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Brugger SW, Grose JH, Decker CH, Pickett BE, Davis MF. Genomic Analyses of Major SARS-CoV-2 Variants Predicting Multiple Regions of Pathogenic and Transmissive Importance. Viruses 2024; 16:276. [PMID: 38400051 PMCID: PMC10891864 DOI: 10.3390/v16020276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/20/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
The rapid evolution of SARS-CoV-2 has fueled its global proliferation since its discovery in 2019, with several notable variants having been responsible for increases in cases of coronavirus disease 2019 (COVID-19). Analyses of codon bias and usage in these variants between phylogenetic clades or lineages may grant insights into the evolution of SARS-CoV-2 and identify target codons indicative of evolutionary or mutative trends that may prove useful in tracking or defending oneself against emerging strains. We processed a cohort of 120 SARS-CoV-2 genome sequences through a statistical and bioinformatic pipeline to identify codons presenting evidence of selective pressure as well as codon coevolution. We report the identification of two codon sites in the orf8 and N genes demonstrating such evidence with real-world impacts on pathogenicity and transmissivity.
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Affiliation(s)
| | | | | | | | - Mary F. Davis
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA (J.H.G.); (B.E.P.)
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Sievers BL, Cheng MTK, Csiba K, Meng B, Gupta RK. SARS-CoV-2 and innate immunity: the good, the bad, and the "goldilocks". Cell Mol Immunol 2024; 21:171-183. [PMID: 37985854 PMCID: PMC10805730 DOI: 10.1038/s41423-023-01104-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
An ancient conflict between hosts and pathogens has driven the innate and adaptive arms of immunity. Knowledge about this interplay can not only help us identify biological mechanisms but also reveal pathogen vulnerabilities that can be leveraged therapeutically. The humoral response to SARS-CoV-2 infection has been the focus of intense research, and the role of the innate immune system has received significantly less attention. Here, we review current knowledge of the innate immune response to SARS-CoV-2 infection and the various means SARS-CoV-2 employs to evade innate defense systems. We also consider the role of innate immunity in SARS-CoV-2 vaccines and in the phenomenon of long COVID.
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Affiliation(s)
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kata Csiba
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
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Bignon E, Grandemange S, Dumont E, Monari A. How SARS-CoV-2 Alters the Regulation of Gene Expression in Infected Cells. J Phys Chem Lett 2023; 14:3199-3207. [PMID: 36971439 PMCID: PMC10068877 DOI: 10.1021/acs.jpclett.3c00582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/23/2023] [Indexed: 06/18/2023]
Abstract
Nonstructural accessory proteins in viruses play a key role in hijacking the basic cellular mechanisms, which is essential to promote the virus survival and evasion of the immune system. The immonuglobulin-like open reading frame 8 (ORF8) protein expressed by SARS-CoV-2 accumulates in the nucleus and may influence the regulation of the gene expression in infected cells. In this contribution, by using microsecond time-scale all-atom molecular dynamics simulations, we unravel the structural bases behind the epigenetic action of ORF8. In particular, we highlight how the protein is able to form stable aggregates with DNA through a histone tail-like motif, and how this interaction is influenced by post-translational modifications, such as acetylation and methylation, which are known epigenetic markers in histones. Our work not only clarifies the molecular mechanisms behind the perturbation of the epigenetic regulation caused by the viral infection but also offers an unusual perspective which may foster the development of original antivirals.
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Affiliation(s)
- Emmanuelle Bignon
- Université
de Lorraine and CNRS, UMR 7019 LPCT, F-54000 Nancy, France
| | | | - Elise Dumont
- Université
Côte d’Azur, Institut de Chimie de Nice, UMR 7272, Parc Valrose, 28 avenue Valrose, F-06108 Nice, France
- Institut
Universitaire de France, 5 rue Descartes, F-75005 Paris, France
| | - Antonio Monari
- Université
Paris Cité and CNRS, ITODYS, F-75006 Paris, France
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Arduini A, Laprise F, Liang C. SARS-CoV-2 ORF8: A Rapidly Evolving Immune and Viral Modulator in COVID-19. Viruses 2023; 15:871. [PMID: 37112851 PMCID: PMC10141009 DOI: 10.3390/v15040871] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
The COVID-19 pandemic has resulted in upwards of 6.8 million deaths over the past three years, and the frequent emergence of variants continues to strain global health. Although vaccines have greatly helped mitigate disease severity, SARS-CoV-2 is likely to remain endemic, making it critical to understand its viral mechanisms contributing to pathogenesis and discover new antiviral therapeutics. To efficiently infect, this virus uses a diverse set of strategies to evade host immunity, accounting for its high pathogenicity and rapid spread throughout the COVID-19 pandemic. Behind some of these critical host evasion strategies is the accessory protein Open Reading Frame 8 (ORF8), which has gained recognition in SARS-CoV-2 pathogenesis due to its hypervariability, secretory property, and unique structure. This review discusses the current knowledge on SARS-CoV-2 ORF8 and proposes actualized functional models describing its pivotal roles in both viral replication and immune evasion. A better understanding of ORF8's interactions with host and viral factors is expected to reveal essential pathogenic strategies utilized by SARS-CoV-2 and inspire the development of novel therapeutics to improve COVID-19 disease outcomes.
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Affiliation(s)
- Ariana Arduini
- Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (A.A.); (F.L.)
- Department of Medicine, McGill University, Montreal, QC H3G 2M1, Canada
| | - Frederique Laprise
- Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (A.A.); (F.L.)
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Chen Liang
- Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (A.A.); (F.L.)
- Department of Medicine, McGill University, Montreal, QC H3G 2M1, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
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Behairy MY, Soltan MA, Eldeen MA, Abdulhakim JA, Alnoman MM, Abdel-Daim MM, Otifi H, Al-Qahtani SM, Zaki MSA, Alsharif G, Albogami S, Jafri I, Fayad E, Darwish KM, Elhady SS, Eid RA. HBD-2 variants and SARS-CoV-2: New insights into inter-individual susceptibility. Front Immunol 2022; 13:1008463. [PMID: 36569842 PMCID: PMC9780532 DOI: 10.3389/fimmu.2022.1008463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
Background A deep understanding of the causes of liability to SARS-CoV-2 is essential to develop new diagnostic tests and therapeutics against this serious virus in order to overcome this pandemic completely. In the light of the discovered role of antimicrobial peptides [such as human b-defensin-2 (hBD-2) and cathelicidin LL-37] in the defense against SARS-CoV-2, it became important to identify the damaging missense mutations in the genes of these molecules and study their role in the pathogenesis of COVID-19. Methods We conducted a comprehensive analysis with multiple in silico approaches to identify the damaging missense SNPs for hBD-2 and LL-37; moreover, we applied docking methods and molecular dynamics analysis to study the impact of the filtered mutations. Results The comprehensive analysis reveals the presence of three damaging SNPs in hBD-2; these SNPs were predicted to decrease the stability of hBD-2 with a damaging impact on hBD-2 structure as well. G51D and C53G mutations were located in highly conserved positions and were associated with differences in the secondary structures of hBD-2. Docking-coupled molecular dynamics simulation analysis revealed compromised binding affinity for hBD-2 SNPs towards the SARS-CoV-2 spike domain. Different protein-protein binding profiles for hBD-2 SNPs, in relation to their native form, were guided through residue-wise levels and differential adopted conformation/orientation. Conclusions The presented model paves the way for identifying patients prone to COVID-19 in a way that would guide the personalization of both the diagnostic and management protocols for this serious disease.
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Affiliation(s)
- Mohammed Y. Behairy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt,*Correspondence: Mohamed A Soltan, ; Mohammed Y. Behairy,
| | - Mohamed A. Soltan
- Department of Microbiology and immunology, Faculty of Pharmacy, Sinai University – Kantara Branch, Ismailia, Egypt,*Correspondence: Mohamed A Soltan, ; Mohammed Y. Behairy,
| | - Muhammad Alaa Eldeen
- Cell Biology, Histology & Genetics Division, Biology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Jawaher A. Abdulhakim
- Medical Laboratory Department, College of Applied Medical Sciences, Taibah University, Yanbu, Saudi Arabia
| | - Maryam M. Alnoman
- Biology Department, Faculty of Science, Taibah University, Yanbu, Saudi Arabia
| | - Mohamed M. Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, Jeddah, Saudi Arabia,Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Hassan Otifi
- Pathology Department, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Saleh M. Al-Qahtani
- Department of Child Health, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Mohamed Samir A. Zaki
- Anatomy Department, College of Medicine, King Khalid University, Abha, Saudi Arabia,Department of Histology and Cell Biology, College of Medicine, Zagazig University, Zagazig, Egypt
| | - Ghadi Alsharif
- College of Clinical Laboratory Sciences, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Sarah Albogami
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Ibrahim Jafri
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Eman Fayad
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Refaat A. Eid
- Pathology Department, College of Medicine, King Khalid University, Abha, Saudi Arabia
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