab, Alexandria 21934, Egypt; Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Moustafa A Badawy
- Industrial Microbiology and Applied Chemistry program, Faculty of Science, Alexandria University, Egypt.
| | - Kareem I Mohamed
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Renad F Ragab
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Hamssa M Moharm
- Genetics, Biotechnology Department, Faculty of Agriculture, Alexandria University, Egypt.
| | - Nada A Abdallah
- Medicinal Plants Department, Faculty of Agriculture, Alexandria University, Egypt.
| | - Esraa M Elgammal
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Alberto Rubio-Casillas
- Autlan Regional Hospital, Health Secretariat, Autlan, JAL 48900, Mexico; Biology Laboratory, Autlan Regional Preparatory School, University of Guadalajara, Autlan, JAL 48900, Mexico.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg EL-Arab, 21934 Alexandria, Egypt.
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3
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Ali MA, Caetano-Anollés G. AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Nucleocapsid Protein Variants. Viruses 2024; 16:1358. [PMID: 39339835 PMCID: PMC11435742 DOI: 10.3390/v16091358] [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: 07/05/2024] [Revised: 08/10/2024] [Accepted: 08/21/2024] [Indexed: 09/30/2024] Open
Abstract
The COVID-19 pandemic saw the emergence of various Variants of Concern (VOCs) that took the world by storm, often replacing the ones that preceded them. The characteristic mutant constellations of these VOCs increased viral transmissibility and infectivity. Their origin and evolution remain puzzling. With the help of data mining efforts and the GISAID database, a chronology of 22 haplotypes described viral evolution up until 23 July 2023. Since the three-dimensional atomic structures of proteins corresponding to the identified haplotypes are not available, ab initio methods were here utilized. Regions of intrinsic disorder proved to be important for viral evolution, as evidenced by the targeted change to the nucleocapsid (N) protein at the sequence, structure, and biochemical levels. The linker region of the N-protein, which binds to the RNA genome and self-oligomerizes for efficient genome packaging, was greatly impacted by mutations throughout the pandemic, followed by changes in structure and intrinsic disorder. Remarkably, VOC constellations acted co-operatively to balance the more extreme effects of individual haplotypes. Our strategy of mapping the dynamic evolutionary landscape of genetically linked mutations to the N-protein structure demonstrates the utility of ab initio modeling and deep learning tools for therapeutic intervention.
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Affiliation(s)
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
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4
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Xu Y, Yi H, Kuang Q, Zheng X, Xu D, Gong L, Yang L, Xiang B. Nucleotide metabolism-related host proteins RNA polymerase II subunit and uridine phosphorylase 1 interacting with porcine epidemic diarrhea virus N proteins affect viral replication. Front Vet Sci 2024; 11:1417348. [PMID: 38933700 PMCID: PMC11200923 DOI: 10.3389/fvets.2024.1417348] [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: 04/14/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a highly infectious pathogen that targets pig intestines to cause disease. It is globally widespread and causes huge economic losses to the pig industry. PEDV N protein is the protein that constitutes the core of PEDV virus particles, and most of it is expressed in the cytoplasm, and a small part can also be expressed in the nucleus. However, the role of related proteins in host nucleotide metabolic pathways in regulating PEDV replication have not been fully elucidated. In this study, PEDV-N-labeled antibodies were co-immunoprecipitated and combined with LC-MS to screen for host proteins that interact with N proteins. Bioinformatics analyses showed that the selected host proteins were mainly enriched in metabolic pathways. Moreover, co-immunoprecipitation and confocal microscopy confirmed that the second-largest subunit of RNA polymerase II (RPB2) and uridine phosphorylase 1 (UPP1) interacted with the N protein. RPB2 is the main subunit of RNA polymerase II and plays an important role in eukaryotic transcription. UPP1 is an enzyme that catalyzes reversible phosphorylation of uridine to uracil and ribo-1-phosphate to promote catabolism and bio anabolism. RPB2 overexpression significantly promoted viral replication, whereas UPP1 overexpression significantly inhibited viral replication. Studies on interactions between the PEDV N and host proteins are helpful in elucidating the pathogenesis and immune escape mechanism of PEDV.
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Affiliation(s)
- Yifan Xu
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Heyou Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiyuan Kuang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiaoyu Zheng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Dan Xu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Lang Gong
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Liangyu Yang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Bin Xiang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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5
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Yadav AK, Basavegowda N, Shirin S, Raju S, Sekar R, Somu P, Uthappa UT, Abdi G. Emerging Trends of Gold Nanostructures for Point-of-Care Biosensor-Based Detection of COVID-19. Mol Biotechnol 2024:10.1007/s12033-024-01157-y. [PMID: 38703305 DOI: 10.1007/s12033-024-01157-y] [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: 01/16/2024] [Accepted: 03/26/2024] [Indexed: 05/06/2024]
Abstract
In 2019, a worldwide pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged. SARS-CoV-2 is the deadly microorganism responsible for coronavirus disease 2019 (COVID-19), which has caused millions of deaths and irreversible health problems worldwide. To restrict the spread of SARS-CoV-2, accurate detection of COVID-19 is essential for the identification and control of infected cases. Although recent detection technologies such as the real-time polymerase chain reaction delivers an accurate diagnosis of SARS-CoV-2, they require a long processing duration, expensive equipment, and highly skilled personnel. Therefore, a rapid diagnosis with accurate results is indispensable to offer effective disease suppression. Nanotechnology is the backbone of current science and technology developments including nanoparticles (NPs) that can biomimic the corona and develop deep interaction with its proteins because of their identical structures on the nanoscale. Various NPs have been extensively applied in numerous medical applications, including implants, biosensors, drug delivery, and bioimaging. Among them, point-of-care biosensors mediated with gold nanoparticles (GNPSs) have received great attention due to their accurate sensing characteristics, which are widely used in the detection of amino acids, enzymes, DNA, and RNA in samples. GNPS have reconstructed the biomedical application of biosensors because of its outstanding physicochemical characteristics. This review provides an overview of emerging trends in GNP-mediated point-of-care biosensor strategies for diagnosing various mutated forms of human coronaviruses that incorporate different transducers and biomarkers. The review also specifically highlights trends in gold nanobiosensors for coronavirus detection, ranging from the initial COVID-19 outbreak to its subsequent evolution into a pandemic.
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Affiliation(s)
- Akhilesh Kumar Yadav
- Department of Environmental Engineering and Management, Chaoyang University of Technology, Taichung, 413310, Taiwan
- Department of Mining Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Nagaraj Basavegowda
- Department of Biotechnology, Yeungnam University, Gyeongsan, 38451, Republic of Korea
| | - Saba Shirin
- Department of Mining Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
- Department of Environmental Science, School of Vocational Studies and Applied Sciences, Gautam Buddha University, Greater Noida, 201312, India
| | - Shiji Raju
- Bioengineering and Nano Medicine Group, Faculty of Medicine and Health Technology, Tampere University, 33720, Tampere, Finland
| | - Rajkumar Sekar
- Department of Chemistry, Karpaga Vinayaga College of Engineering and Technology, GST Road, Chinna Kolambakkam, Chengalpattu, Tamil Nadu, 603308, India
| | - Prathap Somu
- Department of Biotechnology and Chemical Engineering, School of Civil, Biotechnology and Chemical Engineering, Manipal University Jaipur, Dehmi Kalan, Off. Jaipur-Ajmeer Expressway, Jaipur, Rajasthan, 303007, India.
| | - U T Uthappa
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518055, China
- Department of Bioengineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, 602105, India
| | - Gholamreza Abdi
- Department of Biotechnology, Persian Gulf Research Institute, Persian Gulf University, Bushehr, 75169, Iran.
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6
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Ye Q, Wang H, Xu F, Zhang S, Zhang S, Yang Z, Zhang L. Co-Mutations and Possible Variation Tendency of the Spike RBD and Membrane Protein in SARS-CoV-2 by Machine Learning. Int J Mol Sci 2024; 25:4662. [PMID: 38731879 PMCID: PMC11083383 DOI: 10.3390/ijms25094662] [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: 03/23/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, SARS-CoV-2 variants capable of breakthrough infections have attracted global attention. These variants have significant mutations in the receptor-binding domain (RBD) of the spike protein and the membrane (M) protein, which may imply an enhanced ability to evade immune responses. In this study, an examination of co-mutations within the spike RBD and their potential correlation with mutations in the M protein was conducted. The EVmutation method was utilized to analyze the distribution of the mutations to elucidate the relationship between the mutations in the spike RBD and the alterations in the M protein. Additionally, the Sequence-to-Sequence Transformer Model (S2STM) was employed to establish mapping between the amino acid sequences of the spike RBD and M proteins, offering a novel and efficient approach for streamlined sequence analysis and the exploration of their interrelationship. Certain mutations in the spike RBD, G339D-S373P-S375F and Q493R-Q498R-Y505, are associated with a heightened propensity for inducing mutations at specific sites within the M protein, especially sites 3 and 19/63. These results shed light on the concept of mutational synergy between the spike RBD and M proteins, illuminating a potential mechanism that could be driving the evolution of SARS-CoV-2.
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Affiliation(s)
- Qiushi Ye
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Q.Y.)
| | - He Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Q.Y.)
| | - Fanding Xu
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Sijia Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Q.Y.)
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Q.Y.)
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Q.Y.)
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Q.Y.)
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7
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Zheng T, Shen B, Bai Y, Li E, Zhang X, Hu Y, Gao T, Dong Q, Zhu L, Jin R, Shi H, Liu H, Gao Y, Liu X, Cao C. The PKA-CREB1 axis regulates coronavirus proliferation by viral helicase nsp13 association. J Virol 2024; 98:e0156523. [PMID: 38445884 PMCID: PMC11019953 DOI: 10.1128/jvi.01565-23] [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: 10/07/2023] [Accepted: 01/09/2024] [Indexed: 03/07/2024] Open
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a worldwide threat in the past 3 years. Although it has been widely and intensively investigated, the mechanism underlying the coronavirus-host interaction requires further elucidation, which may contribute to the development of new antiviral strategies. Here, we demonstrated that the host cAMP-responsive element-binding protein (CREB1) interacts with the non-structural protein 13 (nsp13) of SARS-CoV-2, a conserved helicase for coronavirus replication, both in cells and in lung tissues subjected to SARS-CoV-2 infection. The ATPase and helicase activity of viral nsp13 were shown to be potentiated by CREB1 association, as well as by Protein kinase A (PKA)-mediated CREB1 activation. SARS-CoV-2 replication is significantly suppressed by PKA Cα, cAMP-activated protein kinase catalytic subunit alpha (PRKACA), and CREB1 knockdown or inhibition. Consistently, the CREB1 inhibitor 666-15 has shown significant antiviral effects against both the WIV04 strain and the Omicron strain of the SARS-CoV-2. Our findings indicate that the PKA-CREB1 signaling axis may serve as a novel therapeutic target against coronavirus infection. IMPORTANCE In this study, we provide solid evidence that host transcription factor cAMP-responsive element-binding protein (CREB1) interacts directly with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) helicase non-structural protein 13 (nsp13) and potentiate its ATPase and helicase activity. And by live SARS-CoV-2 virus infection, the inhibition of CREB1 dramatically impairs SARS-CoV-2 replication in vivo. Notably, the IC50 of CREB1 inhibitor 666-15 is comparable to that of remdesivir. These results may extend to all highly pathogenic coronaviruses due to the conserved nsp13 sequences in the virus.
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Affiliation(s)
- Tong Zheng
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Beilei Shen
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yu Bai
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China
| | - Entao Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Xun Zhang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China
| | - Yong Hu
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Ting Gao
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Qincai Dong
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Lin Zhu
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Rui Jin
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Hui Shi
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Hainan Liu
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Yuwei Gao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xuan Liu
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Cheng Cao
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
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8
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Steiner S, Kratzel A, Barut GT, Lang RM, Aguiar Moreira E, Thomann L, Kelly JN, Thiel V. SARS-CoV-2 biology and host interactions. Nat Rev Microbiol 2024; 22:206-225. [PMID: 38225365 DOI: 10.1038/s41579-023-01003-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
The zoonotic emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing coronavirus disease 2019 (COVID-19) pandemic have profoundly affected our society. The rapid spread and continuous evolution of new SARS-CoV-2 variants continue to threaten global public health. Recent scientific advances have dissected many of the molecular and cellular mechanisms involved in coronavirus infections, and large-scale screens have uncovered novel host-cell factors that are vitally important for the virus life cycle. In this Review, we provide an updated summary of the SARS-CoV-2 life cycle, gene function and virus-host interactions, including recent landmark findings on general aspects of coronavirus biology and newly discovered host factors necessary for virus replication.
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Affiliation(s)
- Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto M Lang
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center, Jena, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
- European Virus Bioinformatics Center, Jena, Germany.
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9
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Dong W, Cheng Y, Zhou Y, Zhang J, Yu X, Guan H, Du J, Zhou X, Yang Y, Fang W, Wang X, Song H. The nucleocapsid protein facilitates p53 ubiquitination-dependent proteasomal degradation via recruiting host ubiquitin ligase COP1 in PEDV infection. J Biol Chem 2024; 300:107135. [PMID: 38447796 PMCID: PMC10998216 DOI: 10.1016/j.jbc.2024.107135] [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: 01/03/2024] [Revised: 01/30/2024] [Accepted: 02/13/2024] [Indexed: 03/08/2024] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a highly contagious enteric pathogen of the coronavirus family and caused severe economic losses to the global swine industry. Previous studies have established that p53 is a host restriction factor for PEDV infection, and p53 degradation occurs in PEDV-infected cells. However, the underlying molecular mechanisms through which PEDV viral proteins regulate p53 degradation remain unclear. In this study, we found that PEDV infection or expression of the nucleocapsid protein downregulates p53 through a post-translational mechanism: increasing the ubiquitination of p53 and preventing its nuclear translocation. We also show that the PEDV N protein functions by recruiting the E3 ubiquitin ligase COP1 and suppressing COP1 self-ubiquitination and protein degradation, thereby augmenting COP1-mediated degradation of p53. Additionally, COP1 knockdown compromises N-mediated p53 degradation. Functional mapping using truncation analysis showed that the N-terminal domains of N protein were responsible for interacting with COP1 and critical for COP1 stability and p53 degradation. The results presented here suggest the COP1-dependent mechanism for PEDV N protein to abolish p53 activity. This study significantly increases our understanding of PEDV in antagonizing the host antiviral factor p53 and will help initiate novel antiviral strategies against PEDV.
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Affiliation(s)
- Wanyu Dong
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Yahao Cheng
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Yingshan Zhou
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Jingmiao Zhang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Xinya Yu
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Haicun Guan
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Jing Du
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Xingdong Zhou
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Yang Yang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Weihuan Fang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Xiaodu Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China.
| | - Houhui Song
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China.
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10
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Fleckenstein F, Stephan S, Hasse H. Elucidating the behavior of the SARS-CoV-2 virus surface at vapor-liquid interfaces using molecular dynamics simulation. Proc Natl Acad Sci U S A 2024; 121:e2317194121. [PMID: 38502700 PMCID: PMC10990154 DOI: 10.1073/pnas.2317194121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/15/2024] [Indexed: 03/21/2024] Open
Abstract
Aerosols play a major role in the transmission of the SARS-CoV-2 virus. The behavior of the virus within aerosols is therefore of fundamental importance. On the surface of a SARS-CoV-2 virus, there are about 40 spike proteins, which each have a length of about 20 nm. They are glycosylated trimers, which are highly flexible, due to their structure. These spike proteins play a central role in the intrusion of the virus into human host cells and are, therefore, a focus of vaccine development. In this work, we have studied the behavior of spike proteins of the SARS-CoV-2 virus in the presence of a vapor-liquid interface by molecular dynamics (MD) simulations. Systematically, the behavior of the spike protein at different distances to a vapor-liquid interface were studied. The results reveal that the spike protein of the SARS-CoV-2 virus is repelled from the vapor-liquid interface and has a strong affinity to stay inside the bulk liquid phase. Therefore, the spike protein bends when a vapor-liquid interface approaches the top of the protein. This has important consequences for understanding the behavior of the virus during the dry-out of aerosol droplets.
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Affiliation(s)
- Florian Fleckenstein
- Laboratory of Engineering Thermodynamics, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau (RPTU), Kaiserslautern67663, Germany
| | - Simon Stephan
- Laboratory of Engineering Thermodynamics, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau (RPTU), Kaiserslautern67663, Germany
| | - Hans Hasse
- Laboratory of Engineering Thermodynamics, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau (RPTU), Kaiserslautern67663, Germany
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11
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Eltayeb A, Al-Sarraj F, Alharbi M, Albiheyri R, Mattar E, Abu Zeid IM, Bouback TA, Bamagoos A, Aljohny BO, Uversky VN, Redwan EM. Overview of the SARS-CoV-2 nucleocapsid protein. Int J Biol Macromol 2024; 260:129523. [PMID: 38232879 DOI: 10.1016/j.ijbiomac.2024.129523] [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: 06/04/2023] [Revised: 01/12/2024] [Accepted: 01/13/2024] [Indexed: 01/19/2024]
Abstract
Since the emergence of SARS-CoV in 2003, researchers worldwide have been toiling away at deciphering this virus's biological intricacies. In line with other known coronaviruses, the nucleocapsid (N) protein is an important structural component of SARS-CoV. As a result, much emphasis has been placed on characterizing this protein. Independent research conducted by a variety of laboratories has clearly demonstrated the primary function of this protein, which is to encapsidate the viral genome. Furthermore, various accounts indicate that this particular protein disrupts diverse intracellular pathways. Such observations imply its vital role in regulating the virus as well. The opening segment of this review will expound upon these distinct characteristics succinctly exhibited by the N protein. Additionally, it has been suggested that the N protein possesses diagnostic and vaccine capabilities when dealing with SARS-CoV. In light of this fact, we will be reviewing some recent headway in the use cases for N protein toward clinical purposes within this article's concluding segments. This forward movement pertains to both developments of COVID-19-oriented therapeutic targets as well as diagnostic measures. The strides made by medical researchers offer encouragement, knowing they are heading toward a brighter future combating global pandemic situations such as these.
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Affiliation(s)
- Ahmed Eltayeb
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Faisal Al-Sarraj
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Raed Albiheyri
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ehab Mattar
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Isam M Abu Zeid
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, P.O. Box 80200, Jeddah, Saudi Arabia
| | - Thamer A Bouback
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, P.O. Box 80200, Jeddah, Saudi Arabia
| | - Atif Bamagoos
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Bassam O Aljohny
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Elrashdy M Redwan
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, 21934 Alexandria, Egypt.
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12
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Lapierre LA, Roland JT, Manning EH, Caldwell C, Glenn HL, Vidalain PO, Tangy F, Hogue BG, de Haan CAM, Goldenring JR. Coronavirus M Protein Trafficking in Epithelial Cells Utilizes a Myosin Vb Splice Variant and Rab10. Cells 2024; 13:126. [PMID: 38247817 PMCID: PMC10814003 DOI: 10.3390/cells13020126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
The membrane (M) glycoprotein of coronaviruses (CoVs) serves as the nidus for virion assembly. Using a yeast two-hybrid screen, we identified the interaction of the cytosolic tail of Murine Hepatitis Virus (MHV-CoV) M protein with Myosin Vb (MYO5B), specifically with the alternative splice variant of cellular MYO5B including exon D (MYO5B+D), which mediates interaction with Rab10. When co-expressed in human lung epithelial A549 and canine kidney epithelial MDCK cells, MYO5B+D co-localized with the MHV-CoV M protein, as well as with the M proteins from Porcine Epidemic Diarrhea Virus (PEDV-CoV), Middle East Respiratory Syndrome (MERS-CoV) and Severe Acute Respiratory Syndrome 2 (SARS-CoV-2). Co-expressed M proteins and MYO5B+D co-localized with endogenous Rab10 and Rab11a. We identified point mutations in MHV-CoV M that blocked the interaction with MYO5B+D in yeast 2-hybrid assays. One of these point mutations (E121K) was previously shown to block MHV-CoV virion assembly and its interaction with MYO5B+D. The E to K mutation at homologous positions in PEDV-CoV, MERS-CoV and SARS-CoV-2 M proteins also blocked colocalization with MYO5B+D. The knockdown of Rab10 blocked the co-localization of M proteins with MYO5B+D and was rescued by re-expression of CFP-Rab10. Our results suggest that CoV M proteins traffic through Rab10-containing systems, in association with MYO5B+D.
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Affiliation(s)
- Lynne A. Lapierre
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (L.A.L.); (J.T.R.); (E.H.M.); (C.C.)
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Nashville VA Medical Center, Nashville, TN 37212, USA
| | - Joseph T. Roland
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (L.A.L.); (J.T.R.); (E.H.M.); (C.C.)
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Elizabeth H. Manning
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (L.A.L.); (J.T.R.); (E.H.M.); (C.C.)
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Nashville VA Medical Center, Nashville, TN 37212, USA
| | - Catherine Caldwell
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (L.A.L.); (J.T.R.); (E.H.M.); (C.C.)
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Nashville VA Medical Center, Nashville, TN 37212, USA
| | - Honor L. Glenn
- Biodesign Institute Center for Immunotherapy, Vaccines & Virotherapy, Tempe, AZ 85287, USA; (H.L.G.); (B.G.H.)
| | - Pierre-Olivier Vidalain
- Equipe Infections Virales, Métabolisme et Immunité, Centre International de Recherche en Infectiologie (CIRI), Univ. Lyon, INSERM U1111, CNRS UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France;
- Unité Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR3569, 75015 Paris, France
| | - Frederic Tangy
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, CNRS UMR3569, 75015 Paris, France;
| | - Brenda G. Hogue
- Biodesign Institute Center for Immunotherapy, Vaccines & Virotherapy, Tempe, AZ 85287, USA; (H.L.G.); (B.G.H.)
- Center for Applied Structural Discovery, Biodesign Institute, Tempe, AZ 85287, USA
- School of Life Sciences, Arizona State University, Phoenix, AZ 85004, USA
| | - C. A. M. de Haan
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Section Virology, University of Utrecht, 3584 CS Utrecht, The Netherlands;
| | - James R. Goldenring
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (L.A.L.); (J.T.R.); (E.H.M.); (C.C.)
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Nashville VA Medical Center, Nashville, TN 37212, USA
- Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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13
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Wu A, Shi K, Wang J, Zhang R, Wang Y. Targeting SARS-CoV-2 entry processes: The promising potential and future of host-targeted small-molecule inhibitors. Eur J Med Chem 2024; 263:115923. [PMID: 37981443 DOI: 10.1016/j.ejmech.2023.115923] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/16/2023] [Accepted: 10/28/2023] [Indexed: 11/21/2023]
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has had a huge impact on global health. To respond to rapidly mutating viruses and to prepare for the next pandemic, there is an urgent need to develop small molecule therapies that target critical stages of the SARS-CoV-2 life cycle. Inhibiting the entry process of the virus can effectively control viral infection and play a role in prevention and treatment. Host factors involved in this process, such as ACE2, TMPRSS2, ADAM17, furin, PIKfyve, TPC2, CTSL, AAK1, V-ATPase, HSPG, and NRP1, have been found to be potentially good targets with stability. Through further exploration of the cell entry process of SARS-CoV-2, small-molecule drugs targeting these host factors have been developed. This review focuses on the structural functions of potential host cell targets during the entry of SARS-CoV-2 into host cells. The research progress, chemical structure, structure-activity relationship, and clinical value of small-molecule inhibitors against COVID-19 are reviewed to provide a reference for the development of small-molecule drugs against COVID-19.
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Affiliation(s)
- Aijia Wu
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Kunyu Shi
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Ruofei Zhang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yuxi Wang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, China.
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14
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Chatterjee S, Zaia J. Proteomics-based mass spectrometry profiling of SARS-CoV-2 infection from human nasopharyngeal samples. MASS SPECTROMETRY REVIEWS 2024; 43:193-229. [PMID: 36177493 PMCID: PMC9538640 DOI: 10.1002/mas.21813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 05/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the on-going global pandemic of coronavirus disease 2019 (COVID-19) that continues to pose a significant threat to public health worldwide. SARS-CoV-2 encodes four structural proteins namely membrane, nucleocapsid, spike, and envelope proteins that play essential roles in viral entry, fusion, and attachment to the host cell. Extensively glycosylated spike protein efficiently binds to the host angiotensin-converting enzyme 2 initiating viral entry and pathogenesis. Reverse transcriptase polymerase chain reaction on nasopharyngeal swab is the preferred method of sample collection and viral detection because it is a rapid, specific, and high-throughput technique. Alternate strategies such as proteomics and glycoproteomics-based mass spectrometry enable a more detailed and holistic view of the viral proteins and host-pathogen interactions and help in detection of potential disease markers. In this review, we highlight the use of mass spectrometry methods to profile the SARS-CoV-2 proteome from clinical nasopharyngeal swab samples. We also highlight the necessity for a comprehensive glycoproteomics mapping of SARS-CoV-2 from biological complex matrices to identify potential COVID-19 markers.
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Affiliation(s)
- Sayantani Chatterjee
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
- Bioinformatics ProgramBoston University School of MedicineBostonMassachusettsUSA
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15
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Logue J, Melville VM, Ardanuy J, Frieman MB. CNP blocks mitochondrial depolarization and inhibits SARS-CoV-2 replication in vitro and in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544327. [PMID: 37333151 PMCID: PMC10274905 DOI: 10.1101/2023.06.09.544327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The COVID-19 pandemic has claimed over 6.5 million lives worldwide and continues to have lasting impacts on the world's healthcare and economic systems. Several approved and emergency authorized therapeutics that inhibit early stages of the virus replication cycle have been developed however, effective late-stage therapeutical targets have yet to be identified. To that end, our lab identified that 2',3' cyclic-nucleotide 3'-phosphodiesterase (CNP) inhibits SARS-CoV-2 virion assembly. We show that CNP inhibits the generation of new SARS-CoV-2 virions, reducing intracellular titers without inhibiting viral structural protein translation. Additionally, we show that targeting of CNP to mitochondria is necessary for inhibition, blocking mitochondrial depolarization and implicating CNP's proposed role as an inhibitor of the mitochondrial permeabilization transition pore (mPTP) as the mechanism of virion assembly inhibition. We also demonstrate that an adenovirus expressing virus expressing both human ACE2 and CNP inhibits SARS-CoV-2 titers to undetectable levels in lungs of mice. Collectively, this work shows the potential of CNP to be a new SARS-CoV-2 antiviral target.
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Affiliation(s)
- James Logue
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore,Maryland, USA
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore,Maryland, USA
| | - Victoria M. Melville
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore,Maryland, USA
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore,Maryland, USA
| | - Jeremy Ardanuy
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore,Maryland, USA
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore,Maryland, USA
| | - Matthew B. Frieman
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore,Maryland, USA
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore,Maryland, USA
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16
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Knupp J, Pletan ML, Arvan P, Tsai B. Autophagy of the ER: the secretome finds the lysosome. FEBS J 2023; 290:5656-5673. [PMID: 37920925 PMCID: PMC11044768 DOI: 10.1111/febs.16986] [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: 08/03/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023]
Abstract
Lysosomal degradation of the endoplasmic reticulum (ER) and its components through the autophagy pathway has emerged as a major regulator of ER proteostasis. Commonly referred to as ER-phagy and ER-to-lysosome-associated degradation (ERLAD), how the ER is targeted to the lysosome has been recently clarified by a growing number of studies. Here, we summarize the discoveries of the molecular components required for lysosomal degradation of the ER and their proposed mechanisms of action. Additionally, we discuss how cells employ these machineries to create the different routes of ER-lysosome-associated degradation. Further, we review the role of ER-phagy in viral infection pathways, as well as the implication of ER-phagy in human disease. In sum, we provide a comprehensive overview of the current field of ER-phagy.
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Affiliation(s)
- Jeffrey Knupp
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Madison L Pletan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter Arvan
- Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Billy Tsai
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA
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17
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Logue J, Melville VM, Ardanuy J, Frieman MB. CNP blocks mitochondrial depolarization and inhibits SARS-CoV-2 replication in vitro and in vivo. PLoS Pathog 2023; 19:e1011870. [PMID: 38117830 PMCID: PMC10766180 DOI: 10.1371/journal.ppat.1011870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 01/04/2024] [Accepted: 11/28/2023] [Indexed: 12/22/2023] Open
Abstract
The COVID-19 pandemic has claimed over 6.5 million lives worldwide and continues to have lasting impacts on the world's healthcare and economic systems. Several approved and emergency authorized therapeutics that inhibit early stages of the virus replication cycle have been developed however, effective late-stage therapeutical targets have yet to be identified. To that end, our lab identified that 2',3' cyclic-nucleotide 3'-phosphodiesterase (CNP) inhibits SARS-CoV-2 virion assembly. We show that CNP inhibits the generation of new SARS-CoV-2 virions, reducing intracellular titers without inhibiting viral structural protein translation. Additionally, we show that targeting of CNP to mitochondria is necessary for inhibition, blocking mitochondrial depolarization and implicating CNP's proposed role as an inhibitor of the mitochondrial permeabilization transition pore (mPTP) as the mechanism of virion assembly inhibition. We also demonstrate that an adenovirus expressing virus expressing both human ACE2 and CNP inhibits SARS-CoV-2 titers to undetectable levels in lungs of mice. Collectively, this work shows the potential of CNP to be a new SARS-CoV-2 antiviral target.
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Affiliation(s)
- James Logue
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Victoria M. Melville
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jeremy Ardanuy
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Matthew B. Frieman
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
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18
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Miura K, Suzuki Y, Ishida K, Arakawa M, Wu H, Fujioka Y, Emi A, Maeda K, Hamajima R, Nakano T, Tenno T, Hiroaki H, Morita E. Distinct motifs in the E protein are required for SARS-CoV-2 virus particle formation and lysosomal deacidification in host cells. J Virol 2023; 97:e0042623. [PMID: 37830820 PMCID: PMC10617393 DOI: 10.1128/jvi.00426-23] [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: 03/20/2023] [Accepted: 07/18/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has caused a global public health crisis. The E protein, a structural protein found in this virus particle, is also known to be a viroporin. As such, it forms oligomeric ion channels or pores in the host cell membrane. However, the relationship between these two functions is poorly understood. In this study, we showed that the roles of E protein in virus particle and viroporin formation are distinct. This study contributes to the development of drugs that inhibit SARS-CoV-2 virus particle formation. Additionally, we designed a highly sensitive and high-throughput virus-like particle detection system using the HiBiT tag, which is a useful tool for studying the release of SARS-CoV-2.
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Affiliation(s)
- Koya Miura
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Youichi Suzuki
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Kotaro Ishida
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Masashi Arakawa
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Hong Wu
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Yoshihiko Fujioka
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Akino Emi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Koki Maeda
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Ryusei Hamajima
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi, Japan
| | - Takashi Nakano
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Takeshi Tenno
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi, Japan
- BeCellBar LLC, Nagoya, Aichi, Japan
| | - Hidekazu Hiroaki
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi, Japan
- BeCellBar LLC, Nagoya, Aichi, Japan
| | - Eiji Morita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
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19
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Bodakuntla S, Kuhn CC, Biertümpfel C, Mizuno N. Cryo-electron microscopy in the fight against COVID-19-mechanism of virus entry. Front Mol Biosci 2023; 10:1252529. [PMID: 37867557 PMCID: PMC10587472 DOI: 10.3389/fmolb.2023.1252529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/20/2023] [Indexed: 10/24/2023] Open
Abstract
Cryogenic electron microscopy (cryo-EM) and electron tomography (cryo-ET) have become a critical tool for studying viral particles. Cryo-EM has enhanced our understanding of viral assembly and replication processes at a molecular resolution. Meanwhile, in situ cryo-ET has been used to investigate how viruses attach to and invade host cells. These advances have significantly contributed to our knowledge of viral biology. Particularly, prompt elucidations of structures of the SARS-CoV-2 spike protein and its variants have directly impacted the development of vaccines and therapeutic measures. This review discusses the progress made by cryo-EM based technologies in comprehending the severe acute respiratory syndrome coronavirus-2 (SARS-Cov-2), the virus responsible for the devastating global COVID-19 pandemic in 2020 with focus on the SARS-CoV-2 spike protein and the mechanisms of the virus entry and replication.
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Affiliation(s)
- Satish Bodakuntla
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Christopher Cyrus Kuhn
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Christian Biertümpfel
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Naoko Mizuno
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
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20
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Ding T, Cheng T, Zhu X, Xiao W, Xia S, Fang L, Fang P, Xiao S. Exosomes mediate the antibody-resistant intercellular transmission of porcine epidemic diarrhea virus. Vet Microbiol 2023; 284:109834. [PMID: 37536161 DOI: 10.1016/j.vetmic.2023.109834] [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: 03/31/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023]
Abstract
Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic enteric coronavirus that causes severe enteritis and lethal watery diarrhea in suckling piglets, leading to tremendous economic losses. Exosomes have been reported to participate in intercellular communication by the transportation of a variety of biological materials, including RNAs, lipids, and proteins. However, PEDV transmission routes have not yet been fully elucidated, and whether exosomes function in PEDV transmission remains unclear. In this study, we extracted and purified exosomes from PEDV-infected Vero cells using a stringent isolation method with a combination of chemical precipitation, ultracentrifugation, and incubation with CD63-labeled magnetic beads. We found that exosomes from PEDV-infected Vero cells contain viral genomic RNA and viral nucleocapsid protein. Furthermore, we demonstrated that the purified exosomes from PEDV-infected cells are capable of transmitting the virus to both PEDV-susceptible and non-susceptible cells. Importantly, exosome-mediated PEDV infection was resistant to neutralization by PEDV-specific neutralizing antibodies that potently neutralized free PEDV. Our study reveals a potential immune evasion mechanism utilized by PEDV and provides new insight into the transmission and infection of this important pathogen.
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Affiliation(s)
- Tong Ding
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Ting Cheng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Xuerui Zhu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Wenwen Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Sijin Xia
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Puxian Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
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21
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Chen P, Wu M, He Y, Jiang B, He ML. Metabolic alterations upon SARS-CoV-2 infection and potential therapeutic targets against coronavirus infection. Signal Transduct Target Ther 2023; 8:237. [PMID: 37286535 DOI: 10.1038/s41392-023-01510-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/18/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by coronavirus SARS-CoV-2 infection has become a global pandemic due to the high viral transmissibility and pathogenesis, bringing enormous burden to our society. Most patients infected by SARS-CoV-2 are asymptomatic or have mild symptoms. Although only a small proportion of patients progressed to severe COVID-19 with symptoms including acute respiratory distress syndrome (ARDS), disseminated coagulopathy, and cardiovascular disorders, severe COVID-19 is accompanied by high mortality rates with near 7 million deaths. Nowadays, effective therapeutic patterns for severe COVID-19 are still lacking. It has been extensively reported that host metabolism plays essential roles in various physiological processes during virus infection. Many viruses manipulate host metabolism to avoid immunity, facilitate their own replication, or to initiate pathological response. Targeting the interaction between SARS-CoV-2 and host metabolism holds promise for developing therapeutic strategies. In this review, we summarize and discuss recent studies dedicated to uncovering the role of host metabolism during the life cycle of SARS-CoV-2 in aspects of entry, replication, assembly, and pathogenesis with an emphasis on glucose metabolism and lipid metabolism. Microbiota and long COVID-19 are also discussed. Ultimately, we recapitulate metabolism-modulating drugs repurposed for COVID-19 including statins, ASM inhibitors, NSAIDs, Montelukast, omega-3 fatty acids, 2-DG, and metformin.
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Affiliation(s)
- Peiran Chen
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China
| | - Mandi Wu
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China
| | - Yaqing He
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, Guangdong, China
| | - Binghua Jiang
- Cell Signaling and Proteomic Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ming-Liang He
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China.
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22
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Bills C, Xie X, Shi PY. The multiple roles of nsp6 in the molecular pathogenesis of SARS-CoV-2. Antiviral Res 2023; 213:105590. [PMID: 37003304 PMCID: PMC10063458 DOI: 10.1016/j.antiviral.2023.105590] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/19/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve and adapt after its emergence in late 2019. As the causative agent of the coronavirus disease 2019 (COVID-19), the replication and pathogenesis of SARS-CoV-2 have been extensively studied by the research community for vaccine and therapeutics development. Given the importance of viral spike protein in viral infection/transmission and vaccine development, the scientific community has thus far primarily focused on studying the structure, function, and evolution of the spike protein. Other viral proteins are understudied. To fill in this knowledge gap, a few recent studies have identified nonstructural protein 6 (nsp6) as a major contributor to SARS-CoV-2 replication through the formation of replication organelles, antagonism of interferon type I (IFN-I) responses, and NLRP3 inflammasome activation (a major factor of severe disease in COVID-19 patients). Here, we review the most recent progress on the multiple roles of nsp6 in modulating SARS-CoV-2 replication and pathogenesis.
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Affiliation(s)
- Cody Bills
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, USA; World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA; Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, Texas, USA.
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23
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Castañeda-Montes FJ, Cerriteño-Sánchez JL, Castañeda-Montes MA, Cuevas-Romero JS, Mendoza-Elvira S. A Candidate Antigen of the Recombinant Membrane Protein Derived from the Porcine Deltacoronavirus Synthetic Gene to Detect Seropositive Pigs. Viruses 2023; 15:v15051049. [PMID: 37243136 DOI: 10.3390/v15051049] [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: 04/04/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 05/28/2023] Open
Abstract
Porcine deltacoronavirus (PDCoV) is an emergent swine coronavirus which infects cells from the small intestine and induces watery diarrhea, vomiting and dehydration, causing mortality in piglets (>40%). The aim of this study was to evaluate the antigenicity and immunogenicity of the recombinant membrane protein (M) of PDCoV (rM-PDCoV), which was developed from a synthetic gene obtained after an in silico analysis with a group of 138 GenBank sequences. A 3D model and phylogenetic analysis confirmed the highly conserved M protein structure. Therefore, the synthetic gene was successfully cloned in a pETSUMO vector and transformed in E. coli BL21 (DE3). The rM-PDCoV was confirmed by SDS-PAGE and Western blot with ~37.7 kDa. The rM-PDCoV immunogenicity was evaluated in immunized (BLAB/c) mice and iELISA. The data showed increased antibodies from 7 days until 28 days (p < 0.001). The rM-PDCoV antigenicity was analyzed using pig sera samples from three states located in "El Bajío" Mexico and positive sera were determined. Our results show that PDCoV has continued circulating on pig farms in Mexico since the first report in 2019; therefore, the impact of PDCoV on the swine industry could be higher than reported in other studies.
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Affiliation(s)
- Francisco Jesus Castañeda-Montes
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Km 15.5 Carretera México-Toluca, Palo Alto, Cuajimalpa, Ciudad de México 05110, Mexico
- Posgrado en Ciencias de la Producción y de la Salud Animal, Facultad de Estudios Superiores Cuautitlán, Estado de México, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - José Luis Cerriteño-Sánchez
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Km 15.5 Carretera México-Toluca, Palo Alto, Cuajimalpa, Ciudad de México 05110, Mexico
| | - María Azucena Castañeda-Montes
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Km 15.5 Carretera México-Toluca, Palo Alto, Cuajimalpa, Ciudad de México 05110, Mexico
| | - Julieta Sandra Cuevas-Romero
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Km 15.5 Carretera México-Toluca, Palo Alto, Cuajimalpa, Ciudad de México 05110, Mexico
| | - Susana Mendoza-Elvira
- Posgrado en Ciencias de la Producción y de la Salud Animal, Facultad de Estudios Superiores Cuautitlán, Estado de México, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
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24
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Khalid T, Hasan A, Fatima JE, Faridi SA, Khan AF, Mir SS. Therapeutic role of mTOR inhibitors in control of SARS-CoV-2 viral replication. Mol Biol Rep 2023; 50:2701-2711. [PMID: 36538171 PMCID: PMC9764303 DOI: 10.1007/s11033-022-08188-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
By the end of 2019, COVID-19 was reported in Wuhan city of China, and through human-human transmission, this virus spread worldwide and became a pandemic. Initial symptoms of the disease include fever, cough, loss of smell, taste, and shortness of breath, but a decrease in the oxygen levels in the body leads, and pneumonia may ultimately lead to the patient's death. However, the symptoms vary from patient to patient. To understand COVID-19 disease pathogenesis, researchers have tried to understand the cellular pathways that could be targeted to suppress viral replication. Thus, this article reviews the markers that could be targeted to inhibit viral replication by inhibiting the translational initiation complex/regulatory kinases and upregulating host autophagic flux that may lead to a reduction in the viral load. The article also highlights that mTOR inhibitors may act as potential inhibitors of viral replication. mTOR inhibitors such as metformin may inhibit the interaction of SARS-CoV-2 Nsp's and ORFs with mTORC1, LARP1, and 4E-BP. They may also increase autophagic flux by decreasing protein degradation via inhibition of Skp2, further promoting viral cell death. These events result in cell cycle arrest at G1 by p27, ultimately causing cell death.
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Affiliation(s)
- Tuba Khalid
- Department of Bioengineering, Faculty of Engineering, Integral University, Kursi Road, 226026, Lucknow, India
| | - Adria Hasan
- Department of Bioengineering, Faculty of Engineering, Integral University, Kursi Road, 226026, Lucknow, India
- Molecular Cell Biology Laboratory, Integral Information and Research Centre-4 (IIRC-4), Integral University, Kursi Road, 226026, Lucknow, India
| | - Jamal E Fatima
- Department of Bioengineering, Faculty of Engineering, Integral University, Kursi Road, 226026, Lucknow, India
| | - Soban Ahmad Faridi
- Department of Bioengineering, Faculty of Engineering, Integral University, Kursi Road, 226026, Lucknow, India
| | - Ahamad Faiz Khan
- Department of Bioengineering, Faculty of Engineering, Integral University, Kursi Road, 226026, Lucknow, India
| | - Snober S Mir
- Molecular Cell Biology Laboratory, Integral Information and Research Centre-4 (IIRC-4), Integral University, Kursi Road, 226026, Lucknow, India.
- Department of Biosciences, Faculty of Science, Integral University, Kursi Road, 226026, Lucknow, Uttar Pradesh, India.
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25
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Zhou S, Lv P, Li M, Chen Z, Xin H, Reilly S, Zhang X. SARS-CoV-2 E protein: Pathogenesis and potential therapeutic development. Biomed Pharmacother 2023; 159:114242. [PMID: 36652729 PMCID: PMC9832061 DOI: 10.1016/j.biopha.2023.114242] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating global pandemic, which has seriously affected human health worldwide. The discovery of therapeutic agents is extremely urgent, and the viral structural proteins are particularly important as potential drug targets. SARS-CoV-2 envelope (E) protein is one of the main structural proteins of the virus, which is involved in multiple processes of the virus life cycle and is directly related to pathogenesis process. In this review, we present the amino acid sequence of the E protein and compare it with other two human coronaviruses. We then explored the role of E protein in the viral life cycle and discussed the pathogenic mechanisms that E protein may be involved in. Next, we summarize the potential drugs against E protein discovered in the current studies. Finally, we described the possible effects of E protein mutation on virus and host. This established a knowledge system of E protein to date, aiming to provide theoretical insights for mitigating the current COVID-19 pandemic and potential future coronavirus outbreaks.
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Affiliation(s)
- Shilin Zhou
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
| | - Panpan Lv
- Clinical Laboratory, Minhang Hospital, Fudan University, Shanghai, China.
| | - Mingxue Li
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
| | - Zihui Chen
- School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Hong Xin
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
| | - Svetlana Reilly
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
| | - Xuemei Zhang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
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26
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Jiang Y, Xue M, Tang M, Zhang D, Yu Y, Zhou S. Adaptation of the infectious bronchitis virus H120 vaccine strain to Vero cell lines. Vet Microbiol 2023; 280:109709. [PMID: 36870205 DOI: 10.1016/j.vetmic.2023.109709] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 02/27/2023]
Abstract
Infectious bronchitis virus (IBV) has restricted cell and tissue tropism. IBVs, except the Beaudette strain, can infect and replicate in chicken embryos, primary chicken embryo kidneys, and primary chicken kidney cells, only. The limited viral cell tropism of IBV substantially hinders in vitro cell-based research on pathogenic mechanisms and vaccine development. Herein, the parental H120 vaccine strain was serially passaged for five generations in chicken embryos, 20 passages in CK cells and 80 passages in Vero cells. This passaging yielded a Vero cell-adapted strain designated HV80. To further understand viral evolution, serial assessments of infection, replication, and transmission in Vero cells were performed for the viruses obtained every tenth passage. The ability to form syncytia and the replication efficiency significantly after the 50th passage (strain HV50). HV80 also displayed tropism extension to DF-1, BHK-21, HEK-293 T, and HeLa cells. Whole genome sequencing of viruses from every tenth generation revealed a total of 19 amino acid point mutations in the viral genome by passage 80, nine of which occurred in the S gene. The second furin cleavage site appeared in viral evolution and may be associated with cell tropism extension of HV80.
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Affiliation(s)
- Yi Jiang
- Poultry Institute, Chinese Academy of Agricultural Sciences, 225125, China; Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, 225009, China
| | - Mei Xue
- Poultry Institute, Chinese Academy of Agricultural Sciences, 225125, China; College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Mengjun Tang
- Poultry Institute, Chinese Academy of Agricultural Sciences, 225125, China; College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Di Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, 225125, China; College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Yan Yu
- Poultry Institute, Chinese Academy of Agricultural Sciences, 225125, China; College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Sheng Zhou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China.
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27
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Harrison CM, Doster JM, Landwehr EH, Kumar NP, White EJ, Beachboard DC, Stobart CC. Evaluating the Virology and Evolution of Seasonal Human Coronaviruses Associated with the Common Cold in the COVID-19 Era. Microorganisms 2023; 11:microorganisms11020445. [PMID: 36838410 PMCID: PMC9961755 DOI: 10.3390/microorganisms11020445] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Approximately 15-30% of all cases of the common cold are due to human coronavirus infections. More recently, the emergence of the more severe respiratory coronaviruses, SARS-CoV and MERS-CoV, have highlighted the increased pathogenic potential of emergent coronaviruses. Lastly, the current emergence of SARS-CoV-2 has demonstrated not only the potential for significant disease caused by emerging coronaviruses, but also the capacity of novel coronaviruses to promote pandemic spread. Largely driven by the global response to the COVID-19 pandemic, significant research in coronavirus biology has led to advances in our understanding of these viruses. In this review, we evaluate the virology, emergence, and evolution of the four endemic coronaviruses associated with the common cold, their relationship to pandemic SARS-CoV-2, and discuss the potential for future emergent human coronaviruses.
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Affiliation(s)
- Cameron M. Harrison
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Jayden M. Doster
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Emily H. Landwehr
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Nidhi P. Kumar
- Department of Biology, DeSales University, Central Valley, PA 18034, USA
| | - Ethan J. White
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Dia C. Beachboard
- Department of Biology, DeSales University, Central Valley, PA 18034, USA
| | - Christopher C. Stobart
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
- Correspondence:
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28
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Abstract
Coronavirus disease (COVID-19) is an infectious airborne viral pneumonia caused by a novel virus belonging to the family coronaviridae. On February 11, 2019, the Internal Committee on Taxonomy of Virus (ICTV) announced the name of the novel virus as "severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). One of the proteins present on its membrane i.e. the Spike protein is responsible for the attachment of the virus to the host. It spreads through the salivary droplets released when an infected person sneezes or coughs. The best way to slow down the disease is by protecting self by washing hands and using the disinfectant. Most of the infected people experience mild to moderate breathing issues. Serious illness might develop in people with underlying cardiovascular problems, diabetes and other immuno-compromised diseases. To date, there is no effective medicine available in the market which is effective in COVID-19. However, healthcare professionals are using ritonavir, flavipiravir, lopinavir, hydroxychloroquine and remdesivir. Along with the medicines, some countries are using convalescent plasma and mesenchymal stem cells for treatment. Till date, it has claimed millions of death worldwide. In this detailed review, we have discussed the structure of SARS-CoV-2, essential proteins, its lifecycle, transmission, symptoms, pathology, clinical features, diagnosis, prevention, treatment and epidemiology of the disease.
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Affiliation(s)
- Heena Rehman
- Department of Biochemistry, Jamia Hamdard, New Delhi, India
| | - Md Iftekhar Ahmad
- Department of Pharmaceutics, Shri Gopichand College of Pharmacy, Baghpat, India
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29
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Chau BA, Chen V, Cochrane AW, Parent LJ, Mouland AJ. Liquid-liquid phase separation of nucleocapsid proteins during SARS-CoV-2 and HIV-1 replication. Cell Rep 2023; 42:111968. [PMID: 36640305 PMCID: PMC9790868 DOI: 10.1016/j.celrep.2022.111968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 10/27/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
The leap of retroviruses and coronaviruses from animal hosts to humans has led to two ongoing pandemics and tens of millions of deaths worldwide. Retrovirus and coronavirus nucleocapsid proteins have been studied extensively as potential drug targets due to their central roles in virus replication, among which is their capacity to bind their respective genomic RNAs for packaging into nascent virions. This review focuses on fundamental studies of these nucleocapsid proteins and how their intrinsic abilities to condense through liquid-liquid phase separation (LLPS) contribute to viral replication. Therapeutic targeting of these condensates and methodological advances are also described to address future questions on how phase separation contributes to viral replication.
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Affiliation(s)
- Bao-An Chau
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Venessa Chen
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Alan W Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Leslie J Parent
- Division of Infectious Diseases and Epidemiology, Departments of Medicine and Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada.
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30
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Wang F, Zhang Q, Zhang F, Zhang E, Li M, Ma S, Guo J, Yang Z, Zhu J. Adenovirus vector-mediated single chain variable fragments target the nucleocapsid protein of porcine epidemic diarrhea virus and protect against viral infection in piglets. Front Immunol 2023; 14:1058327. [PMID: 36761768 PMCID: PMC9902916 DOI: 10.3389/fimmu.2023.1058327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) mainly infects the intestinal epithelial cells of pigs, causing porcine epidemic diarrhea (PED). In particular, the virus causes severe diarrhea, dehydration, and death in neonatal piglets. Maternal immunity effectively protects neonatal piglets from PEDV infection; however, maternal antibodies can only prevent PEDV attachment and entry into target cells, but have no effects on intracellular viruses. Intracellular antibodies targeting virus-encoded proteins are effective in preventing viral infection. We previously identified four single chain variable fragments (scFvs), ZW1-16, ZW3-21, ZW1-41, and ZW4-16, which specifically targeted the PEDV N protein and significantly inhibited PEDV replication and up-regulated interferon-λ1 (IFN-λ1) expression in host cells. In our current study, the four scFvs were subcloned into replication-defective adenovirus vectors to generate recombinant adenoviruses rAdV-ZW1-16, rAdV-ZW3-21, rAdV-ZW1-41, and rAdV-ZW4-16. ScFvs were successfully expressed in Human Embryonic Kidney 293 (HEK293) cells and intestinal porcine epithelial cell line J2 (IPEC-J2) and were biosafe for piglets as indicated by body temperature and weight, scFv excretion in feces, IFN-γ and interleukin-4 (IL-4) expression in jejunum, and pathological changes in porcine tissue after oral administration. Western blotting, immunofluorescence, and immunohistochemical analyses showed that scFvs were expressed in porcine jejunum. The prophylactic effects of rAdV-ZW, a cocktail of the four rAdV-scFvs, on piglet diarrhea caused by PEDV was investigated. Clinical symptoms in piglets orally challenged with PEDV, following a two-time treatment with rAdV-ZW, were significantly reduced when compared with PEDV-infected piglets treated with phosphate buffered saline (PBS) or rAdV-wild-type. Also, no death and jejunal lesions were observed. ScFv co-localization with the PEDV N protein in vivo was also observed. Next, the expression of pro-inflammatory serum cytokines such as tumor necrosis factor-α (TNF-α), IL-6, IL-8, IL-12, and IFN-λ was assessed by enzyme-linked immunosorbent assay (ELISA), which showed that scFvs significantly suppressed PEDV-induced pro-inflammatory cytokine expression and restored PEDV-inhibited IFN-λ expression. Therefore, our study supported a promising role for intracellular scFvs targeting the PEDV N protein to prevent and treat diarrhea in PEDV-infected piglets.
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Affiliation(s)
- Fengqing Wang
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China,Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Zhang
- State Key Laboratory of Advanced Optical Communication Systems and Networks, Key Laboratory for Laser Plasmas (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Qing Zhang, ; Jianguo Zhu,
| | - Fanqing Zhang
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - En Zhang
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Mei Li
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shiwei Ma
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jianming Guo
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhibiao Yang
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jianguo Zhu
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Qing Zhang, ; Jianguo Zhu,
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Yun JS, Song H, Kim NH, Cha SY, Hwang KH, Lee JE, Jeong CH, Song SH, Kim S, Cho ES, Kim HS, Yook JI. Glycogen Synthase Kinase-3 Interaction Domain Enhances Phosphorylation of SARS-CoV-2 Nucleocapsid Protein. Mol Cells 2022; 45:911-922. [PMID: 36572560 PMCID: PMC9794558 DOI: 10.14348/molcells.2022.0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/16/2022] [Indexed: 12/28/2022] Open
Abstract
A structural protein of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), nucleocapsid (N) protein is phosphorylated by glycogen synthase kinase (GSK)-3 on the serine/arginine (SR) rich motif located in disordered regions. Although phosphorylation by GSK-3β constitutes a critical event for viral replication, the molecular mechanism underlying N phosphorylation is not well understood. In this study, we found the putative alpha-helix L/FxxxL/AxxRL motif known as the GSK-3 interacting domain (GID), found in many endogenous GSK-3β binding proteins, such as Axins, FRATs, WWOX, and GSKIP. Indeed, N interacts with GSK-3β similarly to Axin, and Leu to Glu substitution of the GID abolished the interaction, with loss of N phosphorylation. The N phosphorylation is also required for its structural loading in a virus-like particle (VLP). Compared to other coronaviruses, N of Sarbecovirus lineage including bat RaTG13 harbors a CDK1-primed phosphorylation site and Gly-rich linker for enhanced phosphorylation by GSK-3β. Furthermore, we found that the S202R mutant found in Delta and R203K/G204R mutant found in the Omicron variant allow increased abundance and hyper-phosphorylation of N. Our observations suggest that GID and mutations for increased phosphorylation in N may have contributed to the evolution of variants.
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Affiliation(s)
- Jun Seop Yun
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Hyeeun Song
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Nam Hee Kim
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - So Young Cha
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Kyu Ho Hwang
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Jae Eun Lee
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Cheol-Hee Jeong
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Sang Hyun Song
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Seonghun Kim
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Eunae Sandra Cho
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Hyun Sil Kim
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Jong In Yook
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
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Karamese M. All Microbiological Aspects of SARS-CoV-2 Virus. Eurasian J Med 2022; 54:106-114. [PMID: 36655453 PMCID: PMC11163349 DOI: 10.5152/eurasianjmed.2022.22315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/22/2022] [Indexed: 01/19/2023] Open
Abstract
The COVID-19 disease, caused by SARS-CoV-2 virus, which was first seen in Wuhan (China) on December 31, 2019, rapidly spread to cities, countries, and continents and was noted in history as the first pandemic caused by coronaviruses. According to the World Health Organization reports, more than 645 million confirmed SARS-CoV-2-positive cases and more than 6.5 million confirmed deaths were noted all over the world during the pandemic (between December 2020 and December 2022). Although SARS-CoV-2 is a virus belonging to the coronavirus family, our knowledge of the pathogenesis and immune response of SARS-CoV-2 is still limited. Approximately 10 years (2012) after the Middle East Respiratory Syndrome (MERS-CoV) (nearly 2200 confirmed cases and 791 confirmed deaths) and 20 years (2002-2004) after the SARS-CoV epidemic (29 different countries, nearly 8000 confirmed cases, and 774 confirmed deaths), the current COVID-19 pandemic is a reminder of how new pathogens can emerge and spread rapidly, eventually causing serious public health problems. Further research is needed to establish animal models for SARSCoV-2 to investigate replication, transmission dynamics, and pathogenesis in humans in order to develop effective antiviral treatments and vaccines.
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Affiliation(s)
- Murat Karamese
- Faculty of Medicine, Department of Medical Microbiology, Kafkas University, Kars, Turkey
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Zhang Y, Chen Y, Zhou J, Wang X, Ma L, Li J, Yang L, Yuan H, Pang D, Ouyang H. Porcine Epidemic Diarrhea Virus: An Updated Overview of Virus Epidemiology, Virulence Variation Patterns and Virus-Host Interactions. Viruses 2022; 14:2434. [PMID: 36366532 PMCID: PMC9695474 DOI: 10.3390/v14112434] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
The porcine epidemic diarrhea virus (PEDV) is a member of the coronavirus family, causing deadly watery diarrhea in newborn piglets. The global pandemic of PEDV, with significant morbidity and mortality, poses a huge threat to the swine industry. The currently developed vaccines and drugs are only effective against the classic GI strains that were prevalent before 2010, while there is no effective control against the GII variant strains that are currently a global pandemic. In this review, we summarize the latest progress in the biology of PEDV, including its transmission and origin, structure and function, evolution, and virus-host interaction, in an attempt to find the potential virulence factors influencing PEDV pathogenesis. We conclude with the mechanism by which PEDV components antagonize the immune responses of the virus, and the role of host factors in virus infection. Essentially, this review serves as a valuable reference for the development of attenuated virus vaccines and the potential of host factors as antiviral targets for the prevention and control of PEDV infection.
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Affiliation(s)
- Yuanzhu Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Yiwu Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Jian Zhou
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Xi Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Lerong Ma
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Jianing Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Lin Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Hongming Yuan
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
- Chongqing Research Institute, Jilin University, Chongqing 401120, China
| | - Daxin Pang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
- Chongqing Research Institute, Jilin University, Chongqing 401120, China
- Chongqing Jitang Biotechnology Research Institute Co., Ltd., Chongqing 401120, China
| | - Hongsheng Ouyang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
- Chongqing Research Institute, Jilin University, Chongqing 401120, China
- Chongqing Jitang Biotechnology Research Institute Co., Ltd., Chongqing 401120, China
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Tulimilli SV, Dallavalasa S, Basavaraju CG, Kumar Rao V, Chikkahonnaiah P, Madhunapantula SV, Veeranna RP. Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Vaccine Effectiveness. Vaccines (Basel) 2022; 10:1751. [PMID: 36298616 PMCID: PMC9607623 DOI: 10.3390/vaccines10101751] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
The incidence and death toll due to SARS-CoV-2 infection varied time-to-time; and depended on several factors, including severity (viral load), immune status, age, gender, vaccination status, and presence of comorbidities. The RNA genome of SARS-CoV-2 has mutated and produced several variants, which were classified by the SARS-CoV-2 Interagency Group (SIG) into four major categories. The first category; “Variant Being Monitored (VBM)”, consists of Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), Epsilon (B.1.427, B.1.429), Eta (B.1.525), Iota (B.1.526), Kappa (B.1.617.1), Mu (B.1.621), and Zeta (P.2); the second category; “Variants of Concern” consists of Omicron (B.1.1.529). The third and fourth categories include “Variants of Interest (VOI)”, and “Variants of High Consequence (VOHC)”, respectively, and contain no variants classified currently under these categories. The surge in VBM and VOC poses a significant threat to public health globally as they exhibit altered virulence, transmissibility, diagnostic or therapeutic escape, and the ability to evade the host immune response. Studies have shown that certain mutations increase the infectivity and pathogenicity of the virus as demonstrated in the case of SARS-CoV-2, the Omicron variant. It is reported that the Omicron variant has >60 mutations with at least 30 mutations in the Spike protein (“S” protein) and 15 mutations in the receptor-binding domain (RBD), resulting in rapid attachment to target cells and immune evasion. The spread of VBM and VOCs has affected the actual protective efficacy of the first-generation vaccines (ChAdOx1, Ad26.COV2.S, NVX-CoV2373, BNT162b2). Currently, the data on the effectiveness of existing vaccines against newer variants of SARS-CoV-2 are very scanty; hence additional studies are immediately warranted. To this end, recent studies have initiated investigations to elucidate the structural features of crucial proteins of SARS-CoV-2 variants and their involvement in pathogenesis. In addition, intense research is in progress to develop better preventive and therapeutic strategies to halt the spread of COVID-19 caused by variants. This review summarizes the structure and life cycle of SARS-CoV-2, provides background information on several variants of SARS-CoV-2 and mutations associated with these variants, and reviews recent studies on the safety and efficacy of major vaccines/vaccine candidates approved against SARS-CoV-2, and its variants.
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Affiliation(s)
- SubbaRao V. Tulimilli
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR) Laboratory (DST-FIST Supported Center), Department of Biochemistry (DST-FIST Supported Department), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru 570004, Karnataka, India
| | - Siva Dallavalasa
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR) Laboratory (DST-FIST Supported Center), Department of Biochemistry (DST-FIST Supported Department), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru 570004, Karnataka, India
| | - Chaithanya G. Basavaraju
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR) Laboratory (DST-FIST Supported Center), Department of Biochemistry (DST-FIST Supported Department), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru 570004, Karnataka, India
| | - Vinay Kumar Rao
- Department of Medical Genetics, JSS Medical College & Hospital, JSS Academy of Higher Education & Research (JSS AHER), Mysore 570015, Karnataka, India
| | - Prashanth Chikkahonnaiah
- Department of Pulmonary Medicine, Mysore Medical College and Research Institute, Mysuru 570001, Karnataka, India
| | - SubbaRao V. Madhunapantula
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR) Laboratory (DST-FIST Supported Center), Department of Biochemistry (DST-FIST Supported Department), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru 570004, Karnataka, India
- Special Interest Group in Cancer Biology and Cancer Stem Cells (SIG-CBCSC), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru 570004, Karnataka, India
| | - Ravindra P. Veeranna
- Department of Biochemistry, Council of Scientific and Industrial Research (CSIR)-Central Food Technological Research Institute (CFTRI), Mysuru 570020, Karnataka, India
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Panati K, Timmana LV, Reddy AT V, Reddy Saddala R, Ramireddy Narala V. Virology and Molecular Pathogenesis of Coronavirus Disease 2019: An Update. Eurasian J Med 2022; 54:299-304. [PMID: 35971283 PMCID: PMC9797742 DOI: 10.5152/eurasianjmed.2022.21133] [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: 04/02/2021] [Accepted: 07/06/2021] [Indexed: 01/08/2023] Open
Abstract
The pandemic coronavirus disease 2019 outbreak's causative agent was identified as severe acute respiratory syndrome coronavirus 2. It is a positive-sense single-stranded RNA virus with a ~30 kb size genome that belongs to the Nidovirales. Molecular analysis revealed that severe acute respiratory syndrome coronavirus 2 is a variant of severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus with some sequence similarity. The confirmed cases and death toll are high in severe acute respiratory syndrome coronavirus 2 compared to severe acute respiratory syndrome coronavirus and the estimated R0 is >1. The data on pathological findings on severe acute respiratory syndrome coronavirus 2 are scarce and present treatment management is based on symptoms that are similar to severe acute respiratory syndrome coronavirus. In this review, we have discussed the transmission, viral replication, and cytokine storm and highlighted the recent pathological findings of coronavirus disease 2019. The reported severe acute respiratory syndrome coronavirus 2 pathological findings were similar to that of severe acute respiratory syndrome coronavirus. Though these findings help notify the clinical course of the disease, it warrants further in vivo and ex vivo studies with larger samples obtained from the coronavirus disease 2019 patients.
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Affiliation(s)
- Kalpana Panati
- Department of Biotechnology, Government College for Men, Kadapa, A.P, India
| | - Lokesh V Timmana
- Department of Zoology, Yogi Vemana University, Kadapa, A.P, India
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Lachén-Montes M, Mendizuri N, Ausín K, Echaide M, Blanco E, Chocarro L, de Toro M, Escors D, Fernández-Irigoyen J, Kochan G, Santamaría E. Metabolic dyshomeostasis induced by SARS-CoV-2 structural proteins reveals immunological insights into viral olfactory interactions. Front Immunol 2022; 13:866564. [PMID: 36159830 PMCID: PMC9492993 DOI: 10.3389/fimmu.2022.866564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
One of the most common symptoms in COVID-19 is a sudden loss of smell. SARS-CoV-2 has been detected in the olfactory bulb (OB) from animal models and sporadically in COVID-19 patients. To decipher the specific role over the SARS-CoV-2 proteome at olfactory level, we characterized the in-depth molecular imbalance induced by the expression of GFP-tagged SARS-CoV-2 structural proteins (M, N, E, S) on mouse OB cells. Transcriptomic and proteomic trajectories uncovered a widespread metabolic remodeling commonly converging in extracellular matrix organization, lipid metabolism and signaling by receptor tyrosine kinases. The molecular singularities and specific interactome expression modules were also characterized for each viral structural factor. The intracellular molecular imbalance induced by each SARS-CoV-2 structural protein was accompanied by differential activation dynamics in survival and immunological routes in parallel with a differentiated secretion profile of chemokines in OB cells. Machine learning through a proteotranscriptomic data integration uncovered TGF-beta signaling as a confluent activation node by the SARS-CoV-2 structural proteome. Taken together, these data provide important avenues for understanding the multifunctional immunomodulatory properties of SARS-CoV-2 M, N, S and E proteins beyond their intrinsic role in virion formation, deciphering mechanistic clues to the olfactory inflammation observed in COVID-19 patients.
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Affiliation(s)
- Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
- IdiSNA. Navarra Institute for Health Research, Pamplona, Spain
| | - Naroa Mendizuri
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
- IdiSNA. Navarra Institute for Health Research, Pamplona, Spain
| | - Karina Ausín
- IdiSNA. Navarra Institute for Health Research, Pamplona, Spain
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Miriam Echaide
- IdiSNA. Navarra Institute for Health Research, Pamplona, Spain
- Oncoimmunology Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Ester Blanco
- IdiSNA. Navarra Institute for Health Research, Pamplona, Spain
- Oncoimmunology Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Luisa Chocarro
- IdiSNA. Navarra Institute for Health Research, Pamplona, Spain
- Oncoimmunology Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - María de Toro
- Genomics and Bioinformatics Platform, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain
| | - David Escors
- IdiSNA. Navarra Institute for Health Research, Pamplona, Spain
- Oncoimmunology Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- IdiSNA. Navarra Institute for Health Research, Pamplona, Spain
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Grazyna Kochan
- IdiSNA. Navarra Institute for Health Research, Pamplona, Spain
- Oncoimmunology Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
- IdiSNA. Navarra Institute for Health Research, Pamplona, Spain
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Stefano GB, Kream RM. Viruses Broaden the Definition of Life by Genomic Incorporation of Artificial Intelligence and Machine Learning Processes. Curr Neuropharmacol 2022; 20:1888-1893. [PMID: 35450524 PMCID: PMC9886803 DOI: 10.2174/1570159x20666220420121746] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 11/22/2022] Open
Abstract
Viruses have been classified as non-living because they require a cellular host to support their replicative processes. Empirical investigations have significantly advanced our understanding of the many strategies employed by viruses to usurp and divert host regulatory and metabolic processes to drive the synthesis and release of infectious particles. The recent emergence of SARS-CoV-2 has permitted us to evaluate and discuss a potentially novel classification of viruses as living entities. The ability of SARS CoV-2 to engender comprehensive regulatory control of integrative cellular processes is strongly suggestive of an inherently dynamic informational registry that is programmatically encoded by linear ssRNA sequences responding to distinct evolutionary constraints. Responses to positive evolutionary constraints have resulted in a single-stranded RNA viral genome that occupies a threedimensional space defined by conserved base-paring resulting from a complex pattern of both secondary and tertiary structures. Additionally, regulatory control of virus-mediated infectious processes relies on extensive protein-protein interactions that drive conformational matching and shape recognition events to provide a functional link between complementary viral and host nucleic acid and protein domains. We also recognize that the seamless integration of complex replicative processes is highly dependent on the precise temporal matching of complementary nucleotide sequences and their corresponding structural and non-structural viral proteins. Interestingly, the deployment of concerted transcriptional and translational activities within targeted cellular domains may be modeled by artificial intelligence (AI) strategies that are inherently fluid, self-correcting, and adaptive at accommodating temporal changes in host defense mechanisms. An in-depth understanding of multiple self-correcting AIassociated viral processes will most certainly lead to novel therapeutic development platforms, notably the design of efficacious neuropharmacological agents to treat chronic CNS syndromes associated with long-COVID. In summary, it appears that viruses, notably SARS-CoV-2, are very much alive due to acquired genetic advantages that are intimately entrained to existential host processes via evolutionarily constrained AI-associated learning paradigms.
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Affiliation(s)
- George B. Stefano
- Center for Cognitive and Molecular Neuroscience, First Faculty of Medicine, Charles University, Prague, Czech Republic,Address correspondence to this author at the Center for Cognitive and Molecular Neuroscience, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic; Tel: 001 443 540 4545; E-mail:
| | - Richard M. Kream
- Center for Cognitive and Molecular Neuroscience, First Faculty of Medicine, Charles University, Prague, Czech Republic
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Vaccines platforms and COVID-19: what you need to know. Trop Dis Travel Med Vaccines 2022; 8:20. [PMID: 35965345 PMCID: PMC9537331 DOI: 10.1186/s40794-022-00176-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 06/22/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The novel SARS-CoV-2, responsible for the COVID-19 pandemic, is the third zoonotic coronavirus since the beginning of the 21 first century, and it has taken more than 6 million human lives because of the lack of immunity causing global economic losses. Consequently, developing a vaccine against the virus represents the fastest way to finish the threat and regain some "normality." OBJECTIVE Here, we provide information about the main features of the most important vaccine platforms, some of them already approved, to clear common doubts fostered by widespread misinformation and to reassure the public of the safety of the vaccination process and the different alternatives presented. METHODS Articles published in open access databases until January 2022 were identified using the search terms "SARS-CoV-2," "COVID-19," "Coronavirus," "COVID-19 Vaccines," "Pandemic," COVID-19, and LMICs or their combinations. DISCUSSION Traditional first-generation vaccine platforms, such as whole virus vaccines (live attenuated and inactivated virus vaccines), as well as second-generation vaccines, like protein-based vaccines (subunit and viral vector vaccines), and third-generation vaccines, such as nanoparticle and genetic vaccines (mRNA vaccines), are described. CONCLUSIONS SARS-CoV-2 sequence information obtained in a record time provided the basis for the fast development of a COVID-19 vaccine. The adaptability characteristic of the new generation of vaccines is changing our capability to react to emerging threats to future pandemics. Nevertheless, the slow and unfair distribution of vaccines to low- and middle-income countries and the spread of misinformation are a menace to global health since the unvaccinated will increase the chances for resurgences and the surge of new variants that can escape the current vaccines.
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Pereira E, Felipe S, de Freitas R, Araújo V, Soares P, Ribeiro J, Henrique Dos Santos L, Alves JO, Canabrava N, van Tilburg M, Guedes MI, Ceccatto V. ABO blood group and link to COVID-19: A comprehensive review of the reported associations and their possible underlying mechanisms. Microb Pathog 2022; 169:105658. [PMID: 35764188 PMCID: PMC9233352 DOI: 10.1016/j.micpath.2022.105658] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 11/20/2022]
Abstract
ABO blood group is long known to be an influencing factor for the susceptibility to infectious diseases, and many studies have been describing associations between ABO blood types and COVID-19 infection and severity, with conflicting findings. This narrative review aims to summarize the literature regarding associations between the ABO blood group and COVID-19. Blood type O is mostly associated with lower rates of SARS-CoV-2 infection, while blood type A is frequently described as a risk factor. Although results regarding the risk of severe outcomes are more variable, blood type A is the most associated with COVID-19 severity and mortality, while many studies describe O blood type as a protective factor for the disease progression. Furthermore, genetic associations with both the risk of infection and disease severity have been reported for the ABO locus. Some underlying mechanisms have been hypothesized to explain the reported associations, with incipient experimental data. Three major hypotheses emerge: SARS-CoV-2 could carry ABO(H)-like structures in its envelope glycoproteins and would be asymmetrically transmitted due to a protective effect of the ABO antibodies, ABH antigens could facilitate SARS-CoV-2 interaction with the host' cells, and the association of non-O blood types with higher risks of thromboembolic events could confer COVID-19 patients with blood type O a lower risk of severe outcomes. The hypothesized mechanisms would affect distinct aspects of the COVID-19 natural history, with distinct potential implications to the disease transmission and its management.
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Affiliation(s)
- Eric Pereira
- Superior Institute of Biomedical Sciences, State University of Ceará, Dr. Silas Munguba Av., Fortaleza, 60714-903, Ceará, Brazil
| | - Stela Felipe
- Superior Institute of Biomedical Sciences, State University of Ceará, Dr. Silas Munguba Av., Fortaleza, 60714-903, Ceará, Brazil
| | - Raquel de Freitas
- Superior Institute of Biomedical Sciences, State University of Ceará, Dr. Silas Munguba Av., Fortaleza, 60714-903, Ceará, Brazil
| | - Valdevane Araújo
- Superior Institute of Biomedical Sciences, State University of Ceará, Dr. Silas Munguba Av., Fortaleza, 60714-903, Ceará, Brazil
| | - Paula Soares
- Superior Institute of Biomedical Sciences, State University of Ceará, Dr. Silas Munguba Av., Fortaleza, 60714-903, Ceará, Brazil
| | - Jannison Ribeiro
- Hematology and Hemotherapy Center of Ceará, José Bastos Av., Fortaleza, 60431-086, Ceará, Brazil
| | - Luiz Henrique Dos Santos
- Superior Institute of Biomedical Sciences, State University of Ceará, Dr. Silas Munguba Av., Fortaleza, 60714-903, Ceará, Brazil
| | - Juliana Osório Alves
- Superior Institute of Biomedical Sciences, State University of Ceará, Dr. Silas Munguba Av., Fortaleza, 60714-903, Ceará, Brazil
| | - Natália Canabrava
- Biotechnology and Molecular Biology Laboratory, State University of Ceará, Dr. Silas Munguba Av., Fortaleza, 60714-903, Ceará, Brazil
| | - Mauricio van Tilburg
- Biotechnology and Molecular Biology Laboratory, State University of Ceará, Dr. Silas Munguba Av., Fortaleza, 60714-903, Ceará, Brazil
| | - Maria Izabel Guedes
- Biotechnology and Molecular Biology Laboratory, State University of Ceará, Dr. Silas Munguba Av., Fortaleza, 60714-903, Ceará, Brazil
| | - Vânia Ceccatto
- Superior Institute of Biomedical Sciences, State University of Ceará, Dr. Silas Munguba Av., Fortaleza, 60714-903, Ceará, Brazil.
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Pepe A, Pietropaoli S, Vos M, Barba-Spaeth G, Zurzolo C. Tunneling nanotubes provide a route for SARS-CoV-2 spreading. SCIENCE ADVANCES 2022; 8:eabo0171. [PMID: 35857849 PMCID: PMC9299553 DOI: 10.1126/sciadv.abo0171] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/08/2022] [Indexed: 05/10/2023]
Abstract
Neurological manifestations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection represent a major issue in long coronavirus disease. How SARS-CoV-2 gains access to the brain and how infection leads to neurological symptoms are not clear because the principal means of viral entry by endocytosis, the angiotensin-converting enzyme 2 receptor, are barely detectable in the brain. We report that human neuronal cells, nonpermissive to infection through the endocytic pathway, can be infected when cocultured with permissive infected epithelial cells. SARS-CoV-2 induces the formation of tunneling nanotubes (TNTs) and exploits this route to spread to uninfected cells. In cellulo correlative fluorescence and cryo-electron tomography reveal that SARS-CoV-2 is associated with TNTs between permissive cells. Furthermore, multiple vesicular structures such as double-membrane vesicles, sites of viral replication, are observed inside TNTs between permissive and nonpermissive cells. Our data highlight a previously unknown mechanism of SARS-CoV-2 spreading, likely used as a route to invade nonpermissive cells and potentiate infection in permissive cells.
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Affiliation(s)
- Anna Pepe
- Unité de Trafic Membranaire et Pathogénèse, Département de Biologie Cellulaire et Infection, Institut Pasteur, CNRS UMR3691, Université Paris Cité, 75015 Paris, France
| | - Stefano Pietropaoli
- Unité de Virologie Structurale, CNRS UMR 3569 Département de Virologie, Institut Pasteur 28 rue du Docteur Roux, Université Paris Cité, 75015 Paris, France
- Catalent Pharma Solutions, Strada Provinciale 12 Casilina, 41, 03012 Anagni, Frosinone, Italy
| | - Matthijn Vos
- Plateforme Technologique Nanoimagerie Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
| | - Giovanna Barba-Spaeth
- Unité de Virologie Structurale, CNRS UMR 3569 Département de Virologie, Institut Pasteur 28 rue du Docteur Roux, Université Paris Cité, 75015 Paris, France
| | - Chiara Zurzolo
- Unité de Trafic Membranaire et Pathogénèse, Département de Biologie Cellulaire et Infection, Institut Pasteur, CNRS UMR3691, Université Paris Cité, 75015 Paris, France
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Otieno JR, Cherry JL, Spiro DJ, Nelson MI, Trovão NS. Origins and Evolution of Seasonal Human Coronaviruses. Viruses 2022; 14:1551. [PMID: 35891531 PMCID: PMC9320361 DOI: 10.3390/v14071551] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Four seasonal human coronaviruses (sHCoVs) are endemic globally (229E, NL63, OC43, and HKU1), accounting for 5-30% of human respiratory infections. However, the epidemiology and evolution of these CoVs remain understudied due to their association with mild symptomatology. Using a multigene and complete genome analysis approach, we find the evolutionary histories of sHCoVs to be highly complex, owing to frequent recombination of CoVs including within and between sHCoVs, and uncertain, due to the under sampling of non-human viruses. The recombination rate was highest for 229E and OC43 whereas substitutions per recombination event were highest in NL63 and HKU1. Depending on the gene studied, OC43 may have ungulate, canine, or rabbit CoV ancestors. 229E may have origins in a bat, camel, or an unsampled intermediate host. HKU1 had the earliest common ancestor (1809-1899) but fell into two distinct clades (genotypes A and B), possibly representing two independent transmission events from murine-origin CoVs that appear to be a single introduction due to large gaps in the sampling of CoVs in animals. In fact, genotype B was genetically more diverse than all the other sHCoVs. Finally, we found shared amino acid substitutions in multiple proteins along the non-human to sHCoV host-jump branches. The complex evolution of CoVs and their frequent host switches could benefit from continued surveillance of CoVs across non-human hosts.
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Affiliation(s)
- James R. Otieno
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Joshua L. Cherry
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - David J. Spiro
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Martha I. Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
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Sharma A, Virmani T, Pathak V, Sharma A, Pathak K, Kumar G, Pathak D. Artificial Intelligence-Based Data-Driven Strategy to Accelerate Research, Development, and Clinical Trials of COVID Vaccine. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7205241. [PMID: 35845955 PMCID: PMC9279074 DOI: 10.1155/2022/7205241] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/15/2022] [Indexed: 12/12/2022]
Abstract
The global COVID-19 (coronavirus disease 2019) pandemic, which was caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in a significant loss of human life around the world. The SARS-CoV-2 has caused significant problems to medical systems and healthcare facilities due to its unexpected global expansion. Despite all of the efforts, developing effective treatments, diagnostic techniques, and vaccinations for this unique virus is a top priority and takes a long time. However, the foremost step in vaccine development is to identify possible antigens for a vaccine. The traditional method was time taking, but after the breakthrough technology of reverse vaccinology (RV) was introduced in 2000, it drastically lowers the time needed to detect antigens ranging from 5-15 years to 1-2 years. The different RV tools work based on machine learning (ML) and artificial intelligence (AI). Models based on AI and ML have shown promising solutions in accelerating the discovery and optimization of new antivirals or effective vaccine candidates. In the present scenario, AI has been extensively used for drug and vaccine research against SARS-COV-2 therapy discovery. This is more useful for the identification of potential existing drugs with inhibitory human coronavirus by using different datasets. The AI tools and computational approaches have led to speedy research and the development of a vaccine to fight against the coronavirus. Therefore, this paper suggests the role of artificial intelligence in the field of clinical trials of vaccines and clinical practices using different tools.
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Affiliation(s)
- Ashwani Sharma
- School of Pharmaceutical Sciences, MVN University, Haryana 121102, India
| | - Tarun Virmani
- School of Pharmaceutical Sciences, MVN University, Haryana 121102, India
| | - Vipluv Pathak
- GL Bajaj Institute of Technology and Management, Greater Noida, Uttar Pradesh, India
| | | | - Kamla Pathak
- Uttar Pradesh University of Medical Sciences, Etawah, Uttar Pradesh 206001, India
| | - Girish Kumar
- School of Pharmaceutical Sciences, MVN University, Haryana 121102, India
| | - Devender Pathak
- Rajiv Academy for Pharmacy, NH. #2, Mathura Delhi Road P.O, Chhatikara, Mathura, Uttar Pradesh 281001, India
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Rath SL, Tripathy M, Mandal N. How Does Temperature Affect the Dynamics of SARS-CoV-2 M Proteins? Insights from Molecular Dynamics Simulations. J Membr Biol 2022; 255:341-356. [PMID: 35552785 PMCID: PMC9101995 DOI: 10.1007/s00232-022-00244-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/07/2022] [Indexed: 11/30/2022]
Abstract
Enveloped viruses, in general, have several transmembrane proteins and glycoproteins, which assist the virus in entry and attachment onto the host cells. These proteins also play a significant role in determining the shape and size of the newly formed virus particles. The lipid membrane and the embedded proteins affect each other in non-trivial ways during the course of the viral life cycle. Unraveling the nature of the protein-protein and protein-lipid interactions, under various environmental and physiological conditions, could therefore prove to be crucial in development of therapeutics. Here, we study the M protein of SARS-CoV-2 to understand the effect of temperature on the properties of the protein-membrane system. The membrane-embedded dimeric M proteins were studied using atomistic and coarse-grained molecular dynamics simulations at temperatures ranging between 10 and 50 °C. While temperature-induced fluctuations are expected to be monotonic, we observe a steady rise in the protein dynamics up to 40 °C, beyond which it surprisingly reverts back to the low-temperature behavior. Detailed investigation reveals disordering of the membrane lipids in the presence of the protein, which induces additional curvature around the transmembrane region. Coarse-grained simulations indicate temperature-dependent aggregation of M protein dimers. Our study clearly indicates that the dynamics of membrane lipids and integral M protein of SARS-CoV-2 enables it to better associate and aggregate only at a certain temperature range (i.e., ~ 30-40 °C). This can have important implications in the protein aggregation and subsequent viral budding/fission processes.
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Affiliation(s)
- Soumya Lipsa Rath
- Department of Biotechnology, National Institute of Technology Warangal (NITW), Telangana, 506004, India.
| | - Madhusmita Tripathy
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287, Darmstadt, Germany.
| | - Nabanita Mandal
- Department of Biotechnology, National Institute of Technology Warangal (NITW), Telangana, 506004, India
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Ribeiro-Filho HV, Jara GE, Batista FAH, Schleder GR, Costa Tonoli CC, Soprano AS, Guimarães SL, Borges AC, Cassago A, Bajgelman MC, Marques RE, Trivella DBB, Franchini KG, Figueira ACM, Benedetti CE, Lopes-de-Oliveira PS. Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding. PLoS Comput Biol 2022; 18:e1010121. [PMID: 35551296 PMCID: PMC9129039 DOI: 10.1371/journal.pcbi.1010121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/24/2022] [Accepted: 04/19/2022] [Indexed: 12/23/2022] Open
Abstract
The nucleocapsid (N) protein of the SARS-CoV-2 virus, the causal agent of COVID-19, is a multifunction phosphoprotein that plays critical roles in the virus life cycle, including transcription and packaging of the viral RNA. To play such diverse roles, the N protein has two globular RNA-binding modules, the N- (NTD) and C-terminal (CTD) domains, which are connected by an intrinsically disordered region. Despite the wealth of structural data available for the isolated NTD and CTD, how these domains are arranged in the full-length protein and how the oligomerization of N influences its RNA-binding activity remains largely unclear. Herein, using experimental data from electron microscopy and biochemical/biophysical techniques combined with molecular modeling and molecular dynamics simulations, we show that, in the absence of RNA, the N protein formed structurally dynamic dimers, with the NTD and CTD arranged in extended conformations. However, in the presence of RNA, the N protein assumed a more compact conformation where the NTD and CTD are packed together. We also provided an octameric model for the full-length N bound to RNA that is consistent with electron microscopy images of the N protein in the presence of RNA. Together, our results shed new light on the dynamics and higher-order oligomeric structure of this versatile protein. The nucleocapsid (N) protein of the SARS-CoV-2 virus plays an essential role in virus particle assembly as it specifically binds to and wraps the virus genomic RNA into a well-organized structure known as the ribonucleoprotein. Understanding how the N protein wraps around the virus RNA is critical for the development of strategies to inhibit virus assembly within host cells. One of the limitations regarding the molecular structure of the ribonucleoprotein, however, is that the N protein has several unstructured and mobile regions that preclude the resolution of its full atomic structure. Moreover, the N protein can form higher-order oligomers, both in the presence and absence of RNA. Here we employed computational methods, supported by experimental data, to simulate the N protein structural dynamics in the absence and presence of RNA. Our data suggest that the N protein forms structurally dynamic dimers in the absence of RNA, with its structured N- and C-terminal domains oriented in extended conformations. In the presence of RNA, however, the N protein assumes a more compact conformation. Our model for the oligomeric structure of the N protein bound to RNA helps to understand how N protein dimers interact to each other to form the ribonucleoprotein.
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Affiliation(s)
- Helder Veras Ribeiro-Filho
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Gabriel Ernesto Jara
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | | | - Gabriel Ravanhani Schleder
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Celisa Caldana Costa Tonoli
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Adriana Santos Soprano
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Samuel Leite Guimarães
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Antonio Carlos Borges
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Alexandre Cassago
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Marcio Chaim Bajgelman
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | | | - Kleber Gomes Franchini
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | | | - Celso Eduardo Benedetti
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- * E-mail: (CEB); (PSLO)
| | - Paulo Sergio Lopes-de-Oliveira
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- * E-mail: (CEB); (PSLO)
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SARS-CoV-2 Antinucleocapsid Antibody Response of mRNA and Inactivated Virus Vaccines Compared to Unvaccinated Individuals. Vaccines (Basel) 2022; 10:vaccines10050643. [PMID: 35632399 PMCID: PMC9143597 DOI: 10.3390/vaccines10050643] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/07/2022] [Accepted: 04/14/2022] [Indexed: 11/29/2022] Open
Abstract
Comparative studies of SARS-CoV-2 antinucleocapsid (anti-N) antibody response in the context of inactivated virus vaccines versus natural infection are limited. This study aims to determine and compare the anti-N antibody levels in people vaccinated with Sinopharm’s (Wuhan, China) inactivated virus vaccine in comparison with naturally infected unvaccinated and Pfizer’s spike (S) mRNA-based vaccinated subjects. Two hundred ninety-nine Jordanian adults participated in the study including unvaccinated COVID-19-infected patients (n = 99), Pfizer-vaccinated (n = 100), and Sinopharm-vaccinated recipients (n = 100). Serum samples were assayed for anti-N IgG, anti-N IgM, and anti-S IgG. Sera of 64.6% of naturally infected unvaccinated participants had positive anti-S IgG (median = 36.35 U/mL; range: 0.04−532.5 U/mL) compared to 88% of Pfizer-vaccinated (Manhattan, NY, USA) (median = 26.52 U/mL; range: 0.39−1265 U/mL) and 58% of Sinopharm-vaccinated subjects (median = 14.35 U/mL; range: 0.39−870.17 U/mL). Samples of 60.6% of naturally infected unvaccinated people had positive anti-N IgG (median = 15.03 U/mL; range: 0−265.1 U/mL) compared to 25% of Pfizer-vaccinated (median = 0.02 U/mL; range: 0−68 U/mL) and 48% of Sinopharm-vaccinated subjects (median = 0.8 U/mL; range: 0−146.3 U/mL). Anti-N titers among the three groups were significantly different (p < 0.05). Anti-N IgM antibodies appeared in 23.2% of the naturally infected unvaccinated group (median = 0.29 U/mL; range: 0−15 U/mL) compared to only 9.0% of Pfizer-vaccinated (median = 018 U/mL; range: 0−33 U/mL) and 7.0% of Sinopharm-vaccinated subjects (median = 0.2 U/mL; range: 0−12.02 U/mL). A significant negative correlation was found between anti-S and age for both vaccines and between anti-S and the presence of chronic disease in Sinopharm-vaccinated subjects. A significant positive correlation between anti-N and anti-S titers was found among the three groups. This study shows that the inactivated virus vaccine, Sinopharm, induces an anti-N response that can boost that of natural infection or vice versa. On the other hand, the Pfizer mRNA-based vaccine induces a significantly stronger anti-S Ab response.
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Kim J, Kim M, Kim D, Park S, Kang M, Baek K, Choi JK, Maharjan S, Akauliya M, Lee Y, Kwon HJ. Targeting the Interaction Between Spike Protein and Nucleocapsid Protein for Suppression and Detection of Human Coronavirus OC43. Front Immunol 2022; 13:835333. [PMID: 35359936 PMCID: PMC8960273 DOI: 10.3389/fimmu.2022.835333] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/18/2022] [Indexed: 01/09/2023] Open
Abstract
Human coronavirus OC43 (HCoV-OC43) is the coronavirus most associated with "common colds", infections of the upper respiratory tract. Previously, we reported that direct interactions of nucleocapsid (N) protein and C-terminal domain of Spike protein (Spike CD) are essential for replication of SARS-CoV-2 and MERS-CoV. Thus, we developed a novel ELISA-based strategy targeting these specific interactions to detect SARS-CoV-2 and MERS-CoV. Here, we investigated whether the same principles apply to HCoV-OC43. We discovered that the S protein of HCoV-OC43 interacts with N protein and that cell penetrating Spike CD peptide inhibits virus protein expression and replication of HCoV-OC43. The interaction between HCoV-OC43 S and N proteins were recapitulated with a recombinant HCoV-OC43 Spike CD fusion protein and a recombinant HCoV-OC43 N fusion protein in vitro. By producing an anti-HCoV-OC43 N protein-specific monoclonal antibody, we established a virus detection system based on the interaction between recombinant Spike CD and N protein of HCoV-OC43. We suggest that the interaction between Spike CD and N protein is conserved in coronaviruses and therefore could be a target for therapeutics against both novel coronavirus and its variants.
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Affiliation(s)
- Jinsoo Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Minyoung Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Dongbum Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Sangkyu Park
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, South Korea
| | - Mijeong Kang
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Kyeongbin Baek
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Jun-Kyu Choi
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, South Korea
| | - Sony Maharjan
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Madhav Akauliya
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Younghee Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, South Korea
| | - Hyung-Joo Kwon
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, South Korea
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, South Korea
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Hassanein SS, Sharaby MR, Tawfik NM, Rashed SA, Adel M, Fayez A, Mansour H, Amer HM. Latest Insights on the Diagnostic Approaches and Treatment Strategies of COVID-19. Intervirology 2022; 65:167-180. [PMID: 35249006 PMCID: PMC9148896 DOI: 10.1159/000522336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 01/25/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND COVID-19 has emerged as the most serious pandemic in the 21st century to date. COVID-19 patients may develop various disease symptoms that hinder the accurate clinical diagnosis. SUMMARY Routine diagnosis of COVID-19 requires complementary investigations, including computed tomography, immunological assays, and molecular assays like real-time RT-PCR, loop-mediated isothermal amplification, metagenomic next-generation sequencing, and clusters of regularly interspaced short palindromic repeats-based assays. Clinically approved antiviral drugs available for the COVID-19 treatment are very limited. The most common measurements that enhance health condition and patients' viability are conservation fluid management, oxygen therapy, and antibiotics. Several therapeutic options have been developed or repurposed to prevent virus replication and/or modulate the immune response against virus infection. These options include various drugs that affect virus entry and membrane fusion, inhibit polymerase and protease activity, suppress the host pro-inflammatory cytokines, and utilize cell therapy approaches. KEY MESSAGES In this review, we aimed to provide an up-to-date discussion on the current diagnostic options and therapeutic strategies used to control and manage COVID-19 in clinical and point-of-care settings.
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Affiliation(s)
- Sarah S. Hassanein
- Basic and Applied Sciences (BAS) Institute, Biotechnology Program, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, Egypt
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Muhammed R. Sharaby
- Basic and Applied Sciences (BAS) Institute, Biotechnology Program, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, Egypt
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Noran M. Tawfik
- Basic and Applied Sciences (BAS) Institute, Biotechnology Program, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, Egypt
- Zoology Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Suzan A. Rashed
- Basic and Applied Sciences (BAS) Institute, Biotechnology Program, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, Egypt
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Mohamed Adel
- Basic and Applied Sciences (BAS) Institute, Biotechnology Program, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, Egypt
- Botany and Microbiology Department, Faculty of Science, Helwan University, Cairo, Egypt
| | - Ayat Fayez
- Basic and Applied Sciences (BAS) Institute, Biotechnology Program, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, Egypt
| | - Heba Mansour
- Basic and Applied Sciences (BAS) Institute, Biotechnology Program, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, Egypt
- Polymeric Materials Research Department, Advanced Technology and New Materials Research Institute, City of Scientific Research and Technological Applications, Alexandria, Egypt
| | - Haitham M. Amer
- Virology Department, Faculty of Medicine Veterinary, Cairo University, Giza, Egypt
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Abusalah MAH, Khalifa M, Al-Hatamleh MAI, Jarrar M, Mohamud R, Chan YY. Nucleic Acid-Based COVID-19 Therapy Targeting Cytokine Storms: Strategies to Quell the Storm. J Pers Med 2022; 12:386. [PMID: 35330388 PMCID: PMC8948998 DOI: 10.3390/jpm12030386] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has shaken the world and triggered drastic changes in our lifestyle to control it. Despite the non-typical efforts, COVID-19 still thrives and plagues humanity worldwide. The unparalleled degree of infection has been met with an exceptional degree of research to counteract it. Many drugs and therapeutic technologies have been repurposed and discovered, but no groundbreaking antiviral agent has been introduced yet to eradicate COVID-19 and restore normalcy. As lethality is directly correlated with the severity of disease, hospitalized severe cases are of the greatest importance to reduce, especially the cytokine storm phenomenon. This severe inflammatory phenomenon characterized by elevated levels of inflammatory mediators can be targeted to relieve symptoms and save the infected patients. One of the promising therapeutic strategies to combat COVID-19 is nucleic acid-based therapeutic approaches, including microRNAs (miRNAs). This work is an up-to-date review aimed to comprehensively discuss the current nucleic acid-based therapeutics against COVID-19 and their mechanisms of action, taking into consideration the emerging SARS-CoV-2 variants of concern, as well as providing potential future directions. miRNAs can be used to run interference with the expression of viral proteins, while endogenous miRNAs can be targeted as well, offering a versatile platform to control SARS-CoV-2 infection. By targeting these miRNAs, the COVID-19-induced cytokine storm can be suppressed. Therefore, nucleic acid-based therapeutics (miRNAs included) have a latent ability to break the COVID-19 infection in general and quell the cytokine storm in particular.
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Affiliation(s)
- Mai Abdel Haleem Abusalah
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Kelantan, Malaysia;
| | - Moad Khalifa
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Kelantan, Malaysia;
| | - Mohammad A. I. Al-Hatamleh
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Kelantan, Malaysia; (M.A.I.A.-H.); (R.M.)
| | - Mu’taman Jarrar
- College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia;
- Medical Education Department, King Fahd Hospital of the University, Al-Khobar 34445, Saudi Arabia
| | - Rohimah Mohamud
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Kelantan, Malaysia; (M.A.I.A.-H.); (R.M.)
| | - Yean Yean Chan
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Kelantan, Malaysia;
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Lu W, Zhao Z, Huang YW, Wang B. Review: A systematic review of virus-like particles of coronavirus: Assembly, generation, chimerism and their application in basic research and in the clinic. Int J Biol Macromol 2022; 200:487-497. [PMID: 35065135 PMCID: PMC8769907 DOI: 10.1016/j.ijbiomac.2022.01.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/27/2022]
Abstract
Virus-like particles (VLPs) are nano-scale particles that are morphologically similar to a live virus but which lack a genetic component. Since the pandemic spread of COVID-19, much focus has been placed on coronavirus (CoV)-related VLPs. CoVs contain four structural proteins, though the minimum requirement for VLP formation differs among virus species. CoV VLPs are commonly produced in mammalian and insect cell systems, sometimes in the form of chimeric VLPs that enable surface display of CoV epitopes. VLPs are an ideal model for virological research and have been applied as vaccines and diagnostic reagents to aid in clinical disease control. This review summarizes and updates the research progress on the characteristics of VLPs from different known CoVs, mainly focusing on assembly, in vitro expression systems for VLP generation, VLP chimerism, protein-based nanoparticles and their applications in basic research and clinical settings, which may aid in development of novel VLP vaccines against emerging coronavirus diseases such as SARS-CoV-2.
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Affiliation(s)
- Wan Lu
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Zhuangzhuang Zhao
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yao-Wei Huang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Bin Wang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China.
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Strategies for fighting pandemic virus infections: Integration of virology and drug delivery. J Control Release 2022; 343:361-378. [PMID: 35122872 PMCID: PMC8810279 DOI: 10.1016/j.jconrel.2022.01.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 02/07/2023]
Abstract
Respiratory viruses have sometimes resulted in worldwide pandemics, with the influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) being major participants. Long-term efforts have made it possible to control the influenza virus, but seasonal influenza continues to take many lives each year, and a pandemic influenza virus sometimes emerges. Although vaccines for coronavirus disease 2019 (COVID-19) have been developed, we are not yet able to coexist with the SARS-CoV-2. To overcome such viruses, it is necessary to obtain knowledge about international surveillance systems, virology, ecology and to determine that immune responses are effective. The information must then be transferred to drugs. Delivery systems would be expected to contribute to the rational development of drugs. In this review, virologist and drug delivery system (DDS) researchers discuss drug delivery strategies, especially the use of lipid-based nanocarriers, for fighting to respiratory virus infections.
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