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Peters MH. Mutations in the Receptor Binding Domain of Severe Acute Respiratory Coronavirus-2 Omicron Variant Spike Protein Significantly Stabilizes Its Conformation. Viruses 2024; 16:912. [PMID: 38932204 PMCID: PMC11209484 DOI: 10.3390/v16060912] [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: 03/08/2024] [Revised: 05/17/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
The Omicron variant and its sub-lineages are the only current circulating SARS-CoV-2 viruses worldwide. In this study, the conformational stability of the isolated Receptor Binding Domain (RBD) of Omicron's spike protein is examined in detail. The parent Omicron lineage has over ten mutations in the ACE2 binding region of the RBD that are specifically associated with its β hairpin loop domain. It is demonstrated through biophysical molecular computations that the mutations in the β hairpin loop domain significantly increase the intra-protein interaction energies of intra-loop and loop-RBD interactions. The interaction energy increases include the formation of new hydrogen bonds in the β hairpin loop domain that help stabilize this critical ACE2 binding region. Our results also agree with recent experiments on the stability of Omicron's core β barrel domain, outside of its loop domain, and help demonstrate the overall conformational stability of the Omicron RBD. It is further shown here through dynamic simulations that the unbound state of the Omicron RBD remains closely aligned with the bound state configuration, which was not observed for the wild-type RBD. Overall, these studies demonstrate the significantly increased conformational stability of Omicron over its wild-type configuration and raise a number of questions on whether conformational stability could be a positive selection feature of SARS-CoV-2 viral mutational changes.
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Affiliation(s)
- Michael H Peters
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, 601 West Main Street, Richmond, VA 23284, USA
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2
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Kumar S, Dasgupta S, Sajadi MM, Snyder GA, DeVico AL, Ray K. Discordant Antigenic Properties of Soluble and Virion SARS-CoV-2 Spike Proteins. Viruses 2024; 16:407. [PMID: 38543772 PMCID: PMC10974403 DOI: 10.3390/v16030407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 04/01/2024] Open
Abstract
Efforts to develop vaccine and immunotherapeutic countermeasures against the COVID-19 pandemic focus on targeting the trimeric spike (S) proteins of SARS-CoV-2. Vaccines and therapeutic design strategies must impart the characteristics of virion S from historical and emerging variants onto practical constructs such as soluble, stabilized trimers. The virus spike is a heterotrimer of two subunits: S1, which includes the receptor binding domain (RBD) that binds the cell surface receptor ACE2, and S2, which mediates membrane fusion. Previous studies suggest that the antigenic, structural, and functional characteristics of virion S may differ from current soluble surrogates. For example, it was reported that certain anti-glycan, HIV-1 neutralizing monoclonal antibodies bind soluble SARS-CoV-2 S but do not neutralize SARS-CoV-2 virions. In this study, we used single-molecule fluorescence correlation spectroscopy (FCS) under physiologically relevant conditions to examine the reactivity of broadly neutralizing and non-neutralizing anti-S human monoclonal antibodies (mAbs) isolated in 2020. Binding efficiency was assessed by FCS with soluble S trimers, pseudoviruses and inactivated wild-type virions representing variants emerging from 2020 to date. Anti-glycan mAbs were tested and compared. We find that both anti-S specific and anti-glycan mAbs exhibit variable but efficient binding to a range of stabilized, soluble trimers. Across mAbs, the efficiencies of soluble S binding were positively correlated with reactivity against inactivated virions but not pseudoviruses. Binding efficiencies with pseudoviruses were generally lower than with soluble S or inactivated virions. Among neutralizing mAbs, potency did not correlate with binding efficiencies on any target. No neutralizing activity was detected with anti-glycan antibodies. Notably, the virion S released from membranes by detergent treatment gained more efficient reactivity with anti-glycan, HIV-neutralizing antibodies but lost reactivity with all anti-S mAbs. Collectively, the FCS binding data suggest that virion surfaces present appreciable amounts of both functional and nonfunctional trimers, with neutralizing anti-S favoring the former structures and non-neutralizing anti-glycan mAbs binding the latter. S released from solubilized virions represents a nonfunctional structure bound by anti-glycan mAbs, while engineered soluble trimers present a composite structure that is broadly reactive with both mAb types. The detection of disparate antigenicity and immunoreactivity profiles in engineered and virion-associated S highlight the value of single-virus analyses in designing future antiviral strategies against SARS-CoV-2.
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Affiliation(s)
- Sameer Kumar
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Souradip Dasgupta
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Mohammad M. Sajadi
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Division of Clinical Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Greg A. Snyder
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Anthony L. DeVico
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Krishanu Ray
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
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Liana DF, Novianry V, Andriani A, Mahyarudin M, Astuti P. Disappearance of Imported Cases of Omicron Lineage BA.2.40 in West Kalimantan, Indonesia. IRANIAN JOURNAL OF MEDICAL SCIENCES 2024; 49:176-185. [PMID: 38584647 PMCID: PMC10997853 DOI: 10.30476/ijms.2023.97513.2935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/23/2023] [Accepted: 03/29/2023] [Indexed: 04/09/2024]
Abstract
Background The World Health Organization has declared Omicron as the fifth variant of concern with more than 50 mutations, particularly in the spike protein. Given increased viral infectivity due to mutations, worldwide genomic surveillance and detection of severe acute respiratory syndrome 2 (SARS-CoV-2) is essential. The present study aimed to track Omicron lineage BA.2.40 in West Kalimantan, Indonesia. Methods In May-August 2022, nasopharyngeal swab samples (n=3,642) were collected from international travelers to West Kalimantan (active surveillance), and patients hospitalized due to SARS-CoV-2 infection (baseline surveillance). The samples were tested for Omicron lineages based on ORF1ab, N, and HV69-70del genes, followed by whole-genome sequencing. The sequences were then identified using two genomic databases, aligned against the reference genome (Wuhan/Hu-1/2019), and then compared with BA.2.40 lineage detected across the world. Phylogenetic analysis between the samples and other SARS-CoV-2 isolates was performed using molecular evolutionary genetics analysis software. Results Based on the genomic databases, 10 isolates were identified as BA.2.40. All samples tested positive for the ORF1ab and N genes, but negative for the HV69-70del gene, which is a marker to detect the Omicron variant. Phylogenetic analysis showed the isolates were closely related to an isolate from Malaysia, an area dominated by BA.2.40. Conclusion Omicron lineage BA.2.40 has no HV69-70 deletion in the spike protein, a marker used to screen for the Omicron variant. BA.2.40 showed a high similarity to an isolate from Malaysia and was detected only during certain periods, indicating the effect of internationally imported cases.
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Affiliation(s)
- Delima Fajar Liana
- Department of Microbiology, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| | - Virhan Novianry
- Department of Biochemistry and Biomolecular, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| | - Andriani Andriani
- Department of Biochemistry and Biomolecular, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| | - Mahyarudin Mahyarudin
- Department of Microbiology, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| | - Puji Astuti
- Department of Biochemistry and Biomolecular, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
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Novkovic M, Banovic Djeri B, Ristivojevic B, Knezevic A, Jankovic M, Tanasic V, Radojicic V, Keckarevic D, Vidanovic D, Tesovic B, Skakic A, Tolinacki M, Moric I, Djordjevic V. Genome sequence diversity of SARS-CoV-2 in Serbia: insights gained from a 3-year pandemic study. Front Microbiol 2024; 15:1332276. [PMID: 38476954 PMCID: PMC10929721 DOI: 10.3389/fmicb.2024.1332276] [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: 11/03/2023] [Accepted: 01/15/2024] [Indexed: 03/14/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has been evolving rapidly causing emergence of new variants and health uncertainties. Monitoring the evolution of the virus was of the utmost importance for public health interventions and the development of national and global mitigation strategies. Here, we report national data on the emergence of new variants, their distribution, and dynamics in a 3-year study conducted from March 2020 to the end of January 2023 in the Republic of Serbia. Nasopharyngeal and oropharyngeal swabs from 2,398 COVID-19-positive patients were collected and sequenced using three different next generation technologies: Oxford Nanopore, Ion Torrent, and DNBSeq. In the subset of 2,107 SARS-CoV-2 sequences which met the quality requirements, detection of mutations, assignment to SARS-CoV-2 lineages, and phylogenetic analysis were performed. During the 3-year period, we detected three variants of concern, namely, Alpha (5.6%), Delta (7.4%), and Omicron (70.3%) and one variant of interest-Omicron recombinant "Kraken" (XBB1.5) (<1%), whereas 16.8% of the samples belonged to other SARS-CoV-2 (sub)lineages. The detected SARS-CoV-2 (sub)lineages resulted in eight COVID-19 pandemic waves in Serbia, which correspond to the pandemic waves reported in Europe and the United States. Wave dynamics in Serbia showed the most resemblance with the profile of pandemic waves in southern Europe, consistent with the southeastern European location of Serbia. The samples were assigned to sixteen SARS-CoV-2 Nextstrain clades: 20A, 20B, 20C, 20D, 20E, 20G, 20I, 21J, 21K, 21L, 22A, 22B, 22C, 22D, 22E, and 22F and six different Omicron recombinants (XZ, XAZ, XAS, XBB, XBF, and XBK). The 10 most common mutations detected in the coding and untranslated regions of the SARS-CoV-2 genomes included four mutations affecting the spike protein (S:D614G, S:T478K, S:P681H, and S:S477N) and one mutation at each of the following positions: 5'-untranslated region (5'UTR:241); N protein (N:RG203KR); NSP3 protein (NSP3:F106F); NSP4 protein (NSP4:T492I); NSP6 protein (NSP6: S106/G107/F108 - triple deletion), and NSP12b protein (NSP12b:P314L). This national-level study is the most comprehensive in terms of sequencing and genomic surveillance of SARS-CoV-2 during the pandemic in Serbia, highlighting the importance of establishing and maintaining good national practice for monitoring SARS-CoV-2 and other viruses circulating worldwide.
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Affiliation(s)
- Mirjana Novkovic
- Center for Genome Sequencing and Bioinformatics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Bojana Banovic Djeri
- Center for Genome Sequencing and Bioinformatics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Bojan Ristivojevic
- Center for Genome Sequencing and Bioinformatics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Aleksandra Knezevic
- Institute of Microbiology and Immunology, Department of Virology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Marko Jankovic
- Institute of Microbiology and Immunology, Department of Virology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Vanja Tanasic
- Center for Forensic and Applied Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Verica Radojicic
- Center for Forensic and Applied Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Dusan Keckarevic
- Center for Forensic and Applied Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Dejan Vidanovic
- Veterinary Specialized Institute “Kraljevo”, Kraljevo, Serbia
| | - Bojana Tesovic
- Veterinary Specialized Institute “Kraljevo”, Kraljevo, Serbia
| | - Anita Skakic
- Center for Genome Sequencing and Bioinformatics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Maja Tolinacki
- Center for Genome Sequencing and Bioinformatics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Ivana Moric
- Center for Genome Sequencing and Bioinformatics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Valentina Djordjevic
- Center for Genome Sequencing and Bioinformatics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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Parums DV. Editorial: Global Health Concerns as Vaccine-Preventable Infections Including SARS-CoV-2 (JN.1), Influenza, Respiratory Syncytial Virus (RSV), and Measles Continue to Rise. Med Sci Monit 2024; 30:e943911. [PMID: 38298093 PMCID: PMC10845785 DOI: 10.12659/msm.943911] [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: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 02/02/2024] Open
Abstract
In December 2023, the US Centers for Disease Control and Prevention (CDC) published the updated 2024 Advisory Committee on Immunization Practices (ACIP) Adult Immunization Schedule, which is available online for access by the public and healthcare professionals. These new guidelines come at a time when the incidence of vaccine-preventable viral infections from SARS-CoV-2 (JN.1), respiratory syncytial virus (RSV), influenza, and measles are increasing in adults and children due to vaccine hesitancy, or non-compliance. This editorial aims to highlight the ongoing global health concerns for the consequences of increasing reports of vaccine-preventable infections, including SARS-CoV-2 (JN.1), influenza, RSV, and measles, to understand the causes of vaccine hesitancy, and introduce some public health measures that could improve vaccine uptake.
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Affiliation(s)
- Dinah V. Parums
- Science Editor, Medical Science Monitor, International Scientific Information, Inc., Melville, NY, USA, e-mail:
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Liu J, Jaijyan DK, Chen Y, Feng C, Yang S, Xu Z, Zhan N, Hong C, Li S, Cheng T, Zhu H. Cytomegalovirus-vectored COVID-19 vaccines elicit neutralizing antibodies against the SARS-CoV-2 Omicron variant (BA.2) in mice. Microbiol Spectr 2023; 11:e0246323. [PMID: 37971259 PMCID: PMC10883801 DOI: 10.1128/spectrum.02463-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Cytomegalovirus (CMV) has been used as a novel viral vector for vaccine development and gene therapy. Coronavirus disease 2019 is an infectious disease caused by the SARS-CoV-2 virus, which is highly mutable and is still circulating globally. The study showed that the CMV viral vector caused transient systemic infection and induced robust transgene expression in vivo. CMV vectors expressing different SARS-CoV-2 proteins were immunogenic and could elicit neutralizing antibodies against a highly mutated Omicron variant (BA.2). The expression level of receptor-binding domain (RBD) protein was higher than that of full-length S protein using CMV as a vaccine vector, and CMV vector expression RBD protein elicited higher RBD-binding and neutralizing antibodies. Moreover, the study showed that CMV-vectored vaccines would not cause unexpected viral transmission, and pre-existing immunity might impair the immunogenicity of subsequent CMV-vectored vaccines. These works provide meaningful insights for the development of a CMV-based vector vaccine platform and the prevention and control strategies for SARS-CoV-2 infection.
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Affiliation(s)
- Jian Liu
- School of Biological Sciences and Biotechnology, Minnan Normal University , Zhangzhou, Fujian, China
| | - Dabbu Kumar Jaijyan
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School , Newark, New Jersey, USA
| | - Yanling Chen
- School of Biological Sciences and Biotechnology, Minnan Normal University , Zhangzhou, Fujian, China
| | - Changcan Feng
- School of Biological Sciences and Biotechnology, Minnan Normal University , Zhangzhou, Fujian, China
| | - Shaomin Yang
- Shenzhen Municipal Key Laboratory for Pain Medicine, Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital , Shenzhen, Guangdong, China
| | - Zhenglong Xu
- School of Biological Sciences and Biotechnology, Minnan Normal University , Zhangzhou, Fujian, China
| | - Nichun Zhan
- School of Biological Sciences and Biotechnology, Minnan Normal University , Zhangzhou, Fujian, China
| | - Congming Hong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University , Xiamen, Fujian, China
| | - Shuxuan Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University , Xiamen, Fujian, China
| | - Tong Cheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University , Xiamen, Fujian, China
| | - Hua Zhu
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School , Newark, New Jersey, USA
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Pérez-Vargas J, Worrall LJ, Olmstead AD, Ton AT, Lee J, Villanueva I, Thompson CAH, Dudek S, Ennis S, Smith JR, Shapira T, De Guzman J, Gang S, Ban F, Vuckovic M, Bielecki M, Kovacic S, Kenward C, Hong CY, Gordon DG, Levett PN, Krajden M, Leduc R, Boudreault PL, Niikura M, Paetzel M, Young RN, Cherkasov A, Strynadka NCJ, Jean F. A novel class of broad-spectrum active-site-directed 3C-like protease inhibitors with nanomolar antiviral activity against highly immune-evasive SARS-CoV-2 Omicron subvariants. Emerg Microbes Infect 2023; 12:2246594. [PMID: 37555275 PMCID: PMC10453993 DOI: 10.1080/22221751.2023.2246594] [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: 05/24/2023] [Revised: 07/31/2023] [Accepted: 08/06/2023] [Indexed: 08/10/2023]
Abstract
Antivirals with broad coronavirus activity are important for treating high-risk individuals exposed to the constantly evolving SARS-CoV-2 variants of concern (VOCs) as well as emerging drug-resistant variants. We developed and characterized a novel class of active-site-directed 3-chymotrypsin-like protease (3CLpro) inhibitors (C2-C5a). Our lead direct-acting antiviral (DAA), C5a, is a non-covalent, non-peptide with a dissociation constant of 170 nM against recombinant SARS-CoV-2 3CLpro. The compounds C2-C5a exhibit broad-spectrum activity against Omicron subvariants (BA.5, BQ.1.1, and XBB.1.5) and seasonal human coronavirus-229E infection in human cells. Notably, C5a has median effective concentrations of 30-50 nM against BQ.1.1 and XBB.1.5 in two different human cell lines. X-ray crystallography has confirmed the unique binding modes of C2-C5a to the 3CLpro, which can limit virus cross-resistance to emerging Paxlovid-resistant variants. We tested the effect of C5a with two of our newly discovered host-directed antivirals (HDAs): N-0385, a TMPRSS2 inhibitor, and bafilomycin D (BafD), a human vacuolar H+-ATPase [V-ATPase] inhibitor. We demonstrated a synergistic action of C5a in combination with N-0385 and BafD against Omicron BA.5 infection in human Calu-3 lung cells. Our findings underscore that a SARS-CoV-2 multi-targeted treatment for circulating Omicron subvariants based on DAAs (C5a) and HDAs (N-0385 or BafD) can lead to therapeutic benefits by enhancing treatment efficacy. Furthermore, the high-resolution structures of SARS-CoV-2 3CLpro in complex with C2-C5a will facilitate future rational optimization of our novel broad-spectrum active-site-directed 3C-like protease inhibitors.
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Affiliation(s)
- Jimena Pérez-Vargas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Liam J. Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Andrea D. Olmstead
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Anh-Tien Ton
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Jaeyong Lee
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Ivan Villanueva
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Connor A. H. Thompson
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Svenja Dudek
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Jason R. Smith
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Tirosh Shapira
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Joshua De Guzman
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Shutong Gang
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Michael Bielecki
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Suzana Kovacic
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Calem Kenward
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Christopher Yee Hong
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Danielle G. Gordon
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Paul N. Levett
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Richard Leduc
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Canada
| | - Pierre-Luc Boudreault
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Mark Paetzel
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Robert N. Young
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - François Jean
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
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Pastorio C, Noettger S, Nchioua R, Zech F, Sparrer KM, Kirchhoff F. Impact of mutations defining SARS-CoV-2 Omicron subvariants BA.2.12.1 and BA.4/5 on Spike function and neutralization. iScience 2023; 26:108299. [PMID: 38026181 PMCID: PMC10661123 DOI: 10.1016/j.isci.2023.108299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/04/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Additional mutations in the viral Spike protein helped the BA.2.12.1 and BA.4/5 SARS-CoV-2 Omicron subvariants to outcompete the parental BA.2 subvariant. Here, we determined the functional impact of mutations that newly emerged in the BA.2.12.1 (L452Q, S704L) and BA.4/5 (Δ69-70, L452R, F486V, R493Q) Spike proteins. Our results show that mutation of L452Q/R or F486V typically increases and R493Q or S704L impair BA.2 Spike-mediated infection. In combination, changes of Δ69-70, L452R, and F486V contribute to the higher infectiousness and fusogenicity of the BA.4/5 Spike. L452R/Q and F486V in Spike are mainly responsible for reduced sensitivity to neutralizing antibodies. However, the combined mutations are required for full infectivity, reduced TMPRSS2 dependency, and immune escape of BA.4/5 Spike. Thus, it is the specific combination of mutations in BA.4/5 Spike that allows increased functionality and immune evasion, which helps to explain the temporary dominance and increased pathogenicity of these Omicron subvariants.
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Affiliation(s)
- Chiara Pastorio
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany
| | - Sabrina Noettger
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany
| | - Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany
| | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany
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9
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Fan T, Li C, Liu X, Xu H, Li W, Wang M, Mei X, Li D. Development of practical techniques for simultaneous detection and distinction of current and emerging SARS-CoV-2 variants. ANAL SCI 2023; 39:1839-1856. [PMID: 37517003 DOI: 10.1007/s44211-023-00396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023]
Abstract
Countless individuals have fallen victim to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and have generated antibodies, reducing the risk of secondary infection in the short term. However, with the emergence of mutated strains, the probability of subsequent infections remains high. Consequently, the demand for simple and accessible methods for distinguishing between different variants is soaring. Although monitoring viral gene sequencing is an effective approach for differentiating between various types of SARS-CoV-2 variants, it may not be easily accessible to the general public. In this article, we provide an overview of the reported techniques that use combined approaches and adaptable testing methods that use editable recognition receptors for simultaneous detection and distinction of current and emerging SARS-CoV-2 variants. These techniques employ straightforward detection strategies, including tests capable of simultaneously identifying and differentiating between different variants. Furthermore, we recommend advancing the development of uncomplicated protocols for distinguishing between current and emerging variants. Additionally, we propose further development of facile protocols for the differentiation of existing and emerging variants.
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Affiliation(s)
- Tuocen Fan
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Chengjie Li
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Xinlei Liu
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Hongda Xu
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Wenhao Li
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Minghao Wang
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Xifan Mei
- Jinzhou Medical University, Jinzhou, 121000, China.
| | - Dan Li
- Jinzhou Medical University, Jinzhou, 121000, China.
- College of Pharmacy, Jinzhou Medical University, Jinzhou, 121000, China.
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10
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Lagare A, Faye M, Issa M, Hamidou O, Bienvenu B, Mohamed A, Aoula B, Moumouni K, Hassane F, Otto YA, Tambwe DD, Tassiou EI, Seini H, Faye O, Jambou R. First identification of the SARS-COV-2/XBB.1.5 sublineage among indigenous COVID-19 cases through the influenza sentinel surveillance system in Niger. Heliyon 2023; 9:e20916. [PMID: 37954288 PMCID: PMC10637901 DOI: 10.1016/j.heliyon.2023.e20916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023] Open
Abstract
The emergence of the Omicron variant in November 2021, has caused panic worldwide due to the rapid evolution and the ability of the virus to escape the immune system. Since, several Omicron sublineages (BA.1 to BA.5) and their descendent recombinant lineages have been circulating worldwide. Furthermore, in December 2022, a new Omicron subvariant XBB.1.5 characterized by an unusual mutation in the spike protein evolved in the United States and rapidly spread to the other continents. Our study reports on the first cases of XBB.1.5 sublineage among indigenous Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-COV-2) positive cases detected through the influenza sentinel surveillance system in Niger. All influenza suspected cases were tested for both influenza and SARS-COV-2 using the Centre for Disease Control and prevention (CDC) Influenza SARS-COV-2 Multiplex quantitative Reverse-Transcription Polymerase Chain Reaction (qRT-PCR) Assay. SARS-COV-2 positive samples with cycle threshold ≤28 were selected for whole genome sequencing subsequently using the Oxford Nanopore Midnight protocol with rapid barcoding on a MinIon MK1B device. A total of 51 SARS-COV-2 positive samples were confirmed between December 2022 and March 2023. We successfully obtained 19 sequences with a predominance of the XBB.1/XBB.1.5 sublineages (73.7 %). In addition, a recombinant XBD sequence was also first-ever identified in early March 2023. Our findings support the need to strengthen the influenza sentinel surveillance for routine Coronavirus Disease 2019 (COVID-19) surveillance and SARS-COV-2 variants monitoring in Niger.
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Affiliation(s)
- Adamou Lagare
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bd de la Nation, Niamey, YN034, Niger
| | - Martin Faye
- Virology Department, Institut Pasteur de Dakar, 36, Avenue Pasteur Dakar, 220, Dakar, Senegal
| | - Moussa Issa
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bd de la Nation, Niamey, YN034, Niger
| | - Oumou Hamidou
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bd de la Nation, Niamey, YN034, Niger
| | - Baruani Bienvenu
- World Health Organization-Country Office, Boulevard Du Roi Mohamed 6, BP 10739, Niamey, Niger
| | | | - Balki Aoula
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bd de la Nation, Niamey, YN034, Niger
| | | | - Fatima Hassane
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bd de la Nation, Niamey, YN034, Niger
| | - Younoussa Adamou Otto
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bd de la Nation, Niamey, YN034, Niger
| | - Didier D.K. Tambwe
- World Health Organization-Country Office, Boulevard Du Roi Mohamed 6, BP 10739, Niamey, Niger
| | | | - Haoua Seini
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bd de la Nation, Niamey, YN034, Niger
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, 36, Avenue Pasteur Dakar, 220, Dakar, Senegal
| | - Ronan Jambou
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bd de la Nation, Niamey, YN034, Niger
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11
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Parums DV. Editorial: Factors Driving New Variants of SARS-CoV-2, Immune Escape, and Resistance to Antiviral Treatments as the End of the COVID-19 Pandemic is Declared. Med Sci Monit 2023; 29:e942960. [PMID: 37908161 PMCID: PMC10626992 DOI: 10.12659/msm.942960] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 11/02/2023] Open
Abstract
On May 5, 2023, the Director-General of the World Health Organization (WHO) advised the transition to long-term management of the COVID-19 pandemic and that COVID-19 is now an established and ongoing health issue that is no longer a public health emergency of international concern (PHEIC). The WHO decision was based on an analysis of the decreasing trend in mortality, the decline in hospital admissions and Intensive Care Unit (ICU) admissions from COVID-19, and the increasing levels of population immunity to SARS-CoV-2. This Editorial aims to highlight what is known of the factors that drive new variants, subvariants, and lineages of SARS-CoV-2 associated with immune escape to previous infection or vaccines and resistance to antiviral treatments as the end of the COVID-19 pandemic is declared.
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Affiliation(s)
- Dinah V Parums
- Science Editor, Medical Science Monitor, International Scientific Information, Inc., Melville, NY, USA
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12
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Cheng Z, Lai Y, Jin K, Zhang M, Wang J. Modeling the XBB strain of SARS-CoV-2: Competition between variants and impact of reinfection. J Theor Biol 2023; 574:111611. [PMID: 37640233 PMCID: PMC10592017 DOI: 10.1016/j.jtbi.2023.111611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/16/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
XBB, an Omicron subvariant of SARS-CoV-2 that began to circulate in late 2022, has been dominant in the US since early 2023. To quantify the impact of XBB on the progression of COVID-19, we propose a new mathematical model which describes the interplay between XBB and other SARS-CoV-2 variants at the population level and which incorporates the effects of reinfection. We apply the model to COVID-19 data in the US that include surveillance data on the cases and variant proportions from the New York City, the State of New York, and the State of Washington. Our fitting and simulation results show that the transmission rate of XBB is significantly higher than that of other variants and the reinfection from XBB may play an important role in shaping the pandemic/epidemic pattern in the US.
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Affiliation(s)
- Ziqiang Cheng
- School of Mathematics, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Yinglei Lai
- School of Mathematical Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Kui Jin
- Department of Emergency Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Mengping Zhang
- School of Mathematical Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Jin Wang
- Department of Mathematics, University of Tennessee at Chattanooga, Chattanooga, TN 37403, USA.
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13
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Naik R, Avula S, Palleti SK, Gummadi J, Ramachandran R, Chandramohan D, Dhillon G, Gill AS, Paiwal K, Shaik B, Balachandran M, Patel B, Gurugubelli S, Mariswamy Arun Kumar AK, Nanjundappa A, Bellamkonda M, Rathi K, Sakhamuri PL, Nassar M, Bali A. From Emergence to Endemicity: A Comprehensive Review of COVID-19. Cureus 2023; 15:e48046. [PMID: 37916248 PMCID: PMC10617653 DOI: 10.7759/cureus.48046] [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] [Accepted: 10/31/2023] [Indexed: 11/03/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), later renamed coronavirus disease 2019 (COVID-19), was first identified in Wuhan, China, in early December 2019. Initially, the China office of the World Health Organization was informed of numerous cases of pneumonia of unidentified etiology in Wuhan, Hubei Province at the end of 2019. This would subsequently result in a global pandemic with millions of confirmed cases of COVID-19 and millions of deaths reported to the WHO. We have analyzed most of the data published since the beginning of the pandemic to compile this comprehensive review of SARS-CoV-2. We looked at the core ideas, such as the etiology, epidemiology, pathogenesis, clinical symptoms, diagnostics, histopathologic findings, consequences, therapies, and vaccines. We have also included the long-term effects and myths associated with some therapeutics of COVID-19. This study presents a comprehensive assessment of the SARS-CoV-2 virology, vaccines, medicines, and significant variants identified during the course of the pandemic. Our review article is intended to provide medical practitioners with a better understanding of the fundamental sciences, clinical treatment, and prevention of COVID-19. As of May 2023, this paper contains the most recent data made accessible.
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Affiliation(s)
- Roopa Naik
- Medicine, Geisinger Commonwealth School of Medicine, Scranton, USA
- Internal Medicine/Hospital Medicine, Geisinger Health System, Wilkes Barre, USA
| | - Sreekant Avula
- Diabetes, Endocrinology, and Metabolism, University of Minnesota, Minneapolis, USA
| | - Sujith K Palleti
- Nephrology, Louisiana State University Health Sciences Center, Shreveport, USA
| | - Jyotsna Gummadi
- Internal Medicine, MedStar Franklin Square Medical Center, Baltimore, USA
| | | | | | - Gagandeep Dhillon
- Physician Executive MBA, University of Tennessee, Knoxville, USA
- Internal Medicine, University of Maryland Baltimore Washington Medical Center, Glen Burnie, USA
| | | | - Kapil Paiwal
- Oral & Maxillofacial Pathology, Daswani Dental College & Research Center, Kota, IND
| | - Bushra Shaik
- Internal Medicine, Onslow Memorial Hospital, Jacksonville, USA
| | | | - Bhumika Patel
- Oral Medicine and Radiology, Howard University, Washington, D.C., USA
| | | | | | | | - Mahita Bellamkonda
- Hospital Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Kanika Rathi
- Internal Medicine, University of Florida, Gainesville, USA
| | | | - Mahmoud Nassar
- Endocrinology, Diabetes, and Metabolism, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Atul Bali
- Internal Medicine/Nephrology, Geisinger Medical Center, Danville, USA
- Internal Medicine/Nephrology, Geisinger Health System, Wilkes-Barre, USA
- Medicine, Geisinger Commonwealth School of Medicine, Scranton, USA
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14
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Parums DV. Editorial: A Rapid Global Increase in COVID-19 is Due to the Emergence of the EG.5 (Eris) Subvariant of Omicron SARS-CoV-2. Med Sci Monit 2023; 29:e942244. [PMID: 37654205 PMCID: PMC10478578 DOI: 10.12659/msm.942244] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 08/21/2023] [Indexed: 09/02/2023] Open
Abstract
A new variant of SARS-CoV-2 has currently achieved global domination. EG.5 (Eris) was first reported by the World Health Organization (WHO) on February 17, 2023, and designated as a variant under monitoring (VUM) on July 19, 2023. EG.5 (Eris), and its sublineages, EG.5.1, EG.5.1.1, and EG.5.2, is a descendent lineage of XBB.1.9.2, which has the same spike amino acid profile as XBB.1.5 (Kraken). However, EG.5 (Eris) has an additional F456L amino acid mutation in the spike protein compared to these parent subvariants, and the subvariant EG.5.1 has another spike mutation, Q52H. Following risk evaluation by the WHO, EG.5 (Eris) and its sublineages were designated as a variant of interest (VOI) on August 8, 2023. In the US, the Centers for Disease Control and Prevention (CDC) provides two-weekly monitoring data on the incidence and mortality from COVID-19 and SARS-CoV-2 variants. The most recent CDC data for August 19, 2023, showed an increase in cases in the past two weeks, with hospitalizations for COVID-19 increasing by 14.3% and mortality from COVID-19 rising by 8.3%. In the US, the most common COVID-19 cases have been due to three new SARS-CoV-2 Omicron variants: EG.5 (Eris) (20.6%); FL.1.5.1 (Fornax) (13.3%); and XBB.1.16 (Arcturus) (10.7%). This Editorial aims to highlight the importance of rapid virus genomic sequencing and continued global SARS-CoV-2 surveillance to identify rapidly emerging SARS-CoV-2 Omicron variants, such as EG.5 (Eris).
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Affiliation(s)
- Dinah V. Parums
- Science Editor, Medical Science Monitor, International Scientific Information, Inc., Melville, NY, USA, e-mail:
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15
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Xiao S, Alshahrani M, Gupta G, Tao P, Verkhivker G. Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. J Chem Inf Model 2023; 63:5272-5296. [PMID: 37549201 PMCID: PMC11162552 DOI: 10.1021/acs.jcim.3c00778] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
The new generation of SARS-CoV-2 Omicron variants displayed a significant growth advantage and increased viral fitness by acquiring convergent mutations, suggesting that the immune pressure can promote convergent evolution leading to the sudden acceleration of SARS-CoV-2 evolution. In the current study, we combined structural modeling, microsecond molecular dynamics simulations, and Markov state models to characterize conformational landscapes and identify specific dynamic signatures of the SARS-CoV-2 spike complexes with the host receptor ACE2 for the recently emerged highly transmissible XBB.1, XBB.1.5, BQ.1, and BQ.1.1 Omicron variants. Microsecond simulations and Markovian modeling provided a detailed characterization of the functional conformational states and revealed the increased thermodynamic stabilization of the XBB.1.5 subvariant, which can be contrasted to more dynamic BQ.1 and BQ.1.1 subvariants. Despite considerable structural similarities, Omicron mutations can induce unique dynamic signatures and specific distributions of the conformational states. The results suggested that variant-specific changes of the conformational mobility in the functional interfacial loops of the receptor-binding domain in the SARS-CoV-2 spike protein can be fine-tuned through crosstalk between convergent mutations which could provide an evolutionary path for modulation of immune escape. By combining atomistic simulations and Markovian modeling analysis with perturbation-based approaches, we determined important complementary roles of convergent mutation sites as effectors and receivers of allosteric signaling involved in modulation of conformational plasticity and regulation of allosteric communications. This study also revealed hidden allosteric pockets and suggested that convergent mutation sites could control evolution and distribution of allosteric pockets through modulation of conformational plasticity in the flexible adaptable regions.
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Affiliation(s)
- Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Grace Gupta
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
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16
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Yuda Kusuma I, Pratiwi H, Fitri Khairunnisa S, Ayu Eka Pitaloka D, Arizandi Kurnianto A. The assessment of Twitter discourse on the new COVID-19 variant, XBB.1.5, through social network analysis. Vaccine X 2023; 14:100322. [PMID: 37317688 PMCID: PMC10245456 DOI: 10.1016/j.jvacx.2023.100322] [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: 04/10/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023] Open
Abstract
Background XBB.1.5 is a new subvariant of the SARS-CoV-2 Omicron variant with increased transmissibility and immune escape potential. Twitter has been used to share information and assess this subvariant. Objectives This study aims to investigate the channel graph, key influencers, top sources, most trends, and pattern discussion, as well as sentiment measures related to Covid-19 XBB.1.5 variant, by using social network analysis (SNA). Methods This experiment involved the collection of Twitter data through the keywords, "XBB.1.5″, and NodeXL, with the obtained information subsequently cleaned to remove duplication and irrelevant tweets. SNA was also performed by using analytical metrics to identify influential users and understand the patterns of connectivity among those discussing XBB.1.5. on Twitter. Moreover, the results were visualized through Gephi software, with sentiment analysis performed by using Azure Machine Learning to categorize tweets into three categories, namely positive, negative, and neutral. Results A total of 43,394 XBB.1.5-based tweets were identified, with five key users observed with the highest betweenness centrality score (BCS), namely "ojimakohei"(red), mikito_777 (blue), "nagunagumomo" (green), "erictopol" (orange), w2skwn3 (yellow). The other hand, the in-degree, out-degree, betweenness, closeness, and eigenvector centrality scores of the top 10 Twitter users to explain various patterns and trends and "ojimakohei" was highly central in the network. Most of the top domains (sources) used in XBB.1.5 discourse originated from Twitter, Japanese websites (co.jp and or.jp), and scientific analysis links (biorxiv.org and cdc.gov). This analysis indicated that most of the tweets (61.35 %) were positively classified, accompanied by neutral (22.44 %) and negative (16.20 %) sentiments. Conclusion Japan was actively engaged in evaluating the XBB.1.5 variant, with influential users playing a crucial role. The preference for sharing verified sources and the positive sentiment demonstrated a commitment to health awareness. We recommend fostering collaborations between health organizations, the government, and Twitter influencers to address COVID-19-related misinformation and its variants.
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Affiliation(s)
- Ikhwan Yuda Kusuma
- Pharmacy Study Program, Faculty of Health, Universitas Harapan Bangsa, Purwokerto 53182, Indonesia
| | - Hening Pratiwi
- Department of Pharmacy, Faculty of Health Sciences, Jenderal Soedirman University, Purwokerto 53122, Indonesia
| | - Shafa Fitri Khairunnisa
- Center of Excellence in Higher Education for Pharmaceutical Care Innovation, Universitas Padjadjaran, Sumedang 45363, Indonesia
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang 45363, Indonesia
| | - Dian Ayu Eka Pitaloka
- Center of Excellence in Higher Education for Pharmaceutical Care Innovation, Universitas Padjadjaran, Sumedang 45363, Indonesia
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang 45363, Indonesia
| | - Arie Arizandi Kurnianto
- Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
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17
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Xiao S, Alshahrani M, Gupta G, Tao P, Verkhivker G. Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variants Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.20.541592. [PMID: 37292827 PMCID: PMC10245745 DOI: 10.1101/2023.05.20.541592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The new generation of SARS-CoV-2 Omicron variants displayed a significant growth advantage and the increased viral fitness by acquiring convergent mutations, suggesting that the immune pressure can promote convergent evolution leading to the sudden acceleration of SARS-CoV-2 evolution. In the current study, we combined structural modeling, extensive microsecond MD simulations and Markov state models to characterize conformational landscapes and identify specific dynamic signatures of the SARS-CoV-2 spike complexes with the host receptor ACE2 for the recently emerged highly transmissible XBB.1, XBB.1.5, BQ.1, and BQ.1.1 Omicron variants. Microsecond simulations and Markovian modeling provided a detailed characterization of the conformational landscapes and revealed the increased thermodynamic stabilization of the XBB.1.5 subvariant which is contrasted to more dynamic BQ.1 and BQ.1.1 subvariants. Despite considerable structural similarities, Omicron mutations can induce unique dynamic signatures and specific distributions of conformational states. The results suggested that variant-specific changes of conformational mobility in the functional interfacial loops of the spike receptor binding domain can be fine-tuned through cross-talk between convergent mutations thereby providing an evolutionary path for modulation of immune escape. By combining atomistic simulations and Markovian modeling analysis with perturbation-based approaches, we determined important complementary roles of convergent mutation sites as effectors and receivers of allosteric signaling involved in modulating conformational plasticity at the binding interface and regulating allosteric responses. This study also characterized the dynamics-induced evolution of allosteric pockets in the Omicron complexes that revealed hidden allosteric pockets and suggested that convergent mutation sites could control evolution and distribution of allosteric pockets through modulation of conformational plasticity in the flexible adaptable regions. Through integrative computational approaches, this investigation provides a systematic analysis and comparison of the effects of Omicron subvariants on conformational dynamics and allosteric signaling in the complexes with the ACE2 receptor. For Table of Contents Use Only
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18
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Verkhivker G, Alshahrani M, Gupta G. Balancing Functional Tradeoffs between Protein Stability and ACE2 Binding in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic and Energetic Changes. Viruses 2023; 15:1143. [PMID: 37243229 PMCID: PMC10221141 DOI: 10.3390/v15051143] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Evolutionary and functional studies suggested that the emergence of the Omicron variants can be determined by multiple fitness trade-offs including the immune escape, binding affinity for ACE2, conformational plasticity, protein stability and allosteric modulation. In this study, we systematically characterize conformational dynamics, structural stability and binding affinities of the SARS-CoV-2 Spike Omicron complexes with the host receptor ACE2 for BA.2, BA.2.75, XBB.1 and XBB.1.5 variants. We combined multiscale molecular simulations and dynamic analysis of allosteric interactions together with the ensemble-based mutational scanning of the protein residues and network modeling of epistatic interactions. This multifaceted computational study characterized molecular mechanisms and identified energetic hotspots that can mediate the predicted increased stability and the enhanced binding affinity of the BA.2.75 and XBB.1.5 complexes. The results suggested a mechanism driven by the stability hotspots and a spatially localized group of the Omicron binding affinity centers, while allowing for functionally beneficial neutral Omicron mutations in other binding interface positions. A network-based community model for the analysis of epistatic contributions in the Omicron complexes is proposed revealing the key role of the binding hotspots R498 and Y501 in mediating community-based epistatic couplings with other Omicron sites and allowing for compensatory dynamics and binding energetic changes. The results also showed that mutations in the convergent evolutionary hotspot F486 can modulate not only local interactions but also rewire the global network of local communities in this region allowing the F486P mutation to restore both the stability and binding affinity of the XBB.1.5 variant which may explain the growth advantages over the XBB.1 variant. The results of this study are consistent with a broad range of functional studies rationalizing functional roles of the Omicron mutation sites that form a coordinated network of hotspots enabling a balance of multiple fitness tradeoffs and shaping up a complex functional landscape of virus transmissibility.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
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19
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Shevchuk O, Palii S, Pak A, Chantada N, Seoane N, Korda M, Campos-Toimil M, Álvarez E. Vessel-on-a-Chip: A Powerful Tool for Investigating Endothelial COVID-19 Fingerprints. Cells 2023; 12:cells12091297. [PMID: 37174696 PMCID: PMC10177552 DOI: 10.3390/cells12091297] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/21/2023] [Accepted: 04/30/2023] [Indexed: 05/15/2023] Open
Abstract
Coronavirus disease (COVID-19) causes various vascular and blood-related reactions, including exacerbated responses. The role of endothelial cells in this acute response is remarkable and may remain important beyond the acute phase. As we move into a post-COVID-19 era (where most people have been or will be infected by the SARS-CoV-2 virus), it is crucial to define the vascular consequences of COVID-19, including the long-term effects on the cardiovascular system. Research is needed to determine whether chronic endothelial dysfunction following COVID-19 could lead to an increased risk of cardiovascular and thrombotic events. Endothelial dysfunction could also serve as a diagnostic and therapeutic target for post-COVID-19. This review covers these topics and examines the potential of emerging vessel-on-a-chip technology to address these needs. Vessel-on-a-chip would allow for the study of COVID-19 pathophysiology in endothelial cells, including the analysis of SARS-CoV-2 interactions with endothelial function, leukocyte recruitment, and platelet activation. "Personalization" could be implemented in the models through induced pluripotent stem cells, patient-specific characteristics, or genetic modified cells. Adaptation for massive testing under standardized protocols is now possible, so the chips could be incorporated for the personalized follow-up of the disease or its sequalae (long COVID) and for the research of new drugs against COVID-19.
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Affiliation(s)
- Oksana Shevchuk
- Department of Pharmacology and Clinical Pharmacology, I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine
| | - Svitlana Palii
- Department of Pharmacology and Clinical Pharmacology, I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine
| | - Anastasiia Pak
- Department of Medical Biochemistry, I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine
| | - Nuria Chantada
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Nuria Seoane
- Physiology and Pharmacology of Chronic Diseases (FIFAEC) Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Mykhaylo Korda
- Department of Medical Biochemistry, I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine
| | - Manuel Campos-Toimil
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Physiology and Pharmacology of Chronic Diseases (FIFAEC) Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Ezequiel Álvarez
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Travesía da Choupana s/n, 15706 Santiago de Compostela, Spain
- CIBERCV, Institute of Health Carlos III, 28220 Madrid, Spain
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In Silico Binding of 2-Aminocyclobutanones to SARS-CoV-2 Nsp13 Helicase and Demonstration of Antiviral Activity. Int J Mol Sci 2023; 24:ijms24065120. [PMID: 36982188 PMCID: PMC10049026 DOI: 10.3390/ijms24065120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/10/2023] Open
Abstract
The landscape of viral strains and lineages of SARS-CoV-2 keeps changing and is currently dominated by Delta and Omicron variants. Members of the latest Omicron variants, including BA.1, are showing a high level of immune evasion, and Omicron has become a prominent variant circulating globally. In our search for versatile medicinal chemistry scaffolds, we prepared a library of substituted ɑ-aminocyclobutanones from an ɑ-aminocyclobutanone synthon (11). We performed an in silico screen of this actual chemical library as well as other virtual 2-aminocyclobutanone analogs against seven SARS-CoV-2 nonstructural proteins to identify potential drug leads against SARS-CoV-2, and more broadly against coronavirus antiviral targets. Several of these analogs were initially identified as in silico hits against SARS-CoV-2 nonstructural protein 13 (Nsp13) helicase through molecular docking and dynamics simulations. Antiviral activity of the original hits as well as ɑ-aminocyclobutanone analogs that were predicted to bind more tightly to SARS-CoV-2 Nsp13 helicase are reported. We now report cyclobutanone derivatives that exhibit anti-SARS-CoV-2 activity. Furthermore, the Nsp13 helicase enzyme has been the target of relatively few target-based drug discovery efforts, in part due to a very late release of a high-resolution structure accompanied by a limited understanding of its protein biochemistry. In general, antiviral agents initially efficacious against wild-type SARS-CoV-2 strains have lower activities against variants due to heavy viral loads and greater turnover rates, but the inhibitors we are reporting have higher activities against the later variants than the wild-type (10–20X). We speculate this could be due to Nsp13 helicase being a critical bottleneck in faster replication rates of the new variants, so targeting this enzyme affects these variants to an even greater extent. This work calls attention to cyclobutanones as a useful medicinal chemistry scaffold, and the need for additional focus on the discovery of Nsp13 helicase inhibitors to combat the aggressive and immune-evading variants of concern (VOCs).
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