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Xiao B, Wu L, Sun Q, Shu C, Hu S. Dynamic analysis of SARS-CoV-2 evolution based on different countries. Gene 2024; 916:148426. [PMID: 38575101 DOI: 10.1016/j.gene.2024.148426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/18/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Since late 2019, COVID-19 has significantly impacted the world. Understanding the evolution of SARS-CoV-2 is crucial for protecting against future infectious pathogens. In this study, we conducted a comprehensive chronological analysis of SARS-CoV-2 evolution by examining mutation prevalence from the source countries of VOCs: United Kingdom, India, Brazil, South Africa, plus two countries: United States, Russia, utilizing genomic sequences from GISAID. Our methodological approach involved large-scale genomic sequence alignment using MAFFT, Python-based data processing on a high-performance computing platform, and advanced statistical methods the Maximal Information Coefficient (MIC), and also Long Short-Term Memory (LSTM) models for correlation analysis. Our findings elucidate the dynamics of SARS-CoV-2 evolution, highlighting the virus's changing behaviour over various pandemic stages. Key results include the discovery of three temporal mutation patterns-lineage distinct, long-span, and competitive mutations-with varying levels of impact on the virus. Notably, we observed a convergence of advantageous mutations in the spike protein, especially in the later stages of the pandemic, indicating a substantial evolutionary pressure on the virus. One of the most significant revelations is the predominant role of natural immunity over vaccination-induced immunity in driving these evolutionary changes. This emphasizes the critical need for regular vaccine updates to maintain efficacy against evolving strains. In conclusion, our study not only sheds light on the evolutionary trajectory of SARS-CoV-2 but also underscores the urgency for robust, continuous global data collection and sharing. It highlights the necessity for rapid adaptations in medical countermeasures, including vaccine development, to stay ahead of pathogen evolution. This research provides valuable insights for future pandemic preparedness and response strategies.
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Affiliation(s)
- Binghan Xiao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Linhuan Wu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Qinglan Sun
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Chang Shu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China.
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2
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Freidel MR, Vakhariya PA, Sardarni SK, Armen RS. The Dual-Targeted Fusion Inhibitor Clofazimine Binds to the S2 Segment of the SARS-CoV-2 Spike Protein. Viruses 2024; 16:640. [PMID: 38675980 PMCID: PMC11054727 DOI: 10.3390/v16040640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/29/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Clofazimine and Arbidol have both been reported to be effective in vitro SARS-CoV-2 fusion inhibitors. Both are promising drugs that have been repurposed for the treatment of COVID-19 and have been used in several previous and ongoing clinical trials. Small-molecule bindings to expressed constructs of the trimeric S2 segment of Spike and the full-length SARS-CoV-2 Spike protein were measured using a Surface Plasmon Resonance (SPR) binding assay. We demonstrate that Clofazimine, Toremifene, Arbidol and its derivatives bind to the S2 segment of the Spike protein. Clofazimine provided the most reliable and highest-quality SPR data for binding with S2 over the conditions explored. A molecular docking approach was used to identify the most favorable binding sites on the S2 segment in the prefusion conformation, highlighting two possible small-molecule binding sites for fusion inhibitors. Results related to molecular docking and modeling of the structure-activity relationship (SAR) of a newly reported series of Clofazimine derivatives support the proposed Clofazimine binding site on the S2 segment. When the proposed Clofazimine binding site is superimposed with other experimentally determined coronavirus structures in structure-sequence alignments, the changes in sequence and structure may rationalize the broad-spectrum antiviral activity of Clofazimine in closely related coronaviruses such as SARS-CoV, MERS, hCoV-229E, and hCoV-OC43.
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Affiliation(s)
| | | | | | - Roger S. Armen
- Department of Pharmaceutical Sciences, College of Pharmacy, Thomas Jefferson University, 901 Walnut St. Suite 918, Philadelphia, PA 19170, USA (P.A.V.); (S.K.S.)
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3
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Kim Y, Maltseva N, Tesar C, Jedrzejczak R, Endres M, Ma H, Dugan HL, Stamper CT, Chang C, Li L, Changrob S, Zheng NY, Huang M, Ramanathan A, Wilson P, Michalska K, Joachimiak A. Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies. iScience 2024; 27:108976. [PMID: 38327783 PMCID: PMC10847736 DOI: 10.1016/j.isci.2024.108976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/02/2023] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Coronavirus nucleocapsid protein (NP) of SARS-CoV-2 plays a central role in many functions important for virus proliferation including packaging and protecting genomic RNA. The protein shares sequence, structure, and architecture with nucleocapsid proteins from betacoronaviruses. The N-terminal domain (NPRBD) binds RNA and the C-terminal domain is responsible for dimerization. After infection, NP is highly expressed and triggers robust host immune response. The anti-NP antibodies are not protective and not neutralizing but can effectively detect viral proliferation soon after infection. Two structures of SARS-CoV-2 NPRBD were determined providing a continuous model from residue 48 to 173, including RNA binding region and key epitopes. Five structures of NPRBD complexes with human mAbs were isolated using an antigen-bait sorting. Complexes revealed a distinct complement-determining regions and unique sets of epitope recognition. This may assist in the early detection of pathogens and designing peptide-based vaccines. Mutations that significantly increase viral load were mapped on developed, full length NP model, likely impacting interactions with host proteins and viral RNA.
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Affiliation(s)
- Youngchang Kim
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Natalia Maltseva
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Christine Tesar
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Robert Jedrzejczak
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Michael Endres
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Heng Ma
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Haley L. Dugan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Christopher T. Stamper
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Changsoo Chang
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Lei Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Siriruk Changrob
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Nai-Ying Zheng
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Min Huang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Arvind Ramanathan
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Patrick Wilson
- Gale and Ira Drukier Institute for Children’s Health, Weill Cornell Medicine, New York, NY 10021, USA
| | - Karolina Michalska
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Andrzej Joachimiak
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
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Ravi V, Shamim U, Khan MA, Swaminathan A, Mishra P, Singh R, Bharali P, Chauhan NS, Pandey R. Unraveling the genetic evolution of SARS-CoV-2 Recombinants using mutational dynamics across the different lineages. Front Med (Lausanne) 2024; 10:1294699. [PMID: 38288302 PMCID: PMC10823376 DOI: 10.3389/fmed.2023.1294699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/18/2023] [Indexed: 01/31/2024] Open
Abstract
Introduction Recombination serves as a common strategy employed by RNA viruses for their genetic evolution. Extensive genomic surveillance during the COVID-19 pandemic has reported SARS-CoV-2 Recombinant strains indicating recombination events during the viral evolution. This study introspects the phenomenon of genome recombination by tracing the footprint of prominent lineages of SARS-CoV-2 at different time points in the context of on-going evolution and emergence of Recombinants. Method Whole genome sequencing was carried out for 2,516 SARS-CoV-2 (discovery cohort) and 1,126 (validation cohort) using nasopharyngeal samples collected between the time period of March 2020 to August 2022, as part of the genomic surveillance program. The sequences were classified according to the different lineages of SARS-CoV-2 prevailing in India at respective time points. Results Mutational diversity and abundance evaluation across the 12 lineages identified 58 Recombinant sequences as harboring the least number of mutations (n = 111), with 14 low-frequency unique mutations with major chunk of mutations coming from the BA.2. The spontaneously/dynamically increasing and decreasing trends of mutations highlight the loss of mutations in the Recombinants that were associated with the SARS-CoV-2 replication efficiency, infectivity, and disease severity, rendering them functionally with low infectivity and pathogenicity. Linkage disequilibrium (LD) analysis revealed that mutations comprising the LD blocks of BA.1, BA.2, and Recombinants were found as minor alleles or as low-frequency alleles in the LD blocks from the previous SARS-CoV-2 variant samples, especially Pre-VOC. Moreover, a dissipation in the size of LD blocks as well as LD decay along with a high negative regression coefficient (R squared) value was demonstrated in the Omicron and BA.1 and BA.2 lineages, which corroborated with the breakpoint analysis. Conclusion Together, the findings help to understand the evolution and emergence of Recombinants after the Omicron lineages, for sustenance and adaptability, to maintain the epidemic spread of SARS-CoV-2 in the host population already high in immunity levels.
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Affiliation(s)
- Varsha Ravi
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Uzma Shamim
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Md Abuzar Khan
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Aparna Swaminathan
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Pallavi Mishra
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Rajender Singh
- CSIR-Central Drug Research Institute, (CSIR-CDRI), Lucknow, Lucknow, India
| | - Pankaj Bharali
- CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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5
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Xie M. Virus-Induced Cell Fusion and Syncytia Formation. Results Probl Cell Differ 2024; 71:283-318. [PMID: 37996683 DOI: 10.1007/978-3-031-37936-9_14] [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] [Indexed: 11/25/2023]
Abstract
Most enveloped viruses encode viral fusion proteins to penetrate host cell by membrane fusion. Interestingly, many enveloped viruses can also use viral fusion proteins to induce cell-cell fusion, both in vitro and in vivo, leading to the formation of syncytia or multinucleated giant cells (MGCs). In addition, some non-enveloped viruses encode specialized viral proteins that induce cell-cell fusion to facilitate viral spread. Overall, viruses that can induce cell-cell fusion are nearly ubiquitous in mammals. Virus cell-to-cell spread by inducing cell-cell fusion may overcome entry and post-entry blocks in target cells and allow evasion of neutralizing antibodies. However, molecular mechanisms of virus-induced cell-cell fusion remain largely unknown. Here, I summarize the current understanding of virus-induced cell fusion and syncytia formation.
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Affiliation(s)
- Maorong Xie
- Division of Infection and Immunity, UCL, London, UK.
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6
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Zhou B, Zhou R, Chan JFW, Zeng J, Zhang Q, Yuan S, Liu L, Robinot R, Shan S, Liu N, Ge J, Kwong HYH, Zhou D, Xu H, Chan CCS, Poon VKM, Chu H, Yue M, Kwan KY, Chan CY, Chan CCY, Chik KKH, Du Z, Au KK, Huang H, Man HO, Cao J, Li C, Wang Z, Zhou J, Song Y, Yeung ML, To KKW, Ho DD, Chakrabarti LA, Wang X, Zhang L, Yuen KY, Chen Z. SARS-CoV-2 hijacks neutralizing dimeric IgA for nasal infection and injury in Syrian hamsters 1. Emerg Microbes Infect 2023; 12:2245921. [PMID: 37542391 PMCID: PMC10444022 DOI: 10.1080/22221751.2023.2245921] [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: 04/24/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/06/2023]
Abstract
Prevention of robust severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in nasal turbinate (NT) requires in vivo evaluation of IgA neutralizing antibodies. Here, we report the efficacy of receptor binding domain (RBD)-specific monomeric B8-mIgA1 and B8-mIgA2, and dimeric B8-dIgA1, B8-dIgA2 and TH335-dIgA1 against intranasal SARS-CoV-2 challenge in Syrian hamsters. These antibodies exhibited comparable neutralization potency against authentic virus by competing with human angiotensin converting enzyme-2 (ACE2) receptor for RBD binding. While reducing viral loads in lungs significantly, prophylactic intranasal B8-dIgA unexpectedly led to high amount of infectious viruses and extended damage in NT compared to controls. Mechanistically, B8-dIgA failed to inhibit SARS-CoV-2 cell-to-cell transmission, but was hijacked by the virus through dendritic cell-mediated trans-infection of NT epithelia leading to robust nasal infection. Cryo-EM further revealed B8 as a class II antibody binding trimeric RBDs in 3-up or 2-up/1-down conformation. Neutralizing dIgA, therefore, may engage an unexpected mode of SARS-CoV-2 nasal infection and injury.
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Affiliation(s)
- Biao Zhou
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Runhong Zhou
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Jasper Fuk-Woo Chan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
- Hainan-Medical University – The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, and Academician Workstation of Hainan Province, Hainan Medical University, Haikou, People’s Republic of China, and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Jianwei Zeng
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Qi Zhang
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Diseases, School of Medicine, Tsinghua University, Beijing, People’s Republic of China
| | - Shuofeng Yuan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Li Liu
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Rémy Robinot
- Control of Chronic Viral Infections Group, Virus & Immunity Unit, Institute Pasteur, Paris, France; CNRS UMR, Paris, France
| | - Sisi Shan
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Diseases, School of Medicine, Tsinghua University, Beijing, People’s Republic of China
| | - Na Liu
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Jiwan Ge
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Hugo Yat-Hei Kwong
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Dongyan Zhou
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Haoran Xu
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Chris Chung-Sing Chan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Vincent Kwok-Man Poon
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Hin Chu
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Ming Yue
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Ka-Yi Kwan
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Chun-Yin Chan
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Chris Chun-Yiu Chan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Kenn Ka-Heng Chik
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Zhenglong Du
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Ka-Kit Au
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Haode Huang
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Hiu-On Man
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Jianli Cao
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Cun Li
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Ziyi Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Jie Zhou
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Youqiang Song
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Man-Lung Yeung
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Kelvin Kai-Wang To
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lisa A. Chakrabarti
- Control of Chronic Viral Infections Group, Virus & Immunity Unit, Institute Pasteur, Paris, France; CNRS UMR, Paris, France
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Linqi Zhang
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Diseases, School of Medicine, Tsinghua University, Beijing, People’s Republic of China
| | - Kwok-Yung Yuen
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
- Hainan-Medical University – The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, and Academician Workstation of Hainan Province, Hainan Medical University, Haikou, People’s Republic of China, and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Zhiwei Chen
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
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7
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Mykytyn AZ, Fouchier RA, Haagmans BL. Antigenic evolution of SARS coronavirus 2. Curr Opin Virol 2023; 62:101349. [PMID: 37647851 DOI: 10.1016/j.coviro.2023.101349] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 09/01/2023]
Abstract
SARS coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, emerged in China in December 2019. Vaccines developed were very effective initially, however, the virus has shown remarkable evolution with multiple variants spreading globally over the last three years. Nowadays, newly emerging Omicron lineages are gaining substitutions at a fast rate, resulting in escape from neutralization by antibodies that target the Spike protein. Tools to map the impact of substitutions on the further antigenic evolution of SARS-CoV-2, such as antigenic cartography, may be helpful to update SARS-CoV-2 vaccines. In this review, we focus on the antigenic evolution of SARS-CoV-2, highlighting the impact of Spike protein substitutions individually and in combination on immune escape.
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Affiliation(s)
- Anna Z Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ron Am Fouchier
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands.
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8
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McCrudden CM, Bennie L, Chambers P, Wilson J, Kerr M, Ziminska M, Douglas H, Kuhn S, Carroll E, O'Brien G, Buckley N, Dunne NJ, McCarthy HO. Peptide delivery of a multivalent mRNA SARS-CoV-2 vaccine. J Control Release 2023; 362:536-547. [PMID: 37648082 DOI: 10.1016/j.jconrel.2023.08.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/06/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
Lipid nanoparticles (LNP) have been instrumental in the success of mRNA vaccines and have opened up the field to a new wave of therapeutics. However, what is ahead beyond the LNP? The approach herein used a nanoparticle containing a blend of Spike, Membrane and Envelope antigens complexed for the first time with the RALA peptide (RALA-SME). The physicochemical characteristics and functionality of RALA-SME were assessed. With >99% encapsulation, RALA-SME was administered via intradermal injection in vivo, and all three antigen-specific IgG antibodies were highly significant. The IgG2a:IgG1 ratio were all >1.2, indicating a robust TH1 response, and this was further confirmed with the T-Cell response in mice. A complete safety panel of markers from mice were all within normal range, supported by safety data in hamsters. Vaccination of Syrian Golden hamsters with RALA-SME derivatives produced functional antibodies capable of neutralising SARS-CoV-2 from both Wuhan-Hu-1 and Omicron BA.1 lineages after two doses. Antibody levels increased over the study period and provided protection from disease-specific weight loss, with inhibition of viral migration down the respiratory tract. This peptide technology enables the flexibility to interchange and add antigens as required, which is essential for the next generation of adaptable mRNA vaccines.
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Affiliation(s)
- Cian M McCrudden
- School of Pharmacy, Queen's University of Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; pHion Therapeutics, Catalyst Concourse Building 2, 20 Queens Road, Belfast BT3 9DT, UK
| | - Lindsey Bennie
- School of Pharmacy, Queen's University of Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; pHion Therapeutics, Catalyst Concourse Building 2, 20 Queens Road, Belfast BT3 9DT, UK
| | - Philip Chambers
- School of Pharmacy, Queen's University of Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; pHion Therapeutics, Catalyst Concourse Building 2, 20 Queens Road, Belfast BT3 9DT, UK
| | - Jordan Wilson
- School of Pharmacy, Queen's University of Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; pHion Therapeutics, Catalyst Concourse Building 2, 20 Queens Road, Belfast BT3 9DT, UK
| | - Megan Kerr
- School of Pharmacy, Queen's University of Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; pHion Therapeutics, Catalyst Concourse Building 2, 20 Queens Road, Belfast BT3 9DT, UK
| | - Monika Ziminska
- School of Pharmacy, Queen's University of Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; pHion Therapeutics, Catalyst Concourse Building 2, 20 Queens Road, Belfast BT3 9DT, UK
| | - Hayley Douglas
- School of Pharmacy, Queen's University of Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; pHion Therapeutics, Catalyst Concourse Building 2, 20 Queens Road, Belfast BT3 9DT, UK
| | - Sarah Kuhn
- School of Pharmacy, Queen's University of Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; pHion Therapeutics, Catalyst Concourse Building 2, 20 Queens Road, Belfast BT3 9DT, UK
| | - Emma Carroll
- School of Pharmacy, Queen's University of Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; pHion Therapeutics, Catalyst Concourse Building 2, 20 Queens Road, Belfast BT3 9DT, UK
| | - Garrett O'Brien
- School of Pharmacy, Queen's University of Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; pHion Therapeutics, Catalyst Concourse Building 2, 20 Queens Road, Belfast BT3 9DT, UK
| | - Niamh Buckley
- School of Pharmacy, Queen's University of Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Nicholas J Dunne
- School of Pharmacy, Queen's University of Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; pHion Therapeutics, Catalyst Concourse Building 2, 20 Queens Road, Belfast BT3 9DT, UK; School of Chemical Sciences, Dublin City University, Collins Avenue, Dublin 9, Ireland; School of Mechanical & Manufacturing Engineering, Dublin City University, Collins Avenue, Dublin 9, Ireland; Advanced Manufacturing Research Centre (I-Form), School of Mechanical and Manufacturing Engineering, Dublin City University, Dublin 9, Ireland; Advanced Materials and Bioengineering Research Centre (AMBER), Trinity College Dublin, Dublin 2, Ireland; Biodesign Europe, Dublin City University, Dublin 9, Ireland
| | - Helen O McCarthy
- School of Pharmacy, Queen's University of Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; pHion Therapeutics, Catalyst Concourse Building 2, 20 Queens Road, Belfast BT3 9DT, UK; School of Chemical Sciences, Dublin City University, Collins Avenue, Dublin 9, Ireland; Biodesign Europe, Dublin City University, Dublin 9, Ireland.
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9
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Li C, Ma L, Zou D, Zhang R, Bai X, Li L, Wu G, Huang T, Zhao W, Jin E, Bao Y, Song S. RCoV19: A One-stop Hub for SARS-CoV-2 Genome Data Integration, Variant Monitoring, and Risk Pre-warning. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1066-1079. [PMID: 37898309 PMCID: PMC10928372 DOI: 10.1016/j.gpb.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]
Abstract
The Resource for Coronavirus 2019 (RCoV19) is an open-access information resource dedicated to providing valuable data on the genomes, mutations, and variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this updated implementation of RCoV19, we have made significant improvements and advancements over the previous version. Firstly, we have implemented a highly refined genome data curation model. This model now features an automated integration pipeline and optimized curation rules, enabling efficient daily updates of data in RCoV19. Secondly, we have developed a global and regional lineage evolution monitoring platform, alongside an outbreak risk pre-warning system. These additions provide a comprehensive understanding of SARS-CoV-2 evolution and transmission patterns, enabling better preparedness and response strategies. Thirdly, we have developed a powerful interactive mutation spectrum comparison module. This module allows users to compare and analyze mutation patterns, assisting in the detection of potential new lineages. Furthermore, we have incorporated a comprehensive knowledgebase on mutation effects. This knowledgebase serves as a valuable resource for retrieving information on the functional implications of specific mutations. In summary, RCoV19 serves as a vital scientific resource, providing access to valuable data, relevant information, and technical support in the global fight against COVID-19. The complete contents of RCoV19 are available to the public at https://ngdc.cncb.ac.cn/ncov/.
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Affiliation(s)
- Cuiping Li
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Lina Ma
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Rongqin Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue Bai
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Lun Li
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Gangao Wu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianhao Huang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Enhui Jin
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shuhui Song
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China.
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10
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Pondé RADA. Physicochemical effects of emerging exchanges on the spike protein's RBM of the SARS-CoV-2 Omicron subvariants BA.1-BA.5 and its influence on the biological properties and attributes developed by these subvariants. Virology 2023; 587:109850. [PMID: 37562286 DOI: 10.1016/j.virol.2023.109850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/13/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
Emerging in South Africa, SARS-CoV-2 Omicron variant was marked by the expression of an exaggerated number of mutations throughout its genome and by the emergence of subvariants, whose attributes developed by them have been associated with amino acid exchanges that occur mainly in the RBM region of the spike protein. The RBM comprises a region within the RBD and is directly involved in the SARS-CoV-2 spike protein interaction with the host cell ACE2 receptor, during the infection mechanism and viral transmission. Defined as the region from aa 437 to aa 508, there are several residues in certain positions that interact directly with the human ACE-2 receptor during these processes. The occurrence of amino acid exchanges in these positions causes physicochemical alterations in the SARS-CoV-2 spike protein, which confer additional advantages and attributes to the agent. In addition, these exchanges serve as a basis for the characterization of new variants and subvariants of SARS-CoV-2. In this review, the amino acid exchanges that have occurred in the RBM of the subvariants BA.1 to BA.5 of SARS-CoV-2 that emerged from the Omicron are described. The physicochemical effects caused by them on spike protein are also described, as well as their influence on the biological properties and attributes developed by the subvariants BA.1, BA.2, BA.3, BA.4 and BA.5.
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Affiliation(s)
- Robério Amorim de Almeida Pondé
- Secretaria de Estado da Saúde -SES/Superintendência de Vigilância em Saúde-SUVISA/GO, Gerência de Vigilância Epidemiológica de Doenças Transmissíveis-GVEDT/Coordenação de Análises e Pesquisas-CAP, Goiânia, Goiás, Brazil; Laboratory of Human Virology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil.
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11
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Chrysostomou AC, Vrancken B, Haralambous C, Alexandrou M, Gregoriou I, Ioannides M, Ioannou C, Kalakouta O, Karagiannis C, Marcou M, Masia C, Mendris M, Papastergiou P, Patsalis PC, Pieridou D, Shammas C, Stylianou DC, Zinieri B, Lemey P, Network TCOMESSAR, Kostrikis LG. Unraveling the Dynamics of Omicron (BA.1, BA.2, and BA.5) Waves and Emergence of the Deltacton Variant: Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus (Oct 2021-Oct 2022). Viruses 2023; 15:1933. [PMID: 37766339 PMCID: PMC10535466 DOI: 10.3390/v15091933] [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] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Commencing in December 2019 with the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), three years of the coronavirus disease 2019 (COVID-19) pandemic have transpired. The virus has consistently demonstrated a tendency for evolutionary adaptation, resulting in mutations that impact both immune evasion and transmissibility. This ongoing process has led to successive waves of infections. This study offers a comprehensive assessment spanning genetic, phylogenetic, phylodynamic, and phylogeographic dimensions, focused on the trajectory of the SARS-CoV-2 epidemic in Cyprus. Based on a dataset comprising 4700 viral genomic sequences obtained from affected individuals between October 2021 and October 2022, our analysis is presented. Over this timeframe, a total of 167 distinct lineages and sublineages emerged, including variants such as Delta and Omicron (1, 2, and 5). Notably, during the fifth wave of infections, Omicron subvariants 1 and 2 gained prominence, followed by the ascendancy of Omicron 5 in the subsequent sixth wave. Additionally, during the fifth wave (December 2021-January 2022), a unique set of Delta sequences with genetic mutations associated with Omicron variant 1, dubbed "Deltacron", was identified. The emergence of this phenomenon initially evoked skepticism, characterized by concerns primarily centered around contamination or coinfection as plausible etiological contributors. These hypotheses were predominantly disseminated through unsubstantiated assertions within the realms of social and mass media, lacking concurrent scientific evidence to validate their claims. Nevertheless, the exhaustive molecular analyses presented in this study have demonstrated that such occurrences would likely lead to a frameshift mutation-a genetic aberration conspicuously absent in our provided sequences. This substantiates the accuracy of our initial assertion while refuting contamination or coinfection as potential etiologies. Comparable observations on a global scale dispelled doubt, eventually leading to the recognition of Delta-Omicron variants by the scientific community and their subsequent monitoring by the World Health Organization (WHO). As our investigation delved deeper into the intricate dynamics of the SARS-CoV-2 epidemic in Cyprus, a discernible pattern emerged, highlighting the major role of international connections in shaping the virus's local trajectory. Notably, the United States and the United Kingdom were the central conduits governing the entry and exit of the virus to and from Cyprus. Moreover, notable migratory routes included nations such as Greece, South Korea, France, Germany, Brazil, Spain, Australia, Denmark, Sweden, and Italy. These empirical findings underscore that the spread of SARS-CoV-2 within Cyprus was markedly influenced by the influx of new, highly transmissible variants, triggering successive waves of infection. This investigation elucidates the emergence of new waves of infection subsequent to the advent of highly contagious and transmissible viral variants, notably characterized by an abundance of mutations localized within the spike protein. Notably, this discovery decisively contradicts the hitherto hypothesis of seasonal fluctuations in the virus's epidemiological dynamics. This study emphasizes the importance of meticulously examining molecular genetics alongside virus migration patterns within a specific region. Past experiences also emphasize the substantial evolutionary potential of viruses such as SARS-CoV-2, underscoring the need for sustained vigilance. However, as the pandemic's dynamics continue to evolve, a balanced approach between caution and resilience becomes paramount. This ethos encourages an approach founded on informed prudence and self-preservation, guided by public health authorities, rather than enduring apprehension. Such an approach empowers societies to adapt and progress, fostering a poised confidence rooted in well-founded adaptation.
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Affiliation(s)
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Christos Haralambous
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | - Maria Alexandrou
- Microbiology Department, Larnaca General Hospital, 6301 Larnaca, Cyprus
| | - Ioanna Gregoriou
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | | | - Costakis Ioannou
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, 5310 Paralimni, Cyprus
| | - Olga Kalakouta
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | | | - Markella Marcou
- Department of Microbiology, Archbishop Makarios III Hospital, 2012 Nicosia, Cyprus
| | - Christina Masia
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, 5310 Paralimni, Cyprus
| | - Michail Mendris
- Microbiology Department, Limassol General Hospital, 4131 Limassol, Cyprus
| | | | - Philippos C. Patsalis
- Medicover Genetics, 2409 Nicosia, Cyprus
- Medical School, University of Nicosia, 2417 Nicosia, Cyprus
| | - Despo Pieridou
- Microbiology Department, Nicosia General Hospital, 2029 Nicosia, Cyprus
| | - Christos Shammas
- S.C.I.N.A. Bioanalysis Sciomedical Centre Ltd., 4040 Limassol, Cyprus
| | - Dora C. Stylianou
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
| | - Barbara Zinieri
- Microbiology Department, Paphos General Hospital, Achepans, 8026 Paphos, Cyprus
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | | | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, 1011 Nicosia, Cyprus
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12
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Sgorlon G, Roca TP, Passos-Silva AM, Custódio MGF, Queiroz JADS, da Silva ALF, Teixeira KS, Batista FS, Salcedo JMV, Rampazzo RDCP, Naveca FG, Vieira D. SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia. Bioinform Biol Insights 2023; 17:11779322231186477. [PMID: 37461740 PMCID: PMC10350575 DOI: 10.1177/11779322231186477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/18/2023] [Indexed: 07/20/2023] Open
Abstract
The increased transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has generated variants of concern (VOCs) throughout the pandemic, responsible for waves of cases worldwide. To monitor mutations in the S gene of SARS-CoV-2 in different variants, we evaluated 1497 individuals with COVID-19 in western Amazonia in the period April 2021 to July 2022. The epidemiological and clinical data of the individuals were collected; subsequently, the samples were extracted using a commercial kit, the viral load was assessed, and viral genomes were sequenced. We analyzed the quality and mutations of the genomes and maximum likelihood phylogenetic inference. However, 3 main clusters were observed, referring to Gamma (52.91%), Delta (24.38%), and Omicron (20.38%) VOCs with wide distribution in all health regions of the Rondônia state. Regarding the vaccination profile, there was a higher percentage of unvaccinated and partially vaccinated individuals, with more representatives by the Gamma variant. A total of 1412 sequences were suitable for mutation analysis in the S gene region. The Omicron VOC showed 38 mutations, with the Delta and Gamma variants with 16 and 17, respectively. The VOC Omicron and Gamma shared 4 mutations E484K, H655Y, N501Y, and N679K with high frequency, and Delta and Omicron 2 mutations (T478K and T95I). Regarding the comparison between the frequency of mutations for each variant concerning the vaccination groups, there were no changes in mutations for each group. In conclusion, the study showed a temporal increase in mutations and subvariants for characterized strains. Furthermore, the vaccination profile did not impact significant changes in the mutational profile yet remains a determining factor for severe disease.
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Affiliation(s)
- Gabriella Sgorlon
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | - Tárcio Peixoto Roca
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz (IOC), FIOCRUZ, Rio de Janeiro, Brazil
| | - Ana Maisa Passos-Silva
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | | | - Jackson Alves da Silva Queiroz
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | - André Luiz Ferreira da Silva
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | - Karolaine Santos Teixeira
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | | | - Juan Miguel Villalobos Salcedo
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | | | - Felipe Gomes Naveca
- Laboratório de Virologia do Instituto Leônidas e Maria Deane, FIOCRUZ/AM, Manaus, Brazil
| | - Deusilene Vieira
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
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13
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Woods H, Schiano DL, Aguirre JI, Ledwitch KV, McDonald EF, Voehler M, Meiler J, Schoeder CT. Computational modeling and prediction of deletion mutants. Structure 2023; 31:713-723.e3. [PMID: 37119820 PMCID: PMC10247520 DOI: 10.1016/j.str.2023.04.005] [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: 11/16/2022] [Revised: 03/02/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023]
Abstract
In-frame deletion mutations can result in disease. The impact of these mutations on protein structure and subsequent functional changes remain understudied, partially due to the lack of comprehensive datasets including a structural readout. In addition, the recent breakthrough in structure prediction through deep learning demands an update of computational deletion mutation prediction. In this study, we deleted individually every residue of a small α-helical sterile alpha motif domain and investigated the structural and thermodynamic changes using 2D NMR spectroscopy and differential scanning fluorimetry. Then, we tested computational protocols to model and classify observed deletion mutants. We show a method using AlphaFold2 followed by RosettaRelax performs the best overall. In addition, a metric containing pLDDT values and Rosetta ΔΔG is most reliable in classifying tolerated deletion mutations. We further test this method on other datasets and show they hold for proteins known to harbor disease-causing deletion mutations.
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Affiliation(s)
- Hope Woods
- Center of Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN 37235, USA
| | - Dominic L Schiano
- Center of Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Jonathan I Aguirre
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Kaitlyn V Ledwitch
- Center of Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Eli F McDonald
- Center of Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Markus Voehler
- Center of Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Jens Meiler
- Center of Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Institute for Drug Discovery, Leipzig University Medical School, 04103 Leipzig, Germany.
| | - Clara T Schoeder
- Center of Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Institute for Drug Discovery, Leipzig University Medical School, 04103 Leipzig, Germany.
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14
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Kakavandi S, Zare I, VaezJalali M, Dadashi M, Azarian M, Akbari A, Ramezani Farani M, Zalpoor H, Hajikhani B. Structural and non-structural proteins in SARS-CoV-2: potential aspects to COVID-19 treatment or prevention of progression of related diseases. Cell Commun Signal 2023; 21:110. [PMID: 37189112 DOI: 10.1186/s12964-023-01104-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/15/2023] [Indexed: 05/17/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by a new member of the Coronaviridae family known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There are structural and non-structural proteins (NSPs) in the genome of this virus. S, M, H, and E proteins are structural proteins, and NSPs include accessory and replicase proteins. The structural and NSP components of SARS-CoV-2 play an important role in its infectivity, and some of them may be important in the pathogenesis of chronic diseases, including cancer, coagulation disorders, neurodegenerative disorders, and cardiovascular diseases. The SARS-CoV-2 proteins interact with targets such as angiotensin-converting enzyme 2 (ACE2) receptor. In addition, SARS-CoV-2 can stimulate pathological intracellular signaling pathways by triggering transcription factor hypoxia-inducible factor-1 (HIF-1), neuropilin-1 (NRP-1), CD147, and Eph receptors, which play important roles in the progression of neurodegenerative diseases like Alzheimer's disease, epilepsy, and multiple sclerosis, and multiple cancers such as glioblastoma, lung malignancies, and leukemias. Several compounds such as polyphenols, doxazosin, baricitinib, and ruxolitinib could inhibit these interactions. It has been demonstrated that the SARS-CoV-2 spike protein has a stronger affinity for human ACE2 than the spike protein of SARS-CoV, leading the current study to hypothesize that the newly produced variant Omicron receptor-binding domain (RBD) binds to human ACE2 more strongly than the primary strain. SARS and Middle East respiratory syndrome (MERS) viruses against structural and NSPs have become resistant to previous vaccines. Therefore, the review of recent studies and the performance of current vaccines and their effects on COVID-19 and related diseases has become a vital need to deal with the current conditions. This review examines the potential role of these SARS-CoV-2 proteins in the initiation of chronic diseases, and it is anticipated that these proteins could serve as components of an effective vaccine or treatment for COVID-19 and related diseases. Video Abstract.
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Affiliation(s)
- Sareh Kakavandi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Iman Zare
- Research and Development Department, Sina Medical Biochemistry Technologies Co. Ltd., Shiraz, 7178795844, Iran
| | - Maryam VaezJalali
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Dadashi
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Maryam Azarian
- Department of Radiology, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Abdullatif Akbari
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Marzieh Ramezani Farani
- Department of Biological Sciences and Bioengineering, Nano Bio High-Tech Materials Research Center, Inha University, Incheon, 22212, Republic of Korea
| | - Hamidreza Zalpoor
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
| | - Bahareh Hajikhani
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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15
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Chrysostomou AC, Vrancken B, Haralambous C, Alexandrou M, Aristokleous A, Christodoulou C, Gregoriou I, Ioannides M, Kalakouta O, Karagiannis C, Koumbaris G, Loizides C, Mendris M, Papastergiou P, Patsalis PC, Pieridou D, Richter J, Schmitt M, Shammas C, Stylianou DC, Themistokleous G, Lemey P, Kostrikis LG. Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern. Viruses 2022; 15:108. [PMID: 36680148 PMCID: PMC9862594 DOI: 10.3390/v15010108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 resulted in the coronavirus disease 2019 (COVID-19) pandemic, which has had devastating repercussions for public health. Over the course of this pandemic, the virus has continuously been evolving, resulting in new, more infectious variants that have frequently led to surges of new SARS-CoV-2 infections. In the present study, we performed detailed genetic, phylogenetic, phylodynamic and phylogeographic analyses to examine the SARS-CoV-2 epidemic in Cyprus using 2352 SARS-CoV-2 sequences from infected individuals in Cyprus during November 2020 to October 2021. During this period, a total of 61 different lineages and sublineages were identified, with most falling into three groups: B.1.258 & sublineages, Alpha (B.1.1.7 & Q. sublineages), and Delta (B.1.617.2 & AY. sublineages), each encompassing a set of S gene mutations that primarily confer increased transmissibility as well as immune evasion. Specifically, these lineages were coupled with surges of new infections in Cyprus, resulting in the following: the second wave of SARS-CoV-2 infections in Cyprus, comprising B.1.258 & sublineages, during late autumn 2020/beginning of winter 2021; the third wave, comprising Alpha (B.1.1.7 & Q. sublineages), during spring 2021; and the fourth wave, comprising Delta (B.1.617.2 & AY. sublineages) during summer 2021. Additionally, it was identified that these lineages were primarily imported from and exported to the UK, Greece, and Sweden; many other migration links were also identified, including Switzerland, Denmark, Russia, and Germany. Taken together, the results of this study indicate that the SARS-CoV-2 epidemic in Cyprus was characterized by successive introduction of new lineages from a plethora of countries, resulting in the generation of waves of infection. Overall, this study highlights the importance of investigating the spatiotemporal evolution of the SARS-CoV-2 epidemic in the context of Cyprus, as well as the impact of protective measures placed to mitigate transmission of the virus, providing necessary information to safeguard public health.
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Affiliation(s)
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Christos Haralambous
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
| | - Maria Alexandrou
- Microbiology Department, Larnaca General Hospital, Larnaca 6301, Cyprus
| | - Antonia Aristokleous
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
| | - Christina Christodoulou
- Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Ioanna Gregoriou
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
| | | | - Olga Kalakouta
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
| | | | | | | | - Michail Mendris
- Microbiology Department, Limassol General Hospital, Limassol 4131, Cyprus
| | | | - Philippos C. Patsalis
- NIPD Genetics, Nicosia 2409, Cyprus
- Medical School, University of Nicosia, Nicosia 2417, Cyprus
| | - Despo Pieridou
- Microbiology Department, Nicosia General Hospital, Nicosia 2029, Cyprus
| | - Jan Richter
- Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Markus Schmitt
- Eurofins Genomics Sequencing Europe, 85560 Ebersberg, Germany
| | - Christos Shammas
- S.C.I.N.A Bioanalysis Sciomedical Centre Ltd., Limassol 4040, Cyprus
| | - Dora C. Stylianou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
| | | | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, Nicosia 1011, Cyprus
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16
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Molecular and Structural Evolution of Porcine Epidemic Diarrhea Virus. Animals (Basel) 2022; 12:ani12233388. [PMID: 36496909 PMCID: PMC9736354 DOI: 10.3390/ani12233388] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022] Open
Abstract
To analyze the evolutionary characteristics of the highly contagious porcine epidemic diarrhea virus (PEDV) at the molecular and structural levels, we analyzed the complete genomes of 647 strains retrieved from the GenBank database. The results showed that the spike (S) gene exhibited larger dS (synonymous substitutions per synonymous site) values than other PEDV genes. In the selective pressure analysis, eight amino acid (aa) sites of the S protein showed strong signals of positive selection, and seven of them were located on the surface of the S protein (S1 domain), suggesting a high selection pressure of S protein. Topologically, the S gene is more representative of the evolutionary relationship at the genome-wide level than are other genes. Structurally, the evolutionary pattern is highly S1 domain-related. The haplotype networks of the S gene showed that the strains are obviously clustered geographically in the lineages corresponding to genotypes GI and GII. The alignment analysis on representative strains of the main haplotypes revealed three distinguishable nucleic acid sites among those strains, suggesting a putative evolutionary mechanism in PEDV. These findings provide several new fundamental insights into the evolution of PEDV and guidance for developing effective prevention countermeasures against PEDV.
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