1
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Khairnar K, Tomar SS. COVID-19 genome surveillance: A geographical landscape and mutational mapping of SARS-CoV-2 variants in central India over two years. Virus Res 2024; 344:199365. [PMID: 38527669 PMCID: PMC10998191 DOI: 10.1016/j.virusres.2024.199365] [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: 03/28/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 03/27/2024]
Abstract
Reading the viral genome through whole genome sequencing (WGS) enables the detection of changes in the viral genome. The rapid changes in the SARS-CoV-2 viral genome may cause immune escape leading to an increase in the pathogenicity or infectivity. Monitoring mutations through genomic surveillance helps understand the amino acid changes resulting from the mutation. These amino acid changes, especially in the spike glycoprotein, may have implications on the pathogenicity of the virus by rendering it immune-escape. The region of Vidarbha in Maharashtra represents 31.6 % of the state's total area. It holds 21.3 % of the total population. In total, 7457 SARS-CoV-2 positive samples belonging to 16 Indian States were included in the study, out of which 3002 samples passed the sequencing quality control criteria. The metadata of 7457 SARS-CoV-2 positive samples included in the study was sourced from the Integrated Health Information Platform (IHIP). The metadata of 3002 sequenced samples, including the FASTA sequence, was submitted to the Global Initiative on Sharing Avian Influenza Data (GISAID) and the Indian biological data centre (IBDC). This study identified 104 different SARS-CoV-2 pango-lineages classified into 19 clades. We have also analysed the mutation profiles of the variants found in the study, which showed eight mutations of interest, including L18F, K417N, K417T, L452R, S477N, N501Y, P681H, P681R, and mutation of concern E484K in the spike glycoprotein region. The study was from November 2020 to December 2022, making this study the most comprehensive genomic surveillance of SARS-CoV-2 conducted for the region.
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Affiliation(s)
- Krishna Khairnar
- Environmental Epidemiology & Pandemic Management (EE&PM), Council of Scientific and Industrial Research-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, India.
| | - Siddharth Singh Tomar
- Environmental Epidemiology & Pandemic Management (EE&PM), Council of Scientific and Industrial Research-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, India
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2
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Le Pen J, Rice CM. The antiviral state of the cell: lessons from SARS-CoV-2. Curr Opin Immunol 2024; 87:102426. [PMID: 38795501 PMCID: PMC11260430 DOI: 10.1016/j.coi.2024.102426] [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: 06/16/2023] [Revised: 02/20/2024] [Accepted: 05/06/2024] [Indexed: 05/28/2024]
Abstract
In this review, we provide an overview of the intricate host-virus interactions that have emerged from the study of SARS-CoV-2 infection. We focus on the antiviral mechanisms of interferon-stimulated genes (ISGs) and their modulation of viral entry, replication, and release. We explore the role of a selection ISGs, including BST2, CD74, CH25H, DAXX, IFI6, IFITM1-3, LY6E, NCOA7, PLSCR1, OAS1, RTP4, and ZC3HAV1/ZAP, in restricting SARS-CoV-2 infection and discuss the virus's countermeasures. By synthesizing the latest research on SARS-CoV-2 and host antiviral responses, this review aims to provide a deeper understanding of the antiviral state of the cell under SARS-CoV-2 and other viral infections, offering insights for the development of novel antiviral strategies and therapeutics.
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Affiliation(s)
- Jérémie Le Pen
- The Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.
| | - Charles M Rice
- The Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
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3
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Zhang Q, Pavlinov I, Ye Y, Zheng W. Therapeutic development targeting host heparan sulfate proteoglycan in SARS-CoV-2 infection. Front Med (Lausanne) 2024; 11:1364657. [PMID: 38618194 PMCID: PMC11014733 DOI: 10.3389/fmed.2024.1364657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024] Open
Abstract
The global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an urgent need for effective therapeutic options. SARS-CoV-2 is a novel coronavirus responsible for the COVID-19 pandemic that has resulted in significant morbidity and mortality worldwide. The virus is known to enter host cells by binding to the angiotensin-converting enzyme 2 (ACE2) receptor, and emerging evidence suggests that heparan sulfate proteoglycans (HSPGs) play a crucial role in facilitating this process. HSPGs are abundant cell surface proteoglycan present in many tissues, including the lung, and have been shown to interact directly with the spike protein of SARS-CoV-2. This review aims to summarize the current understanding of the role of HSPGs in SARS-CoV-2 infection and the potential of developing new therapies targeting HSPGs.
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Affiliation(s)
- Qi Zhang
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Ivan Pavlinov
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Wei Zheng
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
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4
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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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5
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Korosec CS, Wahl LM, Heffernan JM. Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted from symptomatic infections? Virus Evol 2024; 10:veae006. [PMID: 38425472 PMCID: PMC10904108 DOI: 10.1093/ve/veae006] [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: 11/15/2023] [Revised: 12/20/2023] [Accepted: 01/12/2024] [Indexed: 03/02/2024] Open
Abstract
Despite a relatively low mutation rate, the large number of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has allowed for substantial genetic change, leading to a multitude of emerging variants. Using a recently determined mutation rate (per site replication), as well as within-host parameter estimates for symptomatic SARS-CoV-2 infection, we apply a stochastic transmission-bottleneck model to describe the survival probability of de novo SARS-CoV-2 mutations as a function of bottleneck size and selection coefficient. For narrow bottlenecks, we find that mutations affecting per-target-cell attachment rate (with phenotypes associated with fusogenicity and ACE2 binding) have similar transmission probabilities to mutations affecting viral load clearance (with phenotypes associated with humoral evasion). We further find that mutations affecting the eclipse rate (with phenotypes associated with reorganization of cellular metabolic processes and synthesis of viral budding precursor material) are highly favoured relative to all other traits examined. We find that mutations leading to reduced removal rates of infected cells (with phenotypes associated with innate immune evasion) have limited transmission advantage relative to mutations leading to humoral evasion. Predicted transmission probabilities, however, for mutations affecting innate immune evasion are more consistent with the range of clinically estimated household transmission probabilities for de novo mutations. This result suggests that although mutations affecting humoral evasion are more easily transmitted when they occur, mutations affecting innate immune evasion may occur more readily. We examine our predictions in the context of a number of previously characterized mutations in circulating strains of SARS-CoV-2. Our work offers both a null model for SARS-CoV-2 mutation rates and predicts which aspects of viral life history are most likely to successfully evolve, despite low mutation rates and repeated transmission bottlenecks.
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Affiliation(s)
- Chapin S Korosec
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
- Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
| | - Lindi M Wahl
- Applied Mathematics, Western University, 1151 Richmond St, London, ON N6A 5B7, Canada
| | - Jane M Heffernan
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
- Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
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6
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Marceau T, Braibant M. Role of Viral Envelope Proteins in Determining Susceptibility of Viruses to IFITM Proteins. Viruses 2024; 16:254. [PMID: 38400030 PMCID: PMC10892237 DOI: 10.3390/v16020254] [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: 01/04/2024] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Interferon-induced transmembrane proteins (IFITMs) are a family of proteins which inhibit infections of various enveloped viruses. While their general mechanism of inhibition seems to be non-specific, involving the tightening of membrane structures to prevent fusion between the viral envelope and cell membrane, numerous studies have underscored the importance of viral envelope proteins in determining the susceptibility of viruses to IFITMs. Mutations in envelope proteins may lead to viral escape from direct interaction with IFITM proteins or result in indirect resistance by modifying the viral entry pathway, allowing the virus to modulate its exposure to IFITMs. In a broader context, the nature of viral envelope proteins and their interaction with IFITMs can play a crucial role in the context of adaptive immunity, leading to viral envelope proteins that are more susceptible to antibody neutralization. The precise mechanisms underlying these observations remain unclear, and further studies in this field could contribute to a better understanding of how IFITMs control viral infections.
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7
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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: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [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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8
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Bolland W, Michel V, Planas D, Hubert M, Staropoli I, Guivel-Benhassine F, Porrot F, N'Debi M, Rodriguez C, Fourati S, Prot M, Planchais C, Hocqueloux L, Simon-Lorière E, Mouquet H, Prazuck T, Pawlotsky JM, Bruel T, Schwartz O, Buchrieser J. High fusion and cytopathy of SARS-CoV-2 variant B.1.640.1. J Virol 2024; 98:e0135123. [PMID: 38088562 PMCID: PMC10805008 DOI: 10.1128/jvi.01351-23] [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: 08/31/2023] [Accepted: 11/28/2023] [Indexed: 01/24/2024] Open
Abstract
SARS-CoV-2 variants with undetermined properties have emerged intermittently throughout the COVID-19 pandemic. Some variants possess unique phenotypes and mutations which allow further characterization of viral evolution and Spike functions. Around 1,100 cases of the B.1.640.1 variant were reported in Africa and Europe between 2021 and 2022, before the expansion of Omicron. Here, we analyzed the biological properties of a B.1.640.1 isolate and its Spike. Compared to the ancestral Spike, B.1.640.1 carried 14 amino acid substitutions and deletions. B.1.640.1 escaped binding by some anti-N-terminal domain and anti-receptor-binding domain monoclonal antibodies, and neutralization by sera from convalescent and vaccinated individuals. In cell lines, infection generated large syncytia and a high cytopathic effect. In primary airway cells, B.1.640.1 replicated less than Omicron BA.1 and triggered more syncytia and cell death than other variants. The B.1.640.1 Spike was highly fusogenic when expressed alone. This was mediated by two poorly characterized and infrequent mutations located in the Spike S2 domain, T859N and D936H. Altogether, our results highlight the cytopathy of a hyper-fusogenic SARS-CoV-2 variant, supplanted upon the emergence of Omicron BA.1. (This study has been registered at ClinicalTrials.gov under registration no. NCT04750720.)IMPORTANCEOur results highlight the plasticity of SARS-CoV-2 Spike to generate highly fusogenic and cytopathic strains with the causative mutations being uncharacterized in previous variants. We describe mechanisms regulating the formation of syncytia and the subsequent consequences in a primary culture model, which are poorly understood.
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Affiliation(s)
- William Bolland
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
- Université Paris Cité, Paris, France
| | - Vincent Michel
- Pathogenesis of Vascular Infections Unit, Institut Pasteur, INSERM, Paris, France
| | - Delphine Planas
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
- Vaccine Research Institute, Créteil, France
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Isabelle Staropoli
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | | | - Françoise Porrot
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Mélissa N'Debi
- Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
- Institut Mondor de Recherche Biomédicale, INSERM U955, Créteil, France
| | - Christophe Rodriguez
- Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
- Institut Mondor de Recherche Biomédicale, INSERM U955, Créteil, France
| | - Slim Fourati
- Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
- Institut Mondor de Recherche Biomédicale, INSERM U955, Créteil, France
| | - Matthieu Prot
- Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - Cyril Planchais
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, Paris, France
| | | | - Etienne Simon-Lorière
- Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - Hugo Mouquet
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, Paris, France
| | | | - Jean-Michel Pawlotsky
- Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
- Institut Mondor de Recherche Biomédicale, INSERM U955, Créteil, France
| | - Timothée Bruel
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
- Vaccine Research Institute, Créteil, France
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
- Vaccine Research Institute, Créteil, France
| | - Julian Buchrieser
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
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9
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Ko SH, Radecki P, Belinky F, Bhiman JN, Meiring S, Kleynhans J, Amoako D, Guerra Canedo V, Lucas M, Kekana D, Martinson N, Lebina L, Everatt J, Tempia S, Bylund T, Rawi R, Kwong PD, Wolter N, von Gottberg A, Cohen C, Boritz EA. Rapid Emergence and Evolution of SARS-CoV-2 Variants in Advanced HIV Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574420. [PMID: 38313289 PMCID: PMC10836083 DOI: 10.1101/2024.01.05.574420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Previous studies have linked the evolution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic variants to persistent infections in people with immunocompromising conditions1-4, but the evolutionary processes underlying these observations are incompletely understood. Here we used high-throughput, single-genome amplification and sequencing (HT-SGS) to obtain up to ~103 SARS-CoV-2 spike gene sequences in each of 184 respiratory samples from 22 people with HIV (PWH) and 25 people without HIV (PWOH). Twelve of 22 PWH had advanced HIV infection, defined by peripheral blood CD4 T cell counts (i.e., CD4 counts) <200 cells/μL. In PWOH and PWH with CD4 counts ≥200 cells/μL, most single-genome spike sequences in each person matched one haplotype that predominated throughout the infection. By contrast, people with advanced HIV showed elevated intra-host spike diversity with a median of 46 haplotypes per person (IQR 14-114). Higher intra-host spike diversity immediately after COVID-19 symptom onset predicted longer SARS-CoV-2 RNA shedding among PWH, and intra-host spike diversity at this timepoint was significantly higher in people with advanced HIV than in PWOH. Composition of spike sequence populations in people with advanced HIV fluctuated rapidly over time, with founder sequences often replaced by groups of new haplotypes. These population-level changes were associated with a high total burden of intra-host mutations and positive selection at functionally important residues. In several cases, delayed emergence of detectable serum binding to spike was associated with positive selection for presumptive antibody-escape mutations. Taken together, our findings show remarkable intra-host genetic diversity of SARS-CoV-2 in advanced HIV infection and suggest that adaptive intra-host SARS-CoV-2 evolution in this setting may contribute to the emergence of new variants of concern (VOCs).
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Affiliation(s)
- Sung Hee Ko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pierce Radecki
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frida Belinky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinal N. Bhiman
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- SAMRC Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan Meiring
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jackie Kleynhans
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Daniel Amoako
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Integrative Biology and Bioinformatics, College of Biological Sciences, University of Guelph, Ontario, Canada
| | - Vanessa Guerra Canedo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Margaret Lucas
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dikeledi Kekana
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Neil Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University, Center for TB Research, Baltimore, MD 21218, USA
| | - Limakatso Lebina
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Josie Everatt
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stefano Tempia
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole Wolter
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Eli A. Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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10
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Li J, Zhang K, Lin G, Li J. CRISPR-Cas system: A promising tool for rapid detection of SARS-CoV-2 variants. J Med Virol 2024; 96:e29356. [PMID: 38180237 DOI: 10.1002/jmv.29356] [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: 12/05/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024]
Abstract
COVID-19, caused by SARS-CoV-2, remains a global health crisis. The emergence of multiple variants with enhanced characteristics necessitates their detection and monitoring. Genome sequencing, the gold standard, faces implementation challenges due to complexity, cost, and limited throughput. The CRISPR-Cas system offers promising potential for rapid variant detection, with advantages such as speed, sensitivity, specificity, and programmability. This review provides an in-depth examination of the applications of CRISPR-Cas in mutation detection specifically for SARS-CoV-2. It begins by introducing SARS-CoV-2 and existing variant detection platforms. The principles of the CRISPR-Cas system are then clarified, followed by an exploration of three CRISPR-Cas-based mutation detection platforms, which are evaluated from different perspectives. The review discusses strategies for mutation site selection and the utilization of CRISPR-Cas, offering valuable insights for the development of mutation detection methods. Furthermore, a critical analysis of the clinical applications, advantages, disadvantages, challenges, and prospects of the CRISPR-Cas system is provided.
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Affiliation(s)
- Jing Li
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
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11
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Liu Y, Ye Q. The Key Site Variation and Immune Challenges in SARS-CoV-2 Evolution. Vaccines (Basel) 2023; 11:1472. [PMID: 37766148 PMCID: PMC10537874 DOI: 10.3390/vaccines11091472] [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: 08/07/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a worldwide public health and economic threat, and virus variation amplifies the difficulty in epidemic prevention and control. The structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been studied extensively and is now well defined. The S protein is the most distinguishing feature in terms of infection and immunity, mediating virus entrance and inducing neutralizing antibodies. The S protein and its essential components are also the most promising target to develop vaccines and antibody-based drugs. Therefore, the key site mutation in the S gene is of high interest. Among them, RBD, NTD, and furin cleavage sites are the most mutable regions with the most mutation sites and the most serious consequences for SARS-CoV-2 biological characteristics, including infectivity, pathogenicity, natural immunity, vaccine efficacy, and antibody therapeutics. We are also aware that this outbreak may not be the last. Therefore, in this narrative review, we summarized viral variation and prevalence condition, discussed specific amino acid replacement and associated immune challenges and attempted to sum up some prevention and control strategies by reviewing the literature on previously published research about SARS-CoV-2 variation to assist in clarifying the mutation pathway and consequences of SARS-CoV-2 for developing countermeasures against such viruses as soon as possible.
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Affiliation(s)
| | - Qing Ye
- Department of ‘A’, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China;
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12
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Huang SH, Chen YT, Lin XY, Ly YY, Lien ST, Chen PH, Wang CT, Wu SC, Chen CC, Lin CY. In silico prediction of immune-escaping hot spots for future COVID-19 vaccine design. Sci Rep 2023; 13:13468. [PMID: 37596329 PMCID: PMC10439115 DOI: 10.1038/s41598-023-40741-1] [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: 02/08/2023] [Accepted: 08/16/2023] [Indexed: 08/20/2023] Open
Abstract
The COVID-19 pandemic has had a widespread impact on a global scale, and the evolution of considerable dominants has already taken place. Some variants contained certain key mutations located on the receptor binding domain (RBD) of spike protein, such as E484K and N501Y. It is increasingly worrying that these variants could impair the efficacy of current vaccines or therapies. Therefore, analyzing and predicting the high-risk mutations of SARS-CoV-2 spike glycoprotein is crucial to design future vaccines against the different variants. In this work, we proposed an in silico approach, immune-escaping score (IES), to predict high-risk immune-escaping hot spots on the receptor-binding domain (RBD), implemented through integrated delta binding free energy measured by computational mutagenesis of spike-antibody complexes and mutation frequency calculated from viral genome sequencing data. We identified 23 potentially immune-escaping mutations on the RBD by using IES, nine of which occurred in omicron variants (R346K, K417N, N440K, L452Q, L452R, S477N, T478K, F490S, and N501Y), despite our dataset being curated before the omicron first appeared. The highest immune-escaping score (IES = 1) was found for E484K, which agrees with recent studies stating that the mutation significantly reduced the efficacy of neutralization antibodies. Furthermore, our predicted delta binding free energy and IES show a high correlation with high-throughput deep mutational scanning data (Pearson's r = 0.70) and experimentally measured neutralization titers data (mean Pearson's r = -0.80). In summary, our work presents a new method to identify the potentially immune-escaping mutations on the RBD and provides valuable insights into future COVID-19 vaccine design.
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Affiliation(s)
| | | | | | - Yi-Yi Ly
- Graphen Inc., New York, NY, 10110, USA
| | | | | | | | - Suh-Chin Wu
- Adimmune Corp., Taichung City, 427003, Taiwan
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13
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Castelán-Sánchez HG, Delaye L, Inward RPD, Dellicour S, Gutierrez B, Martinez de la Vina N, Boukadida C, Pybus OG, de Anda Jáuregui G, Guzmán P, Flores-Garrido M, Fontanelli Ó, Hernández Rosales M, Meneses A, Olmedo-Alvarez G, Herrera-Estrella AH, Sánchez-Flores A, Muñoz-Medina JE, Comas-García A, Gómez-Gil B, Zárate S, Taboada B, López S, Arias CF, Kraemer MUG, Lazcano A, Escalera Zamudio M. Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico. eLife 2023; 12:e82069. [PMID: 37498057 PMCID: PMC10431917 DOI: 10.7554/elife.82069] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 07/23/2023] [Indexed: 07/28/2023] Open
Abstract
Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that circulated during the first year of local transmission. For most lineages, peaks in sampling frequencies coincided with different epidemiological waves of infection in Mexico. Lineages B.1.1.222 and B.1.1.519 exhibited similar dynamics, constituting clades that likely originated in Mexico and persisted for >12 months. Lineages B.1.1.7, P.1 and B.1.617.2 also displayed similar dynamics, characterized by multiple introduction events leading to a few successful extended local transmission chains that persisted for several months. For the largest B.1.617.2 clades, we further explored viral lineage movements across Mexico. Many clades were located within the south region of the country, suggesting that this area played a key role in the spread of SARS-CoV-2 in Mexico.
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Affiliation(s)
- Hugo G Castelán-Sánchez
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Programa de Investigadoras e Investigadores por México, Consejo Nacional de Ciencia y TecnologíaMexico CityMexico
| | - Luis Delaye
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Ingeniería Genética, CINVESTAV-Unidad IrapuatoGuanajuatoMexico
| | - Rhys PD Inward
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de BruxellesBruxellesBelgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU LeuvenLeuvenBelgium
| | - Bernardo Gutierrez
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | | | - Celia Boukadida
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades RespiratoriasMexico CityMexico
| | - Oliver G Pybus
- Department of Biology, University of OxfordOxfordUnited Kingdom
- Department of Pathobiology, Royal Veterinary CollegeLondonUnited Kingdom
| | - Guillermo de Anda Jáuregui
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Programa de Investigadoras e Investigadores por México, Consejo Nacional de Ciencia y TecnologíaMexico CityMexico
- Instituto Nacional de Medicina GenómicaMexico CityMexico
| | | | - Marisol Flores-Garrido
- Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de MéxicoMexico CityMexico
- Departamento de Ciencias de la Computación, CINVESTAV-IPNMexico CityMexico
| | - Óscar Fontanelli
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Ingeniería Genética, CINVESTAV-Unidad IrapuatoGuanajuatoMexico
| | - Maribel Hernández Rosales
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Ingeniería Genética, CINVESTAV-Unidad IrapuatoGuanajuatoMexico
| | - Amilcar Meneses
- Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de MéxicoMexico CityMexico
- Departamento de Ciencias de la Computación, CINVESTAV-IPNMexico CityMexico
| | - Gabriela Olmedo-Alvarez
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Ingeniería Genética, CINVESTAV-Unidad IrapuatoGuanajuatoMexico
| | - Alfredo Heriberto Herrera-Estrella
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Laboratorio de expresión génica y desarrollo en hongos, CINVESTAV-Unidad IrapuatoIrapuatoMexico
| | - Alejandro Sánchez-Flores
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de MéxicoChamilpaMexico
| | - José Esteban Muñoz-Medina
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro SocialMexico CityMexico
| | - Andreu Comas-García
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Facultad de Medicina y Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis PotosíSan Luis PotosíMexico
| | - Bruno Gómez-Gil
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Centro de Investigación en Alimentación y Desarrollo-CIAD, Unidad Regional Mazatlán en Acuicultura y Manejo AmbientalSinaloaMexico
| | - Selene Zárate
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de MéxicoMexico CityMexico
| | - Blanca Taboada
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Genética del Desarrollo y Fisiología Molecular, Universidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Susana López
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Genética del Desarrollo y Fisiología Molecular, Universidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Carlos F Arias
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Genética del Desarrollo y Fisiología Molecular, Universidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Moritz UG Kraemer
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Antonio Lazcano
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Facultad de Ciencias, Universidad Nacional Autónoma de MéxicMexico CityMexico
| | - Marina Escalera Zamudio
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Department of Biology, University of OxfordOxfordUnited Kingdom
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14
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Fang L, Xu J, Zhao Y, Fan J, Shen J, Liu W, Cao G. The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2. Front Microbiol 2023; 14:1228128. [PMID: 37560529 PMCID: PMC10409611 DOI: 10.3389/fmicb.2023.1228128] [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: 05/24/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Over three years' pandemic of 2019 novel coronavirus disease (COVID-19), multiple variants and novel subvariants have emerged successively, outcompeted earlier variants and become predominant. The sequential emergence of variants reflects the evolutionary process of mutation-selection-adaption of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Amino acid substitution/insertion/deletion in the spike protein causes altered viral antigenicity, transmissibility, and pathogenicity of SARS-CoV-2. Early in the pandemic, D614G mutation conferred virus with advantages over previous variants and increased transmissibility, and it also laid a conservative background for subsequent substantial mutations. The role of genomic recombination in the evolution of SARS-CoV-2 raised increasing concern with the occurrence of novel recombinants such as Deltacron, XBB.1.5, XBB.1.9.1, and XBB.1.16 in the late phase of pandemic. Co-circulation of different variants and co-infection in immunocompromised patients accelerate the emergence of recombinants. Surveillance for SARS-CoV-2 genomic variations, particularly spike protein mutation and recombination, is essential to identify ongoing changes in the viral genome and antigenic epitopes and thus leads to the development of new vaccine strategies and interventions.
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Affiliation(s)
- Letian Fang
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jie Xu
- Department of Foreign Languages, International Exchange Center for Military Medicine, Second Military Medical University, Shanghai, China
| | - Yue Zhao
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Junyan Fan
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jiaying Shen
- School of Medicine, Tongji University, Shanghai, China
| | - Wenbin Liu
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Guangwen Cao
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
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15
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Ha YR, Kim HJ, Park JS, Chung YS. Genomic surveillance of genes encoding the SARS-CoV-2 spike protein to monitor for emerging variants on Jeju Island, Republic of Korea. Front Microbiol 2023; 14:1170766. [PMID: 37533831 PMCID: PMC10390832 DOI: 10.3389/fmicb.2023.1170766] [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: 02/21/2023] [Accepted: 07/03/2023] [Indexed: 08/04/2023] Open
Abstract
Introduction The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been fueled by new variants emerging from circulating strains. Here, we report results from a genomic surveillance study of SARS-CoV-2 on Jeju Island, Republic of Korea, from February 2021 to September 2022. Methods A total of 3,585 SARS-CoV-2 positive samples were analyzed by Sanger sequencing of the gene encoding the spike protein before performing phylogenetic analyses. Results We found that the Alpha variant (B.1.1.7) was dominant in May 2021 before being replaced by the Delta variant (B.1.617.2) in July 2021, which was dominant until December 2021 before being replaced by the Omicron variant. Mutations in the spike protein, including N440K and G446S, have been proposed to contribute to immune evasion, accelerating the spread of Omicron variants. Discussion Our results from Juju Island, Republic of Korea, are consistent with and contribute to global surveillance efforts crucial for identifying new variants of concern of SARS-CoV-2 and for monitoring the transmission dynamics and characteristics of known strains.
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Affiliation(s)
- Young-Ran Ha
- Jeju Branch Office, Honam Regional Center for Disease Control and Prevention, Korea Disease Control and Prevention Agency, Jeju, Republic of Korea
| | - Hyun-Jeong Kim
- Jeju Branch Office, Honam Regional Center for Disease Control and Prevention, Korea Disease Control and Prevention Agency, Jeju, Republic of Korea
| | - Jae-Sung Park
- Jeju National Quarantine Station, Korea Disease Control and Prevention Agency, Jeju, Republic of Korea
| | - Yoon-Seok Chung
- Division of Infectious Disease Diagnosis Control, Honam Regional Center for Disease Control and Prevention, Korea Disease Control and Prevention Agency, Gwangju, Republic of Korea
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16
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De La Cruz-Montoya AH, Díaz Velásquez CE, Martínez-Gregorio H, Ruiz-De La Cruz M, Bustos-Arriaga J, Castro-Jiménez TK, Olguín-Hernández JE, Rodríguez-Sosa M, Terrazas-Valdes LI, Jiménez-Alvarez LA, Regino-Zamarripa NE, Ramírez-Martínez G, Cruz-Lagunas A, Peralta-Arrieta I, Armas-López L, Contreras-Garza BM, Palma-Cortés G, Cabello-Gutierrez C, Báez-Saldaña R, Zúñiga J, Ávila-Moreno F, Vaca-Paniagua F. Molecular transition of SARS-CoV-2 from critical patients during the first year of the COVID-19 pandemic in Mexico City. Front Cell Infect Microbiol 2023; 13:1155938. [PMID: 37260697 PMCID: PMC10227454 DOI: 10.3389/fcimb.2023.1155938] [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: 02/01/2023] [Accepted: 05/02/2023] [Indexed: 06/02/2023] Open
Abstract
Background The SARS-CoV-2 virus has caused unprecedented mortality since its emergence in late 2019. The continuous evolution of the viral genome through the concerted action of mutational forces has produced distinct variants that became dominant, challenging human immunity and vaccine development. Aim and methods In this work, through an integrative genomic approach, we describe the molecular transition of SARS-CoV-2 by analyzing the viral whole genome sequences from 50 critical COVID-19 patients recruited during the first year of the pandemic in Mexico City. Results Our results revealed differential levels of the evolutionary forces across the genome and specific mutational processes that have shaped the first two epidemiological waves of the pandemic in Mexico. Through phylogenetic analyses, we observed a genomic transition in the circulating SARS-CoV-2 genomes from several lineages prevalent in the first wave to a dominance of the B.1.1.519 variant (defined by T478K, P681H, and T732A mutations in the spike protein) in the second wave. Conclusion This work contributes to a better understanding of the evolutionary dynamics and selective pressures that act at the genomic level, the prediction of more accurate variants of clinical significance, and a better comprehension of the molecular mechanisms driving the evolution of SARS-CoV-2 to improve vaccine and drug development.
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Affiliation(s)
- Aldo Hugo De La Cruz-Montoya
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Mexico
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Clara Estela Díaz Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Mexico
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Héctor Martínez-Gregorio
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Mexico
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Miguel Ruiz-De La Cruz
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Mexico
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Avenida Instituto Politécnico Nacional, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, Ciudad de México, Mexico
| | - José Bustos-Arriaga
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Tannya Karen Castro-Jiménez
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Jonadab Efraín Olguín-Hernández
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Mexico
| | - Miriam Rodríguez-Sosa
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Luis Ignacio Terrazas-Valdes
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Mexico
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Luis Armando Jiménez-Alvarez
- Laboratorio de Inmunobiología y Genética y Departamento de Virología, Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
| | - Nora Elemi Regino-Zamarripa
- Laboratorio de Inmunobiología y Genética y Departamento de Virología, Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ciudad de México, Mexico
| | - Gustavo Ramírez-Martínez
- Laboratorio de Inmunobiología y Genética y Departamento de Virología, Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
| | - Alfredo Cruz-Lagunas
- Laboratorio de Inmunobiología y Genética y Departamento de Virología, Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
| | - Irlanda Peralta-Arrieta
- Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
| | - Leonel Armas-López
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | | | - Gabriel Palma-Cortés
- Department of Research in Virology and Mycology, Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
| | - Carlos Cabello-Gutierrez
- Department of Research in Virology and Mycology, Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
| | - Renata Báez-Saldaña
- Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
| | - Joaquín Zúñiga
- Laboratorio de Inmunobiología y Genética y Departamento de Virología, Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ciudad de México, Mexico
- Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
| | - Federico Ávila-Moreno
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
- Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
- Laboratorio 12 de Enfermedades Pulmonares y Epigenómica del Cáncer, Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Felipe Vaca-Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Mexico
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México, Mexico
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17
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Kenney AD, Zani A, Kawahara J, Eddy AC, Wang X, Mahesh KC, Lu M, Thomas J, Kohlmeier JE, Suthar MS, Hemann EA, Li J, Peeples ME, Hall‐Stoodley L, Forero A, Cai C, Ma J, Yount JS. Interferon-induced transmembrane protein 3 (IFITM3) limits lethality of SARS-CoV-2 in mice. EMBO Rep 2023; 24:e56660. [PMID: 36880581 PMCID: PMC10074051 DOI: 10.15252/embr.202256660] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/07/2023] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
Interferon-induced transmembrane protein 3 (IFITM3) is an antiviral protein that alters cell membranes to block fusion of viruses. Conflicting reports identified opposing effects of IFITM3 on SARS-CoV-2 infection of cells, and its impact on viral pathogenesis in vivo remains unclear. Here, we show that IFITM3 knockout (KO) mice infected with SARS-CoV-2 experience extreme weight loss and lethality compared to mild infection in wild-type (WT) mice. KO mice have higher lung viral titers and increases in inflammatory cytokine levels, immune cell infiltration, and histopathology. Mechanistically, we observe disseminated viral antigen staining throughout the lung and pulmonary vasculature in KO mice, as well as increased heart infection, indicating that IFITM3 constrains dissemination of SARS-CoV-2. Global transcriptomic analysis of infected lungs shows upregulation of gene signatures associated with interferons, inflammation, and angiogenesis in KO versus WT animals, highlighting changes in lung gene expression programs that precede severe lung pathology and fatality. Our results establish IFITM3 KO mice as a new animal model for studying severe SARS-CoV-2 infection and overall demonstrate that IFITM3 is protective in SARS-CoV-2 infections in vivo.
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Affiliation(s)
- Adam D Kenney
- Department of Microbial Infection and ImmunityThe Ohio State UniversityColumbusOHUSA
- Infectious Diseases InstituteThe Ohio State UniversityColumbusOHUSA
| | - Ashley Zani
- Department of Microbial Infection and ImmunityThe Ohio State UniversityColumbusOHUSA
- Infectious Diseases InstituteThe Ohio State UniversityColumbusOHUSA
| | - Jeffrey Kawahara
- Department of Microbial Infection and ImmunityThe Ohio State UniversityColumbusOHUSA
- Infectious Diseases InstituteThe Ohio State UniversityColumbusOHUSA
| | - Adrian C Eddy
- Department of Microbial Infection and ImmunityThe Ohio State UniversityColumbusOHUSA
- Infectious Diseases InstituteThe Ohio State UniversityColumbusOHUSA
| | | | - KC Mahesh
- Infectious Diseases InstituteThe Ohio State UniversityColumbusOHUSA
- Center for Vaccines and ImmunityAbigail Wexner Research Institute at Nationwide Children's HospitalColumbusOHUSA
| | - Mijia Lu
- Infectious Diseases InstituteThe Ohio State UniversityColumbusOHUSA
- Department of Veterinary BiosciencesThe Ohio State UniversityColumbusOHUSA
| | - Jeronay Thomas
- Department of Microbiology and ImmunologyEmory UniversityAtlantaGAUSA
| | - Jacob E Kohlmeier
- Department of Microbiology and ImmunologyEmory UniversityAtlantaGAUSA
| | - Mehul S Suthar
- Department of Microbiology and ImmunologyEmory UniversityAtlantaGAUSA
- Department of PediatricsEmory University School of MedicineAtlantaGAUSA
- Emory Vaccine Center, Yerkes National Primate Research CenterEmory UniversityAtlantaGAUSA
| | - Emily A Hemann
- Department of Microbial Infection and ImmunityThe Ohio State UniversityColumbusOHUSA
- Infectious Diseases InstituteThe Ohio State UniversityColumbusOHUSA
| | - Jianrong Li
- Infectious Diseases InstituteThe Ohio State UniversityColumbusOHUSA
- Department of Veterinary BiosciencesThe Ohio State UniversityColumbusOHUSA
| | - Mark E Peeples
- Infectious Diseases InstituteThe Ohio State UniversityColumbusOHUSA
- Center for Vaccines and ImmunityAbigail Wexner Research Institute at Nationwide Children's HospitalColumbusOHUSA
- Department of PediatricsThe Ohio State UniversityColumbusOHUSA
| | - Luanne Hall‐Stoodley
- Department of Microbial Infection and ImmunityThe Ohio State UniversityColumbusOHUSA
- Infectious Diseases InstituteThe Ohio State UniversityColumbusOHUSA
| | - Adriana Forero
- Department of Microbial Infection and ImmunityThe Ohio State UniversityColumbusOHUSA
- Infectious Diseases InstituteThe Ohio State UniversityColumbusOHUSA
| | - Chuanxi Cai
- Department of SurgeryThe Ohio State UniversityColumbusOHUSA
| | - Jianjie Ma
- Department of SurgeryThe Ohio State UniversityColumbusOHUSA
| | - Jacob S Yount
- Department of Microbial Infection and ImmunityThe Ohio State UniversityColumbusOHUSA
- Infectious Diseases InstituteThe Ohio State UniversityColumbusOHUSA
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18
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González-Vázquez LD, Arenas M. Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic. Genes (Basel) 2023; 14:407. [PMID: 36833334 PMCID: PMC9956206 DOI: 10.3390/genes14020407] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) produced diverse molecular variants during its recent expansion in humans that caused different transmissibility and severity of the associated disease as well as resistance to monoclonal antibodies and polyclonal sera, among other treatments. In order to understand the causes and consequences of the observed SARS-CoV-2 molecular diversity, a variety of recent studies investigated the molecular evolution of this virus during its expansion in humans. In general, this virus evolves with a moderate rate of evolution, in the order of 10-3-10-4 substitutions per site and per year, which presents continuous fluctuations over time. Despite its origin being frequently associated with recombination events between related coronaviruses, little evidence of recombination was detected, and it was mostly located in the spike coding region. Molecular adaptation is heterogeneous among SARS-CoV-2 genes. Although most of the genes evolved under purifying selection, several genes showed genetic signatures of diversifying selection, including a number of positively selected sites that affect proteins relevant for the virus replication. Here, we review current knowledge about the molecular evolution of SARS-CoV-2 in humans, including the emergence and establishment of variants of concern. We also clarify relationships between the nomenclatures of SARS-CoV-2 lineages. We conclude that the molecular evolution of this virus should be monitored over time for predicting relevant phenotypic consequences and designing future efficient treatments.
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Affiliation(s)
- Luis Daniel González-Vázquez
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Miguel Arenas
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310 Vigo, Spain
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19
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Abstract
SARS-CoV-2 spike requires proteolytic processing for viral entry. A polybasic furin-cleavage site (FCS) in spike, and evolution toward an optimized FCS by dominant variants of concern (VOCs), are linked to enhanced infectivity and transmission. Here we show interferon-inducible restriction factors Guanylate-binding proteins (GBP) 2 and 5 interfere with furin-mediated spike cleavage and inhibit the infectivity of early-lineage isolates Wuhan-Hu-1 and VIC. By contrast, VOCs Alpha and Delta escape restriction by GBP2/5 that we map to the spike substitution D614G present in these VOCs. Despite inhibition of spike cleavage, these viruses remained sensitive to plasma membrane IFITM1, but not endosomal IFITM2 and 3, consistent with a preference for TMPRSS2-dependent plasma membrane entry. Strikingly, we find that Omicron is unique among VOCs, being sensitive to restriction factors GBP2/5, and also IFITM1, 2, and 3. Using chimeric spike mutants, we map the Omicron phenotype and show that the S1 domain determines Omicron's sensitivity to GBP2/5, whereas the S2' domain determines its sensitivity to endosomal IFITM2/3 and preferential use of TMPRSS2-independent entry. We propose that evolution of SARS-CoV-2 for the D614G substitution has allowed for escape from GBP restriction factors, but the selective pressures on Omicron for spike changes that mediate antibody escape, and altered tropism, have come at the expense of increased sensitivity to innate immune restriction factors that target virus entry.
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20
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Cocherie T, Zafilaza K, Leducq V, Marot S, Calvez V, Marcelin AG, Todesco E. Epidemiology and Characteristics of SARS-CoV-2 Variants of Concern: The Impacts of the Spike Mutations. Microorganisms 2022; 11:30. [PMID: 36677322 PMCID: PMC9866527 DOI: 10.3390/microorganisms11010030] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2 expresses on its surface the Spike protein responsible for binding with the ACE2 receptor and which carries the majority of immunodominant epitopes. Mutations mainly affect this protein and can modify characteristics of the virus, giving each variant a unique profile concerning its transmissibility, virulence, and immune escape. The first lineage selected is the B.1 lineage characterized by the D614G substitution and from which all SARS-CoV-2 variants of concern have emerged. The first three variants of concern Alpha, Beta, and Gamma spread in early 2021: all shared the N501Y substitution. These variants were replaced by the Delta variant in summer 2021, carrying unique mutations like the L452R substitution and associated with higher virulence. It was in turn quickly replaced by the Omicron variant at the end of 2021, which has predominated since then, characterized by its large number of mutations. The successive appearance of variants of concern showed a dynamic evolution of SARS-CoV-2 through the selection and accumulation of mutations. This has not only allowed progressive improvement of the transmissibility of SARS-CoV-2, but has also participated in a better immune escape of the virus. This review brings together acquired knowledge about SARS-CoV-2 variants of concern and the impacts of the Spike mutations.
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Affiliation(s)
| | | | | | | | | | | | - Eve Todesco
- Institut Pierre Louis d’Épidémiologie et de Santé Publique (iPLESP), INSERM, Sorbonne Université, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Virologie, 75013 Paris, France
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