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McCallum M, Park YJ, Stewart C, Sprouse KR, Brown J, Tortorici MA, Gibson C, Wong E, Ieven M, Telenti A, Veesler D. Human coronavirus HKU1 recognition of the TMPRSS2 host receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574565. [PMID: 38260518 PMCID: PMC10802434 DOI: 10.1101/2024.01.09.574565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain elusive. Here, we designed an active human TMPRSS2 construct enabling high-yield recombinant production in human cells of this key therapeutic target. We determined a cryo-electron microscopy structure of the HKU1 RBD bound to human TMPRSS2 providing a blueprint of the interactions supporting viral entry and explaining the specificity for TMPRSS2 among human type 2 transmembrane serine proteases. We found that human, rat, hamster and camel TMPRSS2 promote HKU1 S-mediated entry into cells and identified key residues governing host receptor usage. Our data show that serum antibodies targeting the HKU1 RBD TMPRSS2 binding-site are key for neutralization and that HKU1 uses conformational masking and glycan shielding to balance immune evasion and receptor engagement.
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | - Cecily Gibson
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Emily Wong
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Margareta Ieven
- Laboratory of Clinical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | | | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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102
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Liu F, Deng P, He J, Chen X, Jiang X, Yan Q, Xu J, Hu S, Yan J. A regional genomic surveillance program is implemented to monitor the occurrence and emergence of SARS-CoV-2 variants in Yubei District, China. Virol J 2024; 21:13. [PMID: 38191416 PMCID: PMC10775548 DOI: 10.1186/s12985-023-02279-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/27/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND In December 2022, Chongqing experienced a significant surge in coronavirus disease 2019 (COVID-19) epidemic after adjusting control measures in China. Given the widespread immunization of the population with the BA.5 variant, it is crucial to actively monitor severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant evolution in Chongqing's Yubei district. METHODS In this retrospective study based on whole genome sequencing, we collected oropharyngeal and nasal swab of native COVID-19 cases from Yubei district between January to May 2023, along with imported cases from January 2022 to January 2023. Through second-generation sequencing, we generated a total of 578 genomes. RESULTS Phylogenetic analyses revealed these genomes belong to 47 SARS-CoV-2 Pango lineages. BA.5.2.48 was dominant from January to April 2023, rapidly replaced by XBB* variants from April to May 2023. Bayesian Skyline Plot reconstructions indicated a higher evolutionary rate (6.973 × 10-4 subs/site/year) for the XBB.1.5* lineage compared to others. The mean time to the most recent common ancestor (tMRCA) of BA.5.2.48* closely matched BA.2.75* (May 27, 2022). Using multinomial logistic regression, we estimated growth advantages, with XBB.1.9.1 showing the highest growth advantage (1.2, 95% HPI:1.1-1.2), followed by lineage FR.1 (1.1, 95% HPI:1.1-1.2). CONCLUSIONS Our monitoring reveals the rapid replacement of the previously prevalent BA.5.2.48 variant by XBB and its sub-variants, underscoring the ineffectiveness of herd immunity and breakthrough BA.5 infections against XBB variants. Given the ongoing evolutionary pressure, sustaining a SARS-CoV-2 genomic surveillance program is imperative.
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Affiliation(s)
- Fangyuan Liu
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Peng Deng
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Jiuhong He
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Xiaofeng Chen
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Xinyu Jiang
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Qi Yan
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Jing Xu
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Sihan Hu
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Jin Yan
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China.
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103
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Pérez-Massón B, Quintana-Pérez Y, Tundidor Y, Pérez-Martínez D, Castro-Martínez C, Pupo-Meriño M, Orosa I, Relova-Hernández E, Villegas R, Guirola O, Rojas G. Studying SARS-CoV-2 interactions using phage-displayed receptor binding domain as a model protein. Sci Rep 2024; 14:712. [PMID: 38184672 PMCID: PMC10771503 DOI: 10.1038/s41598-023-50450-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/20/2023] [Indexed: 01/08/2024] Open
Abstract
SARS-CoV-2 receptor binding domain (RBD) mediates viral entry into human cells through its interaction with angiotensin converting enzyme 2 (ACE2). Most neutralizing antibodies elicited by infection or vaccination target this domain. Such a functional relevance, together with large RBD sequence variability arising during viral spreading, point to the need of exploring the complex landscape of interactions between RBD-derived variants, ACE2 and antibodies. The current work was aimed at developing a simple platform to do so. Biologically active and antigenic Wuhan-Hu-1 RBD, as well as mutated RBD variants found in nature, were successfully displayed on filamentous phages. Mutational scanning confirmed the global plasticity of the receptor binding motif within RBD, highlighted residues playing a critical role in receptor binding, and identified mutations strengthening the interaction. The ability of vaccine-induced antibodies to inhibit ACE2 binding of many mutated RBD variants, albeit at different extents, was shown. Amino acid replacements which could compromise such inhibitory potential were underscored. The expansion of our approach could be the starting point for a large-scale phage-based exploration of diversity within RBD of SARS-CoV-2 and related coronaviruses, useful to understand structure-function relationships, to engineer RBD proteins, and to anticipate changes to watch during viral evolution.
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Affiliation(s)
- Beatriz Pérez-Massón
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Yazmina Quintana-Pérez
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Yaima Tundidor
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Dayana Pérez-Martínez
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Camila Castro-Martínez
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Mario Pupo-Meriño
- Universidad de Ciencias Informáticas, Carretera a San Antonio de los Baños, km 2 1/2, Torrens, Boyeros, CP 19370, Havana, Cuba
| | - Ivette Orosa
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Ernesto Relova-Hernández
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Rosmery Villegas
- Universidad de Ciencias Informáticas, Carretera a San Antonio de los Baños, km 2 1/2, Torrens, Boyeros, CP 19370, Havana, Cuba
| | - Osmany Guirola
- Center for Genetic Engineering and Biotechnology, Ave 31 E/158 y 190, Cubanacán, Playa, CP 11300, Havana, Cuba
| | - Gertrudis Rojas
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba.
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104
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Zaidi AK, Singh RB. Epidemiology of COVID-19. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 202:25-38. [PMID: 38237988 DOI: 10.1016/bs.pmbts.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
This chapter provides a detailed exploration of the epidemiology of COVID-19, focusing on several key aspects that offer valuable insights into the disease progression. A comprehensive comparison is made between the three related coronaviruses: SARS-CoV, MERS-CoV, and SARS-CoV-2, elucidating their similarities and differences in terms of transmission dynamics, clinical presentation, laboratory and radiological findings, infection mechanisms, and mortality rates. The concept of herd immunity is then discussed, exploring its relevance and potential implications for controlling the spread of COVID-19. Next, the chapter delves into the changing epidemiology of the disease, examining how various factors such as human behavior, public health interventions, and viral mutations have influenced its transmission patterns and severity over time. Finally, the timelines and evolution of COVID-19 are outlined, tracing the origins of the virus, its rapid global spread, and the emergence of new variants.
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Affiliation(s)
| | - Rohan Bir Singh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United State; Department of Population, Policy and Practice, Greater Ormond Street Institute of Child Health, University College London, United Kingdom; Discipline of Ophthalmology and Visual Sciences, Adelaide Medical School, University of Adelaide, Australia
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105
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Jia J, Garbarino E, Wang Y, Li J, Song M, Zhang X, Wang X, Li L, Chi J, Cui L, Tang H. Generation of SARS-CoV-2 spike receptor binding domain mutants and functional screening for immune evaders using a novel lentivirus-based system. J Med Virol 2024; 96:e29425. [PMID: 38258313 DOI: 10.1002/jmv.29425] [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: 08/17/2023] [Revised: 12/19/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024]
Abstract
The emergence of rapid and continuous mutations of severe acute respiratory syndrome 2 (SARS-CoV-2) spike glycoprotein that increased with the Omicron variant points out the necessity to anticipate such mutations for conceiving specific and adaptable therapies to avoid another pandemic. The crucial target for the antibody treatment and vaccine design is the receptor binding domain (RBD) of the SARS-CoV-2 spike. It is also the site where the virus has shown its high ability to mutate and consequently escape immune response. We developed a robust and simple method for generating a large number of functional SARS-CoV-2 spike RBD mutants by error-prone PCR and a novel nonreplicative lentivirus-based system. We prepared anti-RBD wild type (WT) polyclonal antibodies and used them to screen and select for mutant libraries that escape inhibition of virion entry into recipient cells expressing human angiotensin-converting enzyme 2 and transmembrane serine protease 2. We isolated, cloned, and sequenced six mutants totally bearing nine mutation sites. Eight mutations were found in successive WT variants, including Omicron and other recombinants, whereas one is novel. These results, together with the detailed functional analyses of two mutants provided the proof of concept for our approach.
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Affiliation(s)
- Junli Jia
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Emanuela Garbarino
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yuhang Wang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
- Department of Blood Transfusion, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jiaming Li
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Minmin Song
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xin Zhang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xinjie Wang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Lingyun Li
- Department of Medical Genetics, Nanjing Medical University, Nanjing, China
| | - Jing Chi
- Department of Microbiological Laboratory, Baoan District Center for Disease Control and Prevention, Shenzhen, China
| | - Lunbiao Cui
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Huamin Tang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
- The Laboratory Center for Basic Medical Sciences, Nanjing Medical University, Nanjing, China
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106
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Alfaleh MA, Alsulaiman RM, Almahboub SA, Nezamuldeen L, Zawawi A, Aljehani ND, Yasir M, Abdulal RH, Alkhaldi R, Helal A, Alamri SS, Malki J, Alhabbab RY, Abujamel TS, Alhakamy NA, Alnami A, Algaissi A, Hassanain M, Hashem AM. ACE2-Fc and DPP4-Fc decoy receptors against SARS-CoV-2 and MERS-CoV variants: a quick therapeutic option for current and future coronaviruses outbreaks. Antib Ther 2024; 7:53-66. [PMID: 38371953 PMCID: PMC10873275 DOI: 10.1093/abt/tbad030] [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: 10/12/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 02/20/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and the Middle East respiratory syndrome coronavirus (MERS-CoV) are highly pathogenic human coronaviruses (CoVs). Anti-CoVs mAbs and vaccines may be effective, but the emergence of neutralization escape variants is inevitable. Angiotensin-converting enzyme 2 and dipeptidyl peptidase 4 enzyme are the getaway receptors for SARS-CoV-2 and MERS-CoV, respectively. Thus, we reformatted these receptors as Fc-fusion decoy receptors. Then, we tested them in parallel with anti-SARS-CoV (ab1-IgG) and anti-MERS-CoV (M336-IgG) mAbs against several variants using pseudovirus neutralization assay. The generated Fc-based decoy receptors exhibited a strong inhibitory effect against all pseudotyped CoVs. Results showed that although mAbs can be effective antiviral drugs, they might rapidly lose their efficacy against highly mutated viruses. We suggest that receptor traps can be engineered as Fc-fusion proteins for highly mutating viruses with known entry receptors, for a faster and effective therapeutic response even against virus harboring antibodies escape mutations.
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Affiliation(s)
- Mohamed A Alfaleh
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Reem M Alsulaiman
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Sarah A Almahboub
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Leena Nezamuldeen
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Ayat Zawawi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Najwa D Aljehani
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Muhammad Yasir
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Rwaa H Abdulal
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Rami Alkhaldi
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Assala Helal
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Sawsan S Alamri
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Jana Malki
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Rowa Y Alhabbab
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Turki S Abujamel
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Nabil A Alhakamy
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Aisha Alnami
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Abdullah Algaissi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mazen Hassanain
- Department of Surgery, Faculty of Medicine, King Saud University, Riyadh 11451, Saudi Arabia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21859, Saudi Arabia
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107
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Gressett TE, Hossen ML, Talkington G, Volic M, Perez H, Tiwari PB, Chapagain P, Bix G. Molecular interactions between perlecan LG3 and the SARS-CoV-2 spike protein receptor binding domain. Protein Sci 2024; 33:e4843. [PMID: 37996967 PMCID: PMC10731540 DOI: 10.1002/pro.4843] [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: 06/18/2023] [Revised: 10/14/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused a global health crisis with significant clinical morbidity and mortality. While angiotensin-converting enzyme 2 (ACE2) is the primary receptor for viral entry, other cell surface and extracellular matrix proteins may also bind to the viral receptor binding domain (RBD) within the SARS-CoV-2 spike protein. Recent studies have implicated heparan sulfate proteoglycans, specifically perlecan LG3, in facilitating SARS-CoV-2 binding to ACE2. However, the role of perlecan LG3 in SARS-CoV-2 pathophysiology is not well understood. In this study, we investigated the binding interactions between the SARS-CoV-2 spike protein RBD and perlecan LG3 through molecular modeling simulations and surface plasmon resonance (SPR) experiments. Our results indicate stable binding between LG3 and SARS-CoV-2 spike protein RBD, which may potentially enhance RBD-ACE2 interactions. These findings shed light on the role of perlecan LG3 in SARS-CoV-2 infection and provide insight into SARS-CoV-2 pathophysiology and potential therapeutic strategy for COVID-19.
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Affiliation(s)
- Timothy E. Gressett
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
- Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
| | - Md Lokman Hossen
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
- Department of PhysicsUniversity of BarishalKornokathiBangladesh
| | - Grant Talkington
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
- Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
| | - Milla Volic
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
| | - Hugo Perez
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
| | | | - Prem Chapagain
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
- Biomolecular Sciences InstituteFlorida International UniversityMiamiFloridaUSA
| | - Gregory Bix
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
- Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
- Department of NeurologyTulane University School of MedicineNew OrleansLouisianaUSA
- Department of Microbiology and ImmunologyTulane University School of MedicineNew OrleansLouisianaUSA
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108
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Nawaz S, Janiad S, Fatima A, Saleem M, Fatima U, Ali A. Rapidly Evolving SARS-CoV-2: A Brief Review Regarding the Variants and their Effects on Vaccine Efficacies. Infect Disord Drug Targets 2024; 24:58-66. [PMID: 38178666 DOI: 10.2174/0118715265271109231129112515] [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: 07/29/2023] [Revised: 10/14/2023] [Accepted: 10/26/2023] [Indexed: 01/06/2024]
Abstract
Since the commencement of Corona Virus Disease 2019 (COVID-19) pandemic, which has resulted in millions of mortalities globally, the efforts to minimize the damages have equally been up to the task. One of those efforts includes the mass vaccine development initiative targeting the deadly Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). So far, vaccines have tremendously decreased the rate of transmission and infection in most parts of the world. However, the repeated resurgence of different types of mutated versions of the virus, also known as variants, has somehow created uncertainties about the efficacies of different types of vaccines. This review discusses some of the interesting SARS-CoV-2 features, including general structure, genomics, and mechanisms of variants development and their consequent immune escape. This review also focuses very briefly on antigenic drift, shift, and vaccine-developing platforms.
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Affiliation(s)
- Shahid Nawaz
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Sara Janiad
- Department of Microbiology and Molecular Genetics, The Women University Multan, Multan, Pakistan
| | - Aiman Fatima
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Maira Saleem
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Urooj Fatima
- Department of Microbiology and Molecular Genetics, The Women University Multan, Multan, Pakistan
| | - Asad Ali
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
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109
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Yisimayi A, Song W, Wang J, Jian F, Yu Y, Chen X, Xu Y, Yang S, Niu X, Xiao T, Wang J, Zhao L, Sun H, An R, Zhang N, Wang Y, Wang P, Yu L, Lv Z, Gu Q, Shao F, Jin R, Shen Z, Xie XS, Wang Y, Cao Y. Repeated Omicron exposures override ancestral SARS-CoV-2 immune imprinting. Nature 2024; 625:148-156. [PMID: 37993710 PMCID: PMC10764275 DOI: 10.1038/s41586-023-06753-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/17/2023] [Indexed: 11/24/2023]
Abstract
The continuing emergence of SARS-CoV-2 variants highlights the need to update COVID-19 vaccine compositions. However, immune imprinting induced by vaccination based on the ancestral (hereafter referred to as WT) strain would compromise the antibody response to Omicron-based boosters1-5. Vaccination strategies to counter immune imprinting are critically needed. Here we investigated the degree and dynamics of immune imprinting in mouse models and human cohorts, especially focusing on the role of repeated Omicron stimulation. In mice, the efficacy of single Omicron boosting is heavily limited when using variants that are antigenically distinct from WT-such as the XBB variant-and this concerning situation could be mitigated by a second Omicron booster. Similarly, in humans, repeated Omicron infections could alleviate WT vaccination-induced immune imprinting and generate broad neutralization responses in both plasma and nasal mucosa. Notably, deep mutational scanning-based epitope characterization of 781 receptor-binding domain (RBD)-targeting monoclonal antibodies isolated from repeated Omicron infection revealed that double Omicron exposure could induce a large proportion of matured Omicron-specific antibodies that have distinct RBD epitopes to WT-induced antibodies. Consequently, immune imprinting was largely mitigated, and the bias towards non-neutralizing epitopes observed in single Omicron exposures was restored. On the basis of the deep mutational scanning profiles, we identified evolution hotspots of XBB.1.5 RBD and demonstrated that these mutations could further boost the immune-evasion capability of XBB.1.5 while maintaining high ACE2-binding affinity. Our findings suggest that the WT component should be abandoned when updating COVID-19 vaccines, and individuals without prior Omicron exposure should receive two updated vaccine boosters.
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Affiliation(s)
- Ayijiang Yisimayi
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Weiliang Song
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Jing Wang
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Fanchong Jian
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | | | - Xiaosu Chen
- Institute for Immunology, College of Life Sciences, Nankai University, Tianjin, P. R. China
| | - Yanli Xu
- Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
| | - Sijie Yang
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, P. R. China
| | - Xiao Niu
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Tianhe Xiao
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Joint Graduate Program of Peking-Tsinghua-NIBS, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P. R. China
| | - Jing Wang
- Changping Laboratory, Beijing, P. R. China
| | | | - Haiyan Sun
- Changping Laboratory, Beijing, P. R. China
| | - Ran An
- Changping Laboratory, Beijing, P. R. China
| | - Na Zhang
- Changping Laboratory, Beijing, P. R. China
| | - Yao Wang
- Changping Laboratory, Beijing, P. R. China
| | - Peng Wang
- Changping Laboratory, Beijing, P. R. China
| | | | - Zhe Lv
- Sinovac Biotech, Beijing, P. R. China
| | | | - Fei Shao
- Changping Laboratory, Beijing, P. R. China
| | - Ronghua Jin
- Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
| | - Zhongyang Shen
- Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, P. R. China
| | - Xiaoliang Sunney Xie
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Youchun Wang
- Changping Laboratory, Beijing, P. R. China
- Institute of Medical Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, P. R. China
| | - Yunlong Cao
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China.
- Changping Laboratory, Beijing, P. R. China.
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110
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Quezada A, Annapareddy A, Javanmardi K, Cooper J, Finkelstein IJ. Mammalian Antigen Display for Pandemic Countermeasures. Methods Mol Biol 2024; 2762:191-216. [PMID: 38315367 DOI: 10.1007/978-1-0716-3666-4_12] [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: 02/07/2024]
Abstract
Pandemic countermeasures require the rapid design of antigens for vaccines, profiling patient antibody responses, assessing antigen structure-function landscapes, and the surveillance of emerging viral lineages. Cell surface display of a viral antigen or its subdomains can facilitate these goals by coupling the phenotypes of protein variants to their DNA sequence. Screening surface-displayed proteins via flow cytometry also eliminates time-consuming protein purification steps. Prior approaches have primarily relied on yeast as a display chassis. However, yeast often cannot express large viral glycoproteins, requiring their truncation into subdomains. Here, we describe a method to design and express antigens on the surface of mammalian HEK293T cells. We discuss three use cases, including screening of stabilizing mutations, deep mutational scanning, and epitope mapping. The mammalian antigen display platform described herein will accelerate ongoing and future pandemic countermeasures.
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Affiliation(s)
- Andrea Quezada
- Department of Molecular BioSciences, University of Texas at Austin, Austin, TX, USA
| | - Ankur Annapareddy
- Department of Molecular BioSciences, University of Texas at Austin, Austin, TX, USA
| | - Kamyab Javanmardi
- Department of Molecular BioSciences, University of Texas at Austin, Austin, TX, USA
| | - John Cooper
- Department of Molecular BioSciences, University of Texas at Austin, Austin, TX, USA
| | - Ilya J Finkelstein
- Department of Molecular BioSciences, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
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111
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Zhao J, Kang M, Wu H, Sun B, Baele G, He WT, Lu M, Suchard MA, Ji X, He N, Su S, Veit M. Risk assessment of SARS-CoV-2 replicating and evolving in animals. Trends Microbiol 2024; 32:79-92. [PMID: 37541811 DOI: 10.1016/j.tim.2023.07.002] [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: 03/16/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
The retransmissions of SARS-CoV-2 from several mammals - primarily mink and white-tailed deer - to humans have raised concerns for the emergence of a new animal-derived SARS-CoV-2 variant to worsen the pandemic. Here, we discuss animal species that are susceptible to natural or experimental infection with SARS-CoV-2 and can transmit the virus to mates or humans. We describe cutting-edge techniques to assess the impact of a mutation in the viral spike (S) protein on its receptor and on antibody binding. Our review of spike sequences of animal-derived viruses identified nine unique amino acid exchanges in the receptor-binding domain (RBD) that are not present in any variant of concern (VOC). These mutations are present in SARS-CoV-2 found in companion animals such as dogs and cats, and they exhibit a higher frequency in SARS-CoV-2 found in mink and white-tailed deer, suggesting that sustained transmissions may contribute to maintaining novel mutations. Four of these exchanges, such as Leu452Met, could undermine acquired immune protection in humans while maintaining high affinity for the human angiotensin-converting enzyme 2 (ACE2) receptor. Finally, we discuss important avenues of future research into animal-derived viruses with public health risks.
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Affiliation(s)
- Jin Zhao
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Mei Kang
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China; Clinical Research Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongyan Wu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Bowen Sun
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Guy Baele
- Department of Microbiology, Immunology, and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Wan-Ting He
- School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Meng Lu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA; Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | - Na He
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Shuo Su
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China.
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin, Germany.
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112
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Schwab B, Yin J. Computational multigene interactions in virus growth and infection spread. Virus Evol 2023; 10:vead082. [PMID: 38361828 PMCID: PMC10868543 DOI: 10.1093/ve/vead082] [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: 08/31/2023] [Revised: 11/29/2023] [Accepted: 12/19/2023] [Indexed: 02/17/2024] Open
Abstract
Viruses persist in nature owing to their extreme genetic heterogeneity and large population sizes, which enable them to evade host immune defenses, escape antiviral drugs, and adapt to new hosts. The persistence of viruses is challenging to study because mutations affect multiple virus genes, interactions among genes in their impacts on virus growth are seldom known, and measures of viral fitness are yet to be standardized. To address these challenges, we employed a data-driven computational model of cell infection by a virus. The infection model accounted for the kinetics of viral gene expression, functional gene-gene interactions, genome replication, and allocation of host cellular resources to produce progeny of vesicular stomatitis virus, a prototype RNA virus. We used this model to computationally probe how interactions among genes carrying up to eleven deleterious mutations affect different measures of virus fitness: single-cycle growth yields and multicycle rates of infection spread. Individual mutations were implemented by perturbing biophysical parameters associated with individual gene functions of the wild-type model. Our analysis revealed synergistic epistasis among deleterious mutations in their effects on virus yield; so adverse effects of single deleterious mutations were amplified by interaction. For the same mutations, multicycle infection spread indicated weak or negligible epistasis, where single mutations act alone in their effects on infection spread. These results were robust to simulation in high- and low-host resource environments. Our work highlights how different types and magnitudes of epistasis can arise for genetically identical virus variants, depending on the fitness measure. More broadly, gene-gene interactions can differently affect how viruses grow and spread.
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Affiliation(s)
- Bradley Schwab
- Wisconsin Institute for Discovery, Chemical and Biological Engineering, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI 53715, USA
| | - John Yin
- Wisconsin Institute for Discovery, Chemical and Biological Engineering, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI 53715, USA
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113
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Kim TH, Bae S, Goo S, Myoung J. Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant. J Microbiol Biotechnol 2023; 33:1587-1295. [PMID: 37915256 PMCID: PMC10772562 DOI: 10.4014/jmb.2308.08020] [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: 08/14/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 11/03/2023]
Abstract
Since its first report in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a grave threat to public health. Virus-specific countermeasures, such as vaccines and therapeutics, have been developed and have contributed to the control of the viral pandemic, which has become endemic. Nonetheless, new variants continue to emerge and could cause a new pandemic. Consequently, it is important to comprehensively understand viral evolution and the roles of mutations in viral infectivity and transmission. SARS-CoV-2 beta variant encode mutations (D614G, N501Y, E484K, and K417N) in the spike which are frequently found in other variants as well. While their individual role in viral infectivity has been elucidated against various therapeutic antibodies, it still remains unclear whether those mutations may act additively or synergistically when combined. Here, we report that N501Y mutation shows differential effect on two therapeutic antibodies tested. Interestingly, the relative importance of E484K and K417N mutations in antibody evasion varies depending on the antibody type. Collectively, these findings suggest that continuous efforts to develop effective antibody therapeutics and combinatorial treatment with multiple antibodies are more rational and effective forms of treatment.
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Affiliation(s)
- Tae-Hun Kim
- Korea Zoonosis Research Institute, Department of Bioactive Material Science and Genetic Engineering Research Institute, Jeonbuk National University, Jeonju 54531, Republic of Korea
| | - Sojung Bae
- Korea Zoonosis Research Institute, Department of Bioactive Material Science and Genetic Engineering Research Institute, Jeonbuk National University, Jeonju 54531, Republic of Korea
| | - Sunggeun Goo
- Korea Zoonosis Research Institute, Department of Bioactive Material Science and Genetic Engineering Research Institute, Jeonbuk National University, Jeonju 54531, Republic of Korea
| | - Jinjong Myoung
- Korea Zoonosis Research Institute, Department of Bioactive Material Science and Genetic Engineering Research Institute, Jeonbuk National University, Jeonju 54531, Republic of Korea
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114
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Nemoto T, Ocari T, Planul A, Tekinsoy M, Zin EA, Dalkara D, Ferrari U. ACIDES: on-line monitoring of forward genetic screens for protein engineering. Nat Commun 2023; 14:8504. [PMID: 38148337 PMCID: PMC10751290 DOI: 10.1038/s41467-023-43967-9] [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: 04/07/2023] [Accepted: 11/24/2023] [Indexed: 12/28/2023] Open
Abstract
Forward genetic screens of mutated variants are a versatile strategy for protein engineering and investigation, which has been successfully applied to various studies like directed evolution (DE) and deep mutational scanning (DMS). While next-generation sequencing can track millions of variants during the screening rounds, the vast and noisy nature of the sequencing data impedes the estimation of the performance of individual variants. Here, we propose ACIDES that combines statistical inference and in-silico simulations to improve performance estimation in the library selection process by attributing accurate statistical scores to individual variants. We tested ACIDES first on a random-peptide-insertion experiment and then on multiple public datasets from DE and DMS studies. ACIDES allows experimentalists to reliably estimate variant performance on the fly and can aid protein engineering and research pipelines in a range of applications, including gene therapy.
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Affiliation(s)
- Takahiro Nemoto
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 17 rue Moreau, 75012, Paris, France.
- Graduate School of Informatics, Kyoto University, Yoshida Hon-machi, Sakyo-ku, Kyoto, 606-8501, Japan.
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Tommaso Ocari
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 17 rue Moreau, 75012, Paris, France
| | - Arthur Planul
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 17 rue Moreau, 75012, Paris, France
| | - Muge Tekinsoy
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 17 rue Moreau, 75012, Paris, France
| | - Emilia A Zin
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 17 rue Moreau, 75012, Paris, France
| | - Deniz Dalkara
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 17 rue Moreau, 75012, Paris, France.
| | - Ulisse Ferrari
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 17 rue Moreau, 75012, Paris, France.
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115
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Parsons RJ, Acharya P. Evolution of the SARS-CoV-2 Omicron spike. Cell Rep 2023; 42:113444. [PMID: 37979169 PMCID: PMC10782855 DOI: 10.1016/j.celrep.2023.113444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/21/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern, first identified in November 2021, rapidly spread worldwide and diversified into several subvariants. The Omicron spike (S) protein accumulated an unprecedented number of sequence changes relative to previous variants. In this review, we discuss how Omicron S protein structural features modulate host cell receptor binding, virus entry, and immune evasion and highlight how these structural features differentiate Omicron from previous variants. We also examine how key structural properties track across the still-evolving Omicron subvariants and the importance of continuing surveillance of the S protein sequence evolution over time.
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Affiliation(s)
- Ruth J Parsons
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA.
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA.
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116
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Lee J, Zepeda SK, Park YJ, Taylor AL, Quispe J, Stewart C, Leaf EM, Treichel C, Corti D, King NP, Starr TN, Veesler D. Broad receptor tropism and immunogenicity of a clade 3 sarbecovirus. Cell Host Microbe 2023; 31:1961-1973.e11. [PMID: 37989312 PMCID: PMC10913562 DOI: 10.1016/j.chom.2023.10.018] [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: 09/05/2023] [Revised: 10/12/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023]
Abstract
Although Rhinolophus bats harbor diverse clade 3 sarbecoviruses, the structural determinants of receptor tropism along with the antigenicity of their spike (S) glycoproteins remain uncharacterized. Here, we show that the African Rhinolophus bat clade 3 sarbecovirus PRD-0038 S has a broad angiotensin-converting enzyme 2 (ACE2) usage and that receptor-binding domain (RBD) mutations further expand receptor promiscuity and enable human ACE2 utilization. We determine a cryo-EM structure of the PRD-0038 RBD bound to Rhinolophus alcyone ACE2, explaining receptor tropism and highlighting differences with SARS-CoV-1 and SARS-CoV-2. Characterization of PRD-0038 S using cryo-EM and monoclonal antibody reactivity reveals its distinct antigenicity relative to SARS-CoV-2 and identifies PRD-0038 cross-neutralizing antibodies for pandemic preparedness. PRD-0038 S vaccination elicits greater titers of antibodies cross-reacting with vaccine-mismatched clade 2 and clade 1a sarbecoviruses compared with SARS-CoV-2 S due to broader antigenic targeting, motivating the inclusion of clade 3 antigens in next-generation vaccines for enhanced resilience to viral evolution.
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Affiliation(s)
- Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ashley L Taylor
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Elizabeth M Leaf
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Catherine Treichel
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Tyler N Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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117
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Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. AlphaFold2-Enabled Atomistic Modeling of Epistatic Binding Mechanisms for the SARS-CoV-2 Spike Omicron XBB.1.5, EG.5 and FLip Variants: Convergent Evolution Hotspots Cooperate to Control Stability and Conformational Adaptability in Balancing ACE2 Binding and Antibody Resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571185. [PMID: 38168257 PMCID: PMC10760024 DOI: 10.1101/2023.12.11.571185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In this study, we combined AI-based atomistic structural modeling and microsecond molecular simulations of the SARS-CoV-2 Spike complexes with the host receptor ACE2 for XBB.1.5+L455F, XBB.1.5+F456L(EG.5) and XBB.1.5+L455F/F456L (FLip) lineages to examine the mechanisms underlying the role of convergent evolution hotspots in balancing ACE2 binding and antibody evasion. Using the ensemble-based mutational scanning of the spike protein residues and physics-based rigorous computations of binding affinities, we identified binding energy hotspots and characterized molecular basis underlying epistatic couplings between convergent mutational hotspots. Consistent with the experiments, the results revealed the mediating role of Q493 hotspot in synchronization of epistatic couplings between L455F and F456L mutations providing a quantitative insight into the mechanism underlying differences between XBB lineages. Mutational profiling is combined with network-based model of epistatic couplings showing that the Q493, L455 and F456 sites mediate stable communities at the binding interface with ACE2 and can serve as stable mediators of non-additive couplings. Structure-based mutational analysis of Spike protein binding with the class 1 antibodies quantified the critical role of F456L and F486P mutations in eliciting strong immune evasion response. The results of this analysis support a mechanism in which the emergence of EG.5 and FLip variants may have been dictated by leveraging strong epistatic effects between several convergent revolutionary hotspots that provide synergy between the improved ACE2 binding and broad neutralization resistance. This interpretation is consistent with the notion that functionally balanced substitutions which simultaneously optimize immune evasion and high ACE2 affinity may continue to emerge through lineages with beneficial pair or triplet combinations of RBD mutations involving mediators of epistatic couplings and sites in highly adaptable RBD regions.
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118
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Welsh FC, Eguia RT, Lee JM, Haddox HK, Galloway J, Chau NVV, Loes AN, Huddleston J, Yu TC, Le MQ, Nhat NTD, Thanh NTL, Greninger AL, Chu HY, Englund JA, Bedford T, Matsen FA, Boni MF, Bloom JD. Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571235. [PMID: 38168237 PMCID: PMC10760046 DOI: 10.1101/2023.12.12.571235] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Human influenza virus evolves to escape neutralization by polyclonal antibodies. However, we have a limited understanding of how the antigenic effects of viral mutations vary across the human population, and how this heterogeneity affects virus evolution. Here we use deep mutational scanning to map how mutations to the hemagglutinin (HA) proteins of the A/Hong Kong/45/2019 (H3N2) and A/Perth/16/2009 (H3N2) strains affect neutralization by serum from individuals of a variety of ages. The effects of HA mutations on serum neutralization differ across age groups in ways that can be partially rationalized in terms of exposure histories. Mutations that fixed in influenza variants after 2020 cause the greatest escape from sera from younger individuals. Overall, these results demonstrate that influenza faces distinct antigenic selection regimes from different age groups, and suggest approaches to understand how this heterogeneous selection shapes viral evolution.
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Affiliation(s)
- Frances C Welsh
- Molecular and Cellular Biology Graduate Program, University of Washington, and Basic Sciences Division, Fred Hutch Cancer Center, Seattle, WA, 98109, USA
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Rachel T Eguia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - Juhye M Lee
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - Hugh K Haddox
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Jared Galloway
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Nguyen Van Vinh Chau
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Andrea N Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Timothy C Yu
- Molecular and Cellular Biology Graduate Program, University of Washington, and Basic Sciences Division, Fred Hutch Cancer Center, Seattle, WA, 98109, USA
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Mai Quynh Le
- National Institutes for Hygiene and Epidemiology, Hanoi, Vietnam
| | - Nguyen T D Nhat
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Nguyen Thi Le Thanh
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Janet A Englund
- Seattle Children's Research Institute, Seattle, WA, 98109, USA
| | - Trevor Bedford
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Frederick A Matsen
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - Maciej F Boni
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
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119
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Fan J, Li S, Zhang Y, Zheng J, Wang D, Liao Y, Cui Z, Zhao D, Barouch DH, Yu J. Early Emerging SARS-CoV-2 Spike Mutants Are Diversified in Virologic Properties but Elicit Compromised Antibody Responses. Viruses 2023; 15:2401. [PMID: 38140642 PMCID: PMC10747620 DOI: 10.3390/v15122401] [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: 11/21/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Despite the effective antivirals and vaccines, COVID-19 remains a public health concern. The mutations that occurred during the early stage of the pandemic can be valuable in assessing the viral fitness and evolutionary trajectory. In this study, we analyzed a panel of 2969 spike sequences deposited in GISAID before April 2020 and characterized nine representative spike single-point mutants in detail. Compared with the WA01/2020, most (8 out of 9) mutants demonstrated an equivalent or diminished protein expression or processing, pseudovirus infectivity, and cell-cell fusion. Interestingly, most of the mutants in native form elicited minimum antibody responses in mice despite unaltered CD4+ and CD8+ T cell responses. The mutants remained sensitive to the antisera and the type I interferon. Taken together, these data suggest that the early emerging mutants are virologically divergent, and some of which showed transmission fitness. Our findings have important implications for the retrospective tracing of the early SARS-CoV-2 transmission and future pandemic preparedness.
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Affiliation(s)
- Junhao Fan
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, China;
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
| | - Shixiong Li
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yao Zhang
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jihao Zheng
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
| | - Dongfang Wang
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
| | - Yunxi Liao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; (Y.L.); (D.Z.)
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Zhibo Cui
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Dongyu Zhao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; (Y.L.); (D.Z.)
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jingyou Yu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, China;
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
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120
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Notin P, Kollasch AW, Ritter D, van Niekerk L, Paul S, Spinner H, Rollins N, Shaw A, Weitzman R, Frazer J, Dias M, Franceschi D, Orenbuch R, Gal Y, Marks DS. ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570727. [PMID: 38106144 PMCID: PMC10723403 DOI: 10.1101/2023.12.07.570727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Predicting the effects of mutations in proteins is critical to many applications, from understanding genetic disease to designing novel proteins that can address our most pressing challenges in climate, agriculture and healthcare. Despite a surge in machine learning-based protein models to tackle these questions, an assessment of their respective benefits is challenging due to the use of distinct, often contrived, experimental datasets, and the variable performance of models across different protein families. Addressing these challenges requires scale. To that end we introduce ProteinGym, a large-scale and holistic set of benchmarks specifically designed for protein fitness prediction and design. It encompasses both a broad collection of over 250 standardized deep mutational scanning assays, spanning millions of mutated sequences, as well as curated clinical datasets providing high-quality expert annotations about mutation effects. We devise a robust evaluation framework that combines metrics for both fitness prediction and design, factors in known limitations of the underlying experimental methods, and covers both zero-shot and supervised settings. We report the performance of a diverse set of over 70 high-performing models from various subfields (eg., alignment-based, inverse folding) into a unified benchmark suite. We open source the corresponding codebase, datasets, MSAs, structures, model predictions and develop a user-friendly website that facilitates data access and analysis.
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Affiliation(s)
| | | | | | | | | | | | | | - Ada Shaw
- Applied Mathematics, Harvard University
| | | | | | - Mafalda Dias
- Centre for Genomic Regulation, Universitat Pompeu Fabra
| | | | | | - Yarin Gal
- Computer Science, University of Oxford
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Zeng Y, Xia F, Guo C, Hu C, Li Y, Wang X, Wu Q, Chen Z, Lu J, Wang Z. Virological Characteristics of Five SARS-CoV-2 Variants, Including Beta, Delta and Omicron BA.1, BA.2, BA.5. Viruses 2023; 15:2394. [PMID: 38140635 PMCID: PMC10747097 DOI: 10.3390/v15122394] [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: 11/07/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
SARS-CoV-2 variants of concern (VOCs) show increasing transmissibility and infectivity and induce substantial injuries to human health and the ecology. Therefore, it is vital to understand the related features for controlling infection. In this study, SARS-CoV-2 WIV04 (prototype) and five VOCs (Beta, Delta, Omicron BA.1, BA.2 and BA.5 variants) were inoculated in Vero cells to observe their growth activities. Apart from evaluating the environmental stability at different temperatures, residual virus titers and infectivity at different temperatures (4 °C, room temperature (RT) and 37 °C) were measured over 7 days. The experiment also assessed the infectivity for different incubation durations. The growth capacity assay suggested that the WIV04, Beta and Delta variants replicated efficiently in Vero cells compared with Omicron Variants, and BA.2 replicated more efficiently in Vero cells than BA.1 and BA.5. In addition, all variants exhibited longer survivals at 4 °C and could remain infectious after 7 days, compared to RT' survival after 5 days and at 37 °C after 1 day. The virus infection assay indicated that the Omicron variant had a weaker ability to infect cells compared to the WIV04, Beta and Delta strains, and a longer infection time was required for these strains, except for BA.2.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jia Lu
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (Y.Z.); (F.X.); (C.G.); (C.H.); (Y.L.); (X.W.); (Q.W.); (Z.C.)
| | - Zejun Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (Y.Z.); (F.X.); (C.G.); (C.H.); (Y.L.); (X.W.); (Q.W.); (Z.C.)
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122
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Aktaş E, Saygılı İ, Kahveci E, Tekbıyık Z, Özgentürk NÖ. Bioinformatic investigation of Nipah virus surface protein mutations: Molecular docking with Ephrin B2 receptor, molecular dynamics simulation, and structural impact analysis. Microbiol Immunol 2023; 67:501-513. [PMID: 37812043 DOI: 10.1111/1348-0421.13098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023]
Abstract
The SARS-CoV-2 outbreak resulted in significant challenges and loss of life. The Nipah virus, known for its high infectivity and severity, was designated an emergency concern by the World Health Organization. To understand its mutations, the Nipah virus proteins were analyzed extensively, with a focus on the essential G and F proteins responsible for viral entry into host cells. Our bioinformatics analysis unveiled multiple mutations, including simultaneous mutations within a single sequence. Notably, the G273S mutation in the F protein was identified as a potential cause of structural damage, which carries significant implications for vaccine development. Comparing the docking scores of G and F proteins with the Ephrin B2 receptor, it was found that the Y228H mutation in the G protein and the D252G mutation in the F protein likely affect virus entry into host cells. Moreover, our investigation into stability and deformability highlighted the impact of the Y228H mutation in the G protein complex. Molecular dynamics simulations revealed increased flexibility and conformational changes in the G protein complex with the Y228H mutation compared with the known complex. Furthermore, evaluating the root mean square deviation variation demonstrated greater dynamic behavior in the G protein complex and the Ephrin B2 receptor complex. This comprehensive study provides valuable insights into Nipah virus mutations, their significance for vaccine development, and the importance of understanding protein complex behavior in drug discovery. The identified mutations, especially G273S and Y228H, hold crucial implications for future research and potential interventions against the Nipah virus.
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Affiliation(s)
- Emre Aktaş
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
| | - İrem Saygılı
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
| | - Elif Kahveci
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
| | - Zeynep Tekbıyık
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
| | - Nehir Özdemir Özgentürk
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
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123
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Kim DG, Kim U, Park IH, Ryu B, Yoo Y, Cha JS, Yoon GY, Kim SH, Oh H, Seo JY, Nam KT, Seong JK, Shin JS, Cho HS, Kim HS. A bivalent form of a RBD-specific synthetic antibody effectively neutralizes SARS-CoV-2 variants. Antiviral Res 2023; 220:105738. [PMID: 37944822 DOI: 10.1016/j.antiviral.2023.105738] [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: 05/10/2023] [Revised: 10/03/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
Coronavirus Disease 2019 (COVID-19) pandemic is severely impacting the world, and tremendous efforts have been made to deal with it. Despite many advances in vaccines and therapeutics, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants remains an intractable challenge. We present a bivalent Receptor Binding Domain (RBD)-specific synthetic antibody, specific for the RBD of wild-type (lineage A), developed from a non-antibody protein scaffold composed of LRR (Leucine-rich repeat) modules through phage display. We further reinforced the unique feature of the synthetic antibody by constructing a tandem dimeric form. The resulting bivalent form showed a broader neutralizing activity against the variants. The in vivo neutralizing efficacy of the bivalent synthetic antibody was confirmed using a human ACE2-expressing mouse model that significantly alleviated viral titer and lung infection. The present approach can be used to develop a synthetic antibody showing a broader neutralizing activity against a multitude of SARS-CoV-2 variants.
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Affiliation(s)
- Dong-Gun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Uijin Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, South Korea
| | - In Ho Park
- Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, South Korea; Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Bumhan Ryu
- Institute for Basic Science (IBS), Daejeon, 34126, South Korea
| | - Youngki Yoo
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, South Korea
| | - Jeong Seok Cha
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, South Korea
| | - Ga-Yeon Yoon
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, South Korea
| | - Sung-Hee Kim
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 03722, South Korea; Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Heeju Oh
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 03722, South Korea; Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Jun-Young Seo
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 03722, South Korea; Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Ki Taek Nam
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 03722, South Korea; Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Je Kyung Seong
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, 08826, South Korea
| | - Jeon-Soo Shin
- Department of Microbiology, Yonsei University College of Medicine, Seoul, 03722, South Korea; Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, South Korea; Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 03722, South Korea; Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea.
| | - Hyun-Soo Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, South Korea.
| | - Hak-Sung Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea.
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124
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Lässig M, Mustonen V, Nourmohammad A. Steering and controlling evolution - from bioengineering to fighting pathogens. Nat Rev Genet 2023; 24:851-867. [PMID: 37400577 PMCID: PMC11137064 DOI: 10.1038/s41576-023-00623-8] [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] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Control interventions steer the evolution of molecules, viruses, microorganisms or other cells towards a desired outcome. Applications range from engineering biomolecules and synthetic organisms to drug, therapy and vaccine design against pathogens and cancer. In all these instances, a control system alters the eco-evolutionary trajectory of a target system, inducing new functions or suppressing escape evolution. Here, we synthesize the objectives, mechanisms and dynamics of eco-evolutionary control in different biological systems. We discuss how the control system learns and processes information about the target system by sensing or measuring, through adaptive evolution or computational prediction of future trajectories. This information flow distinguishes pre-emptive control strategies by humans from feedback control in biotic systems. We establish a cost-benefit calculus to gauge and optimize control protocols, highlighting the fundamental link between predictability of evolution and efficacy of pre-emptive control.
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Affiliation(s)
- Michael Lässig
- Institute for Biological Physics, University of Cologne, Cologne, Germany.
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Armita Nourmohammad
- Department of Physics, University of Washington, Seattle, WA, USA.
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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125
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Wang Q, Guo Y, Liu L, Schwanz LT, Li Z, Nair MS, Ho J, Zhang RM, Iketani S, Yu J, Huang Y, Qu Y, Valdez R, Lauring AS, Huang Y, Gordon A, Wang HH, Liu L, Ho DD. Antigenicity and receptor affinity of SARS-CoV-2 BA.2.86 spike. Nature 2023; 624:639-644. [PMID: 37871613 DOI: 10.1038/s41586-023-06750-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariant, BA.2.86, has emerged and spread to numerous countries worldwide, raising alarm because its spike protein contains 34 additional mutations compared with its BA.2 predecessor1. We examined its antigenicity using human sera and monoclonal antibodies (mAbs). Reassuringly, BA.2.86 was no more resistant to human sera than the currently dominant XBB.1.5 and EG.5.1, indicating that the new subvariant would not have a growth advantage in this regard. Importantly, sera from people who had XBB breakthrough infection exhibited robust neutralizing activity against all viruses tested, suggesting that upcoming XBB.1.5 monovalent vaccines could confer added protection. Although BA.2.86 showed greater resistance to mAbs to subdomain 1 (SD1) and receptor-binding domain (RBD) class 2 and 3 epitopes, it was more sensitive to mAbs to class 1 and 4/1 epitopes in the 'inner face' of the RBD that is exposed only when this domain is in the 'up' position. We also identified six new spike mutations that mediate antibody resistance, including E554K that threatens SD1 mAbs in clinical development. The BA.2.86 spike also had a remarkably high receptor affinity. The ultimate trajectory of this new SARS-CoV-2 variant will soon be revealed by continuing surveillance, but its worldwide spread is worrisome.
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Affiliation(s)
- Qian Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Liyuan Liu
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Logan T Schwanz
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Pathobiology and Mechanisms of Disease, Columbia University Irving Medical Center, New York, NY, USA
| | - Zhiteng Li
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jerren Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Richard M Zhang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yiming Huang
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yiming Qu
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Riccardo Valdez
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Adam S Lauring
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Aubree Gordon
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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126
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Thakur S, Planeta Kepp K, Mehra R. Predicting virus Fitness: Towards a structure-based computational model. J Struct Biol 2023; 215:108042. [PMID: 37931730 DOI: 10.1016/j.jsb.2023.108042] [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: 07/25/2023] [Revised: 10/12/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]
Abstract
Predicting the impact of new emerging virus mutations is of major interest in surveillance and for understanding the evolutionary forces of the pathogens. The SARS-CoV-2 surface spike-protein (S-protein) binds to human ACE2 receptors as a critical step in host cell infection. At the same time, S-protein binding to human antibodies neutralizes the virus and prevents interaction with ACE2. Here we combine these two binding properties in a simple virus fitness model, using structure-based computation of all possible mutation effects averaged over 10 ACE2 complexes and 10 antibody complexes of the S-protein (∼380,000 computed mutations), and validated the approach against diverse experimental binding/escape data of ACE2 and antibodies. The ACE2-antibody selectivity change caused by mutation (i.e., the differential change in binding to ACE2 vs. immunity-inducing antibodies) is proposed to be a key metric of fitness model, enabling systematic error cancelation when evaluated. In this model, new mutations become fixated if they increase the selective binding to ACE2 relative to circulating antibodies, assuming that both are present in the host in a competitive binding situation. We use this model to categorize viral mutations that may best reach ACE2 before being captured by antibodies. Our model may aid the understanding of variant-specific vaccines and molecular mechanisms of viral evolution in the context of a human host.
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Affiliation(s)
- Shivani Thakur
- Department of Chemistry, Indian Institute of Technology Bhilai, Kutelabhata, Durg - 491001, Chhattisgarh, India
| | - Kasper Planeta Kepp
- DTU Chemistry, Technical University of Denmark, Building 206, 2800 Kongens Lyngby, Denmark
| | - Rukmankesh Mehra
- Department of Chemistry, Indian Institute of Technology Bhilai, Kutelabhata, Durg - 491001, Chhattisgarh, India; Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Bhilai, Kutelabhata, Durg - 491001, Chhattisgarh, India.
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127
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Taylor AL, Starr TN. Deep mutational scans of XBB.1.5 and BQ.1.1 reveal ongoing epistatic drift during SARS-CoV-2 evolution. PLoS Pathog 2023; 19:e1011901. [PMID: 38157379 PMCID: PMC10783747 DOI: 10.1371/journal.ppat.1011901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/11/2024] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
Substitutions that fix between SARS-CoV-2 variants can transform the mutational landscape of future evolution via epistasis. For example, large epistatic shifts in mutational effects caused by N501Y underlied the original emergence of Omicron, but whether such epistatic saltations continue to define ongoing SARS-CoV-2 evolution remains unclear. We conducted deep mutational scans to measure the impacts of all single amino acid mutations and single-codon deletions in the spike receptor-binding domain (RBD) on ACE2-binding affinity and protein expression in the recent Omicron BQ.1.1 and XBB.1.5 variants, and we compared mutational patterns to earlier viral strains that we have previously profiled. As with previous deep mutational scans, we find many mutations that are tolerated or even enhance binding to ACE2 receptor. The tolerance of sites to single-codon deletion largely conforms with tolerance to amino acid mutation. Though deletions in the RBD have not yet been seen in dominant lineages, we observe tolerated deletions including at positions that exhibit indel variation across broader sarbecovirus evolution and in emerging SARS-CoV-2 variants of interest, most notably the well-tolerated Δ483 deletion in BA.2.86. The substitutions that distinguish recent viral variants have not induced as dramatic of epistatic perturbations as N501Y, but we identify ongoing epistatic drift in SARS-CoV-2 variants, including interaction between R493Q reversions and mutations at positions 453, 455, and 456, including F456L that defines the XBB.1.5-derived EG.5 lineage. Our results highlight ongoing drift in the effects of mutations due to epistasis, which may continue to direct SARS-CoV-2 evolution into new regions of sequence space.
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Affiliation(s)
- Ashley L. Taylor
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Tyler N. Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
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128
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Chen C, Wang X, Zhang Z. Humoral and cellular immunity against diverse SARS-CoV-2 variants. J Genet Genomics 2023; 50:934-947. [PMID: 37865193 DOI: 10.1016/j.jgg.2023.10.003] [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: 06/29/2023] [Revised: 09/27/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023]
Abstract
Since the outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019, the virus has rapidly spread worldwide. This has led to an unprecedented global pandemic, marked by millions of COVID-19 cases and a significant number of fatalities. Over a relatively short period, several different vaccine platforms are developed and deployed for use globally to curb the pandemic. However, the genome of SARS-CoV-2 continuously undergoes mutation and/or recombination, resulting in the emergence of several variants of concern (VOC). These VOCs can elevate viral transmission and evade the neutralizing antibodies induced by vaccines, leading to reinfections. Understanding the impact of the SARS-CoV-2 genomic mutation on viral pathogenesis and immune escape is crucial for assessing the threat of new variants to public health. This review focuses on the emergence and pathogenesis of VOC, with particular emphasis on their evasion of neutralizing antibodies. Furthermore, the memory B cell, CD4+, and CD8+ T cell memory induced by different COVID-19 vaccines or infections are discussed, along with how these cells recognize VOC. This review summarizes the current knowledge on adaptive immunology regarding SARS-CoV-2 infection and vaccines. Such knowledge may also be applied to vaccine design for other pathogens.
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Affiliation(s)
- Changxu Chen
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China
| | - Xin Wang
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China
| | - Zeli Zhang
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China.
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129
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Li Y, Arcos S, Sabsay KR, te Velthuis AJW, Lauring AS. Deep mutational scanning reveals the functional constraints and evolutionary potential of the influenza A virus PB1 protein. J Virol 2023; 97:e0132923. [PMID: 37882522 PMCID: PMC10688322 DOI: 10.1128/jvi.01329-23] [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: 08/28/2023] [Accepted: 10/08/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE The influenza virus polymerase is important for adaptation to new hosts and, as a determinant of mutation rate, for the process of adaptation itself. We performed a deep mutational scan of the polymerase basic 1 (PB1) protein to gain insights into the structural and functional constraints on the influenza RNA-dependent RNA polymerase. We find that PB1 is highly constrained at specific sites that are only moderately predicted by the global structure or larger domain. We identified a number of beneficial mutations, many of which have been shown to be functionally important or observed in influenza virus' natural evolution. Overall, our atlas of PB1 mutations and their fitness impacts serves as an important resource for future studies of influenza replication and evolution.
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Affiliation(s)
- Yuan Li
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sarah Arcos
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kimberly R. Sabsay
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute, Princeton University, Princeton, New Jersey, USA
| | | | - Adam S. Lauring
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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130
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Lei R, Qing E, Odle A, Yuan M, Tan TJ, So N, Ouyang WO, Wilson IA, Gallagher T, Perlman S, Wu NC, Wong LYR. Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569051. [PMID: 38076875 PMCID: PMC10705381 DOI: 10.1101/2023.11.28.569051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The fusion peptide of SARS-CoV-2 spike protein is functionally important for membrane fusion during virus entry and is part of a broadly neutralizing epitope. However, sequence determinants at the fusion peptide and its adjacent regions for pathogenicity and antigenicity remain elusive. In this study, we performed a series of deep mutational scanning (DMS) experiments on an S2 region spanning the fusion peptide of authentic SARS-CoV-2 in different cell lines and in the presence of broadly neutralizing antibodies. We identified mutations at residue 813 of the spike protein that reduced TMPRSS2-mediated entry with decreased virulence. In addition, we showed that an F823Y mutation, present in bat betacoronavirus HKU9 spike protein, confers resistance to broadly neutralizing antibodies. Our findings provide mechanistic insights into SARS-CoV-2 pathogenicity and also highlight a potential challenge in developing broadly protective S2-based coronavirus vaccines.
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Affiliation(s)
- Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Abby Odle
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Timothy J.C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Natalie So
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wenhao O. Ouyang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
- Center for Virus-Host-Innate Immunity, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
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131
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Teo QW, Wang Y, Lv H, Tan TJC, Lei R, Mao KJ, Wu NC. Stringent and complex sequence constraints of an IGHV1-69 broadly neutralizing antibody to influenza HA stem. Cell Rep 2023; 42:113410. [PMID: 37976161 PMCID: PMC10872586 DOI: 10.1016/j.celrep.2023.113410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/29/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023] Open
Abstract
IGHV1-69 is frequently utilized by broadly neutralizing influenza antibodies to the hemagglutinin (HA) stem. These IGHV1-69 HA stem antibodies have diverse complementarity-determining region (CDR) H3 sequences. Besides, their light chains have minimal to no contact with the epitope. Consequently, sequence determinants that confer IGHV1-69 antibodies with HA stem specificity remain largely elusive. Using high-throughput experiments, this study reveals the importance of light-chain sequence for the IGHV1-69 HA stem antibody CR9114, which is the broadest influenza antibody known to date. Moreover, we demonstrate that the CDR H3 sequences from many other IGHV1-69 antibodies, including those to the HA stem, are incompatible with CR9114. Along with mutagenesis and structural analysis, our results indicate that light-chain and CDR H3 sequences coordinately determine the HA stem specificity of IGHV1-69 antibodies. Overall, this work provides molecular insights into broadly neutralizing antibody responses to influenza virus, which have important implications for universal influenza vaccine development.
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Affiliation(s)
- Qi Wen Teo
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Huibin Lv
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruipeng Lei
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Kevin J Mao
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
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132
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Deng Y, Atyeo C, Yuan D, Chicz TM, Tibbitts T, Gorman M, Taylor S, Lecouturier V, Lauffenburger DA, Chicz RM, Alter G, McNamara RP. Beta-spike-containing boosters induce robust and functional antibody responses to SARS-CoV-2 in macaques primed with distinct vaccines. Cell Rep 2023; 42:113292. [PMID: 38007686 DOI: 10.1016/j.celrep.2023.113292] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/29/2023] [Accepted: 09/29/2023] [Indexed: 11/27/2023] Open
Abstract
The reduced effectiveness of COVID-19 vaccines due to the emergence of variants of concern (VOCs) necessitated the use of vaccine boosters to bolster protection against disease. However, it remains unclear how boosting expands protective breadth when primary vaccine platforms are distinct and how boosters containing VOC spike(s) broaden humoral responses. Here, we report that boosters composed of recombinant spike antigens of ancestral (prototype) and Beta VOCs elicit a robust, pan-VOC, and multi-functional humoral response in non-human primates largely independent of the primary vaccine series platform. Interestingly, Beta-spike-containing boosters stimulate immunoglobulin A (IgA) with a greater breadth of recognition in protein-primed recipients when administered with adjuvant system 03 (AS03). Our results highlight the utility of a component-based booster strategy for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for broad humoral recognition, independent of primary vaccine series. This is of high global health importance given the heterogeneity of primary vaccination platforms distributed.
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Affiliation(s)
- Yixiang Deng
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Dansu Yuan
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Taras M Chicz
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Matthew Gorman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Sabian Taylor
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | | | | | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Ryan P McNamara
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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133
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Zaman N, Parvaiz N, Gul F, Yousaf R, Gul K, Azam SS. Dynamics of water-mediated interaction effects on the stability and transmission of Omicron. Sci Rep 2023; 13:20894. [PMID: 38017052 PMCID: PMC10684572 DOI: 10.1038/s41598-023-48186-2] [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: 11/24/2022] [Accepted: 11/23/2023] [Indexed: 11/30/2023] Open
Abstract
SARS-Cov-2 Omicron variant and its highly transmissible sublineages amidst news of emerging hybrid variants strengthen the evidence of its ability to rapidly spread and evolve giving rise to unprecedented future waves. Owing to the presence of isolated RBD, monomeric and trimeric Cryo-EM structures of spike protein in complex with ACE2 receptor, comparative analysis of Alpha, Beta, Gamma, Delta, and Omicron assist in a rational assessment of their probability to evolve as new or hybrid variants in future. This study proposes the role of hydration forces in mediating Omicron function and dynamics based on a stronger interplay between protein and solvent with each Covid wave. Mutations of multiple hydrophobic residues into hydrophilic residues underwent concerted interactions with water leading to variations in charge distribution in Delta and Omicron during molecular dynamics simulations. Moreover, comparative analysis of interacting moieties characterized a large number of mutations lying at RBD into constrained, homologous and low-affinity groups referred to as mutational drivers inferring that the probability of future mutations relies on their function. Furthermore, the computational findings reveal a significant difference in angular distances among variants of concern due 3 amino acid insertion (EPE) in Omicron variant that not only facilitates tight domain organization but also seems requisite for characterization of mutational processes. The outcome of this work signifies the possible relation between hydration forces, their impact on conformation and binding affinities, and viral fitness that will significantly aid in understanding dynamics of drug targets for Covid-19 countermeasures. The emerging scenario is that hydration forces and hydrophobic interactions are crucial variables to probe in mutational analysis to explore conformational landscape of macromolecules and reveal the molecular origins of protein behaviors.
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Affiliation(s)
- Naila Zaman
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Nousheen Parvaiz
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Fouzia Gul
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Rimsha Yousaf
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Kainat Gul
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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134
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Lorenzo-Redondo R, de Sant’Anna Carvalho AM, Hultquist JF, Ozer EA. SARS-CoV-2 genomics and impact on clinical care for COVID-19. J Antimicrob Chemother 2023; 78:ii25-ii36. [PMID: 37995357 PMCID: PMC10667012 DOI: 10.1093/jac/dkad309] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/02/2023] [Indexed: 11/25/2023] Open
Abstract
The emergence and worldwide spread of SARS-CoV-2 during the COVID-19 pandemic necessitated the adaptation and rapid deployment of viral WGS and analysis techniques that had been previously applied on a more limited basis to other viral pathogens, such as HIV and influenza viruses. The need for WGS was driven in part by the low mutation rate of SARS-CoV-2, which necessitated measuring variation along the entire genome sequence to effectively differentiate lineages and characterize viral evolution. Several WGS approaches designed to maximize throughput and accuracy were quickly adopted by surveillance labs around the world. These broad-based SARS-CoV-2 genomic sequencing efforts revealed ongoing evolution of the virus, highlighted by the successive emergence of new viral variants throughout the course of the pandemic. These genomic insights were instrumental in characterizing the effects of viral mutations on transmissibility, immune escape and viral tropism, which in turn helped guide public health policy, the use of monoclonal antibody therapeutics and vaccine development strategies. As the use of direct-acting antivirals for the treatment of COVID-19 became more widespread, the potential for emergence of antiviral resistance has driven ongoing efforts to delineate resistance mutations and to monitor global sequence databases for their emergence. Given the critical role of viral genomics in the international effort to combat the COVID-19 pandemic, coordinated efforts should be made to expand global genomic surveillance capacity and infrastructure towards the anticipation and prevention of future pandemics.
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Affiliation(s)
- Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Alexandre Machado de Sant’Anna Carvalho
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
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135
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Tsishyn M, Pucci F, Rooman M. Quantification of biases in predictions of protein-protein binding affinity changes upon mutations. Brief Bioinform 2023; 25:bbad491. [PMID: 38197311 PMCID: PMC10777193 DOI: 10.1093/bib/bbad491] [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: 06/30/2023] [Revised: 10/02/2023] [Accepted: 12/05/2023] [Indexed: 01/11/2024] Open
Abstract
Understanding the impact of mutations on protein-protein binding affinity is a key objective for a wide range of biotechnological applications and for shedding light on disease-causing mutations, which are often located at protein-protein interfaces. Over the past decade, many computational methods using physics-based and/or machine learning approaches have been developed to predict how protein binding affinity changes upon mutations. They all claim to achieve astonishing accuracy on both training and test sets, with performances on standard benchmarks such as SKEMPI 2.0 that seem overly optimistic. Here we benchmarked eight well-known and well-used predictors and identified their biases and dataset dependencies, using not only SKEMPI 2.0 as a test set but also deep mutagenesis data on the severe acute respiratory syndrome coronavirus 2 spike protein in complex with the human angiotensin-converting enzyme 2. We showed that, even though most of the tested methods reach a significant degree of robustness and accuracy, they suffer from limited generalizability properties and struggle to predict unseen mutations. Interestingly, the generalizability problems are more severe for pure machine learning approaches, while physics-based methods are less affected by this issue. Moreover, undesirable prediction biases toward specific mutation properties, the most marked being toward destabilizing mutations, are also observed and should be carefully considered by method developers. We conclude from our analyses that there is room for improvement in the prediction models and suggest ways to check, assess and improve their generalizability and robustness.
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Affiliation(s)
- Matsvei Tsishyn
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Roosevelt Ave, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Roosevelt Ave, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Roosevelt Ave, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium
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136
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Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Accurate Characterization of Conformational Ensembles and Binding Mechanisms of the SARS-CoV-2 Omicron BA.2 and BA.2.86 Spike Protein with the Host Receptor and Distinct Classes of Antibodies Using AlphaFold2-Augmented Integrative Computational Modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.18.567697. [PMID: 38045395 PMCID: PMC10690158 DOI: 10.1101/2023.11.18.567697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The latest wave SARS-CoV-2 Omicron variants displayed a growth advantage and the increased viral fitness through convergent evolution of functional hotspots that work synchronously to balance fitness requirements for productive receptor binding and efficient immune evasion. In this study, we combined AlphaFold2-based structural modeling approaches with all-atom MD simulations and mutational profiling of binding energetics and stability for prediction and comprehensive analysis of the structure, dynamics, and binding of the SARS-CoV-2 Omicron BA.2.86 spike variant with ACE2 host receptor and distinct classes of antibodies. We adapted several AlphaFold2 approaches to predict both structure and conformational ensembles of the Omicron BA.2.86 spike protein in the complex with the host receptor. The results showed that AlphaFold2-predicted conformational ensemble of the BA.2.86 spike protein complex can accurately capture the main dynamics signatures obtained from microscond molecular dynamics simulations. The ensemble-based dynamic mutational scanning of the receptor binding domain residues in the BA.2 and BA.2.86 spike complexes with ACE2 dissected the role of the BA.2 and BA.2.86 backgrounds in modulating binding free energy changes revealing a group of conserved hydrophobic hotspots and critical variant-specific contributions of the BA.2.86 mutational sites R403K, F486P and R493Q. To examine immune evasion properties of BA.2.86 in atomistic detail, we performed large scale structure-based mutational profiling of the S protein binding interfaces with distinct classes of antibodies that displayed significantly reduced neutralization against BA.2.86 variant. The results quantified specific function of the BA.2.86 mutations to ensure broad resistance against different classes of RBD antibodies. This study revealed the molecular basis of compensatory functional effects of the binding hotspots, showing that BA.2.86 lineage may have primarily evolved to improve immune escape while modulating binding affinity with ACE2 through cooperative effect of R403K, F486P and R493Q mutations. The study supports a hypothesis that the impact of the increased ACE2 binding affinity on viral fitness is more universal and is mediated through cross-talk between convergent mutational hotspots, while the effect of immune evasion could be more variant-dependent.
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137
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Maes S, Deploey N, Peelman F, Eyckerman S. Deep mutational scanning of proteins in mammalian cells. CELL REPORTS METHODS 2023; 3:100641. [PMID: 37963462 PMCID: PMC10694495 DOI: 10.1016/j.crmeth.2023.100641] [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: 05/12/2023] [Revised: 07/06/2023] [Accepted: 10/20/2023] [Indexed: 11/16/2023]
Abstract
Protein mutagenesis is essential for unveiling the molecular mechanisms underlying protein function in health, disease, and evolution. In the past decade, deep mutational scanning methods have evolved to support the functional analysis of nearly all possible single-amino acid changes in a protein of interest. While historically these methods were developed in lower organisms such as E. coli and yeast, recent technological advancements have resulted in the increased use of mammalian cells, particularly for studying proteins involved in human disease. These advancements will aid significantly in the classification and interpretation of variants of unknown significance, which are being discovered at large scale due to the current surge in the use of whole-genome sequencing in clinical contexts. Here, we explore the experimental aspects of deep mutational scanning studies in mammalian cells and report the different methods used in each step of the workflow, ultimately providing a useful guide toward the design of such studies.
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Affiliation(s)
- Stefanie Maes
- VIB Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Nick Deploey
- VIB Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Frank Peelman
- VIB Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.
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138
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Yousefbeigi S, Marsusi F. Structural insights into ACE2 interactions and immune activation of SARS-CoV-2 and its variants: an in-silico study. J Biomol Struct Dyn 2023:1-14. [PMID: 37982275 DOI: 10.1080/07391102.2023.2283158] [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: 10/15/2022] [Accepted: 11/08/2023] [Indexed: 11/21/2023]
Abstract
The initial interaction between COVID-19 and the human body involves the receptor-binding domain (RBD) of the viral spike protein with the angiotensin-converting enzyme 2 (ACE2) receptor. Likewise, the spike protein can engage with immune-related proteins, such as toll-like receptors (TLRs) and pulmonary surfactant proteins A (SP-A) and D (SP-D), thereby triggering immune responses. In this study, we utilize computational methods to investigate the interactions between the spike protein and TLRs (specifically TLR2 and TLR4), as well as (SP-A) and (SP-D). The study is conducted on four variants of concern (VOC) to differentiate and identify common virus behaviours. An assessment of the structural stability of various variants indicates slight changes attributed to mutations, yet overall structural integrity remains preserved. Our findings reveal the spike protein's ability to bind with TLR4 and TLR2, prompting immune activation. In addition, our in-silico results reveal almost similar docking scores and therefore affinity for both ACE2-spike and TLR4-spike complexes. We demonstrate that even minor changes due to mutations in all variants, surfactant A and D proteins can function as inhibitors against the spike in all variants, hindering the ACE2-RBD interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sarina Yousefbeigi
- Department of Physics and Energy Engineering, Amirkabir University of Technology, Tehran, Iran
| | - Farah Marsusi
- Department of Physics and Energy Engineering, Amirkabir University of Technology, Tehran, Iran
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139
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Hoskins I, Rao S, Tante C, Cenik C. Integrated multiplexed assays of variant effect reveal cis-regulatory determinants of catechol- O-methyltransferase gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551517. [PMID: 38014045 PMCID: PMC10680568 DOI: 10.1101/2023.08.02.551517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Multiplexed assays of variant effect are powerful methods to profile the consequences of rare variants on gene expression and organismal fitness. Yet, few studies have integrated several multiplexed assays to map variant effects on gene expression in coding sequences. Here, we pioneered a multiplexed assay based on polysome profiling to measure variant effects on translation at scale, uncovering single-nucleotide variants that increase and decrease ribosome load. By combining high-throughput ribosome load data with multiplexed mRNA and protein abundance readouts, we mapped the cis-regulatory landscape of thousands of catechol-O-methyltransferase (COMT) variants from RNA to protein and found numerous coding variants that alter COMT expression. Finally, we trained machine learning models to map signatures of variant effects on COMT gene expression and uncovered both directional and divergent impacts across expression layers. Our analyses reveal expression phenotypes for thousands of variants in COMT and highlight variant effects on both single and multiple layers of expression. Our findings prompt future studies that integrate several multiplexed assays for the readout of gene expression.
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Affiliation(s)
- Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Charisma Tante
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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140
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Gomez-Romero N, Basurto-Alcantara FJ, Velazquez-Salinas L. Assessing the Potential Role of Cats ( Felis catus) as Generators of Relevant SARS-CoV-2 Lineages during the Pandemic. Pathogens 2023; 12:1361. [PMID: 38003825 PMCID: PMC10675002 DOI: 10.3390/pathogens12111361] [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: 10/07/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Several questions regarding the evolution of SARS-CoV-2 remain poorly elucidated. One of these questions is the possible evolutionary impact of SARS-CoV-2 after the infection in domestic animals. In this study, we aimed to evaluate the potential role of cats as generators of relevant SARS-CoV-2 lineages during the pandemic. A total of 105 full-length genome viral sequences obtained from naturally infected cats during the pandemic were evaluated by distinct evolutionary algorithms. Analyses were enhanced, including a set of highly related SARS-CoV-2 sequences recovered from human populations. Our results showed the apparent high susceptibility of cats to the infection SARS-CoV-2 compared with other animal species. Evolutionary analyses indicated that the phylogenomic characteristics displayed by cat populations were influenced by the dominance of specific SARS-CoV-2 genetic groups affecting human populations. However, disparate dN/dS rates at some genes between populations recovered from cats and humans suggested that infection in these two species may suggest a different evolutionary constraint for SARS-CoV-2. Interestingly, the branch selection analysis showed evidence of the potential role of natural selection in the emergence of five distinct cat lineages during the pandemic. Although these lineages were apparently irrelevant to public health during the pandemic, our results suggested that additional studies are needed to understand the role of other animal species in the evolution of SARS-CoV-2 during the pandemic.
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Affiliation(s)
- Ninnet Gomez-Romero
- Comisión México-Estados Unidos para la Prevención de Fiebre Aftosa y Otras Enfermedades Exóticas de los Animales, Carretera Mexico-Toluca Km 15.5 Piso 4 Col. Palo Alto, Cuajimalpa de Morelos, Mexico City 05110, Mexico;
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Av. Universidad No. 3000 Col Copilco Universidad, Mexico City 14510, Mexico;
| | - Francisco Javier Basurto-Alcantara
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Av. Universidad No. 3000 Col Copilco Universidad, Mexico City 14510, Mexico;
| | - Lauro Velazquez-Salinas
- Plum Island Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Greenport, NY 11944, USA
- National Bio and Agro-Defense Facility (NBAF), Agricultural Research Service, United States Department of Agriculture, Manhattan, KS 66502, USA
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141
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Schröder S, Richter A, Veith T, Emanuel J, Gudermann L, Friedmann K, Jeworowski LM, Mühlemann B, Jones TC, Müller MA, Corman VM, Drosten C. Characterization of intrinsic and effective fitness changes caused by temporarily fixed mutations in the SARS-CoV-2 spike E484 epitope and identification of an epistatic precondition for the evolution of E484A in variant Omicron. Virol J 2023; 20:257. [PMID: 37940989 PMCID: PMC10633978 DOI: 10.1186/s12985-023-02154-4] [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: 06/23/2023] [Accepted: 08/08/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Intrinsic fitness costs are likely to have guided the selection of lineage-determining mutations during emergence of variants of SARS-CoV-2. Whereas changes in receptor affinity and antibody neutralization have been thoroughly mapped for individual mutations in spike, their influence on intrinsic replicative fitness remains understudied. METHODS We analyzed mutations in immunodominant spike epitope E484 that became temporarily fixed over the pandemic. We engineered the resulting immune escape mutations E484K, -A, and -Q in recombinant SARS-CoV-2. We characterized viral replication, entry, and competitive fitness with and without immune serum from humans with defined exposure/vaccination history and hamsters monospecifically infected with the E484K variant. We additionally engineered a virus containing the Omicron signature mutations N501Y and Q498R that were predicted to epistatically enhance receptor binding. RESULTS Multistep growth kinetics in Vero-, Calu-3, and NCI-H1299 were identical between viruses. Synchronized entry experiments based on cold absorption and temperature shift identified only an insignificant trend toward faster entry of the E484K variant. Competitive passage experiments revealed clear replicative fitness differences. In absence of immune serum, E484A and E484Q, but not E484K, were replaced by wildtype (WT) in competition assays. In presence of immune serum, all three mutants outcompeted WT. Decreased E484A fitness levels were over-compensated for by N501Y and Q498R, identifying a putative Omicron founder background that exceeds the intrinsic and effective fitness of WT and matches that of E484K. Critically, the E484A/Q498R/N501Y mutant and E484K have equal fitness also in presence of pre-Omicron vaccinee serum, whereas the fitness gain by E484K is lost in the presence of serum raised against the E484K variant in hamsters. CONCLUSIONS The emergence of E484A and E484Q prior to widespread population immunity may have been limited by fitness costs. In populations already exposed to the early immune escape epitope E484K, the Omicron founder background may have provided a basis for alternative immune escape evolution via E484A. Studies of major antigenic epitope changes with and without their epistatic context help reconstruct the sequential adjustments of intrinsic fitness versus neutralization escape during the evolution of major SARS-CoV-2 variants in an increasingly immune human population.
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Affiliation(s)
- Simon Schröder
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Anja Richter
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Talitha Veith
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jackson Emanuel
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Luca Gudermann
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Kirstin Friedmann
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lara M Jeworowski
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Barbara Mühlemann
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Terry C Jones
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Downing St, CB2 3EJ, Cambridge, U.K
| | - Marcel A Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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142
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Ogbunugafor CB, Guerrero RF, Miller-Dickson MD, Shakhnovich EI, Shoulders MD. Epistasis and pleiotropy shape biophysical protein subspaces associated with drug resistance. Phys Rev E 2023; 108:054408. [PMID: 38115433 PMCID: PMC10935598 DOI: 10.1103/physreve.108.054408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 09/19/2023] [Indexed: 12/21/2023]
Abstract
Protein space is a rich analogy for genotype-phenotype maps, where amino acid sequence is organized into a high-dimensional space that highlights the connectivity between protein variants. It is a useful abstraction for understanding the process of evolution, and for efforts to engineer proteins towards desirable phenotypes. Few mentions of protein space consider how protein phenotypes can be described in terms of their biophysical components, nor do they rigorously interrogate how forces like epistasis-describing the nonlinear interaction between mutations and their phenotypic consequences-manifest across these components. In this study, we deconstruct a low-dimensional protein space of a bacterial enzyme (dihydrofolate reductase; DHFR) into "subspaces" corresponding to a set of kinetic and thermodynamic traits [k_{cat}, K_{M}, K_{i}, and T_{m} (melting temperature)]. We then examine how combinations of three mutations (eight alleles in total) display pleiotropy, or unique effects on individual subspace traits. We examine protein spaces across three orthologous DHFR enzymes (Escherichia coli, Listeria grayi, and Chlamydia muridarum), adding a genotypic context dimension through which epistasis occurs across subspaces. In doing so, we reveal that protein space is a deceptively complex notion, and that future applications to bioengineering should consider how interactions between amino acid substitutions manifest across different phenotypic subspaces.
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Affiliation(s)
- C. Brandon Ogbunugafor
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Rafael F. Guerrero
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | | | - Eugene I. Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Matthew D. Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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143
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Roemer C, Sheward DJ, Hisner R, Gueli F, Sakaguchi H, Frohberg N, Schoenmakers J, Sato K, O'Toole Á, Rambaut A, Pybus OG, Ruis C, Murrell B, Peacock TP. SARS-CoV-2 evolution in the Omicron era. Nat Microbiol 2023; 8:1952-1959. [PMID: 37845314 DOI: 10.1038/s41564-023-01504-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 09/13/2023] [Indexed: 10/18/2023]
Abstract
Since SARS-CoV-2 BA.5 (Omicron) emerged and spread in 2022, Omicron lineages have markedly diversified. Here we review the evolutionary trajectories and processes that underpin the emergence of these lineages, and identify the most prevalent sublineages. We discuss the potential origins of second-generation BA.2 lineages. Simple and complex recombination, antigenic drift and convergent evolution have enabled SARS-CoV-2 to accumulate mutations that alter its antigenicity. We also discuss the potential evolutionary trajectories of SARS-CoV-2 in the future.
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Affiliation(s)
- Cornelius Roemer
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ryan Hisner
- University of Cape Town, Rondebosch, South Africa
| | | | | | | | | | - Kenta Sato
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Áine O'Toole
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
| | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK.
- The Pirbright Institute, Woking, UK.
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144
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Frisby TS, Langmead CJ. Identifying promising sequences for protein engineering using a deep transformer protein language model. Proteins 2023; 91:1471-1486. [PMID: 37337902 DOI: 10.1002/prot.26536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/10/2023] [Accepted: 05/23/2023] [Indexed: 06/21/2023]
Abstract
Protein engineers aim to discover and design novel sequences with targeted, desirable properties. Given the near limitless size of the protein sequence landscape, it is no surprise that these desirable sequences are often a relative rarity. This makes identifying such sequences a costly and time-consuming endeavor. In this work, we show how to use a deep transformer protein language model to identify sequences that have the most promise. Specifically, we use the model's self-attention map to calculate a Promise Score that weights the relative importance of a given sequence according to predicted interactions with a specified binding partner. This Promise Score can then be used to identify strong binders worthy of further study and experimentation. We use the Promise Score within two protein engineering contexts-Nanobody (Nb) discovery and protein optimization. With Nb discovery, we show how the Promise Score provides an effective way to select lead sequences from Nb repertoires. With protein optimization, we show how to use the Promise Score to select site-specific mutagenesis experiments that identify a high percentage of improved sequences. In both cases, we also show how the self-attention map used to calculate the Promise Score can indicate which regions of a protein are involved in intermolecular interactions that drive the targeted property. Finally, we describe how to fine-tune the transformer protein language model to learn a predictive model for the targeted property, and discuss the capabilities and limitations of fine-tuning with and without knowledge transfer within the context of protein engineering.
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Affiliation(s)
- Trevor S Frisby
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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145
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Pitsillou E, Yu Y, Beh RC, Liang JJ, Hung A, Karagiannis TC. Chronicling the 3-year evolution of the COVID-19 pandemic: analysis of disease management, characteristics of major variants, and impacts on pathogenicity. Clin Exp Med 2023; 23:3277-3298. [PMID: 37615803 DOI: 10.1007/s10238-023-01168-0] [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] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
Announced on December 31, 2019, the novel coronavirus arising in Wuhan City, Hubei Province resulted in millions of cases and lives lost. Following intense tracking, coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health Organization (WHO) in 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of COVID-19 and the continuous evolution of the virus has given rise to several variants. In this review, a comprehensive analysis of the response to the pandemic over the first three-year period is provided, focusing on disease management, development of vaccines and therapeutics, and identification of variants. The transmissibility and pathogenicity of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron are compared. The binding characteristics of the SARS-CoV-2 spike protein to the angiotensin-converting enzyme 2 (ACE2) receptor and reproduction numbers are evaluated. The effects of major variants on disease severity, hospitalisation, and case-fatality rates are outlined. In addition to the spike protein, open reading frames mutations are investigated. We also compare the pathogenicity of SARS-CoV-2 with SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Overall, this study highlights the strengths and weaknesses of the global response to the pandemic, as well as the importance of prevention and preparedness. Monitoring the evolution of SARS-CoV-2 is critical in identifying and potentially predicting the health outcomes of concerning variants as they emerge. The ultimate goal would be a position in which existing vaccines and therapeutics could be adapted to suit new variants in as close to real-time as possible.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Yiping Yu
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Raymond C Beh
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Julia J Liang
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia.
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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146
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Sevilya Z, Kuzmina A, Cipok M, Hershkovitz V, Keidar-Friedman D, Taube R, Lev EI. Differential platelet activation through an interaction with spike proteins of different SARS-CoV-2 variants. J Thromb Thrombolysis 2023; 56:538-547. [PMID: 37736784 DOI: 10.1007/s11239-023-02891-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
Abstract
COVID-19 disease is associated with an increased risk of thrombotic complications, which contribute to high short-term mortality. Patients with COVID-19 demonstrate enhanced platelet turnover and reactivity, which may have a role in the development of thrombotic events and disease severity. Evidence has suggested direct interaction between SARS-CoV-2 and platelets, resulting in platelets activation. Here, we compare the effect of various SARS-CoV-2 spike variants on platelet activation. Engineered lentiviral particles were pseudotyped with spike SARS-CoV-2 variants and incubated with Platelet Rich Plasma obtained from healthy individuals. The pseudotyped SARS-CoV-2 exhibiting the wild-type Wuhan-Hu spike protein stimulated platelets to increase expression of the surface CD62P and activated αIIbβ3 markers by 3.5 ± 1.2 and 3.3 ± 0.7 fold, respectively (P = 0.004 and 0.003). The Delta variant induced much higher levels of platelet activation; CD62P expression was increased by 6.6 ± 2.2 fold and activated αIIbβ3 expression was increased by 5.0 ± 1.5 fold (P = 0.005 and 0.026, respectively). The Omicron BA.1 and the Alpha variants induced the lowest level of activation; CD62P expression was increased by 1.7 ± 0.4 and 1.6 ± 0.9 fold, respectively (P = 0.003 and 0.008), and activated αIIbβ3 expression by 1.8 ± 1.1 and 1.6 ± 0.8, respectively (P = 0.003 and 0.001). The Omicron BA.2 variant induced an increase of platelets activation comparable to the Wuhan-Hu (2.8 ± 1.2 and 2.1 ± 1.3 fold for CD62P and activated αIIbβ3 markers, respectively). The results obtained for various COVID-19 variants are in correlation with the clinical severity and mortality reported for these variants.
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Affiliation(s)
- Ziv Sevilya
- Cardiology Department, Assuta Ashdod Medical Center, Ashdod, Israel.
| | - Alona Kuzmina
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Michal Cipok
- Hematology Laboratory, Assuta Ashdod Medical Center, Ashdod, Israel
| | - Vera Hershkovitz
- Hematology Laboratory, Assuta Ashdod Medical Center, Ashdod, Israel
| | | | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Eli I Lev
- Cardiology Department, Assuta Ashdod Medical Center, Ashdod, Israel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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147
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Bhattacharya M, Chatterjee S, Lee SS, Dhama K, Chakraborty C. Antibody evasion associated with the RBD significant mutations in several emerging SARS-CoV-2 variants and its subvariants. Drug Resist Updat 2023; 71:101008. [PMID: 37757651 DOI: 10.1016/j.drup.2023.101008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
Since the origin of the wild strain of SARS-CoV-2, several variants have emerged, which were designated as VOC, VOI, and VUM from time to time. The Omicron variant is noted as the recent VOC. After the origin of the Omicron variant on November 2021, several subvariants of Omicron have originated subsequently, like BA.1/2, BA.2.75/2.75.2, BA.4/5, BF.7, BQ.1/1.1, XBB.1/1.5, etc. which are circulated throughout the globe. Scientists reported that antibody escape is a common phenomenon observed in all the previous VOCs, VOIs, including Omicron and its subvariants. The mutations in the NTD (N-terminal domain) and RBD (Receptor-binding domain) of the spike of these variants and subvariants are responsible for antibody escape. At the same time, it has been noted that spike RBD mutations have been increasing in the last few months. This review illustrates significant RBD mutations namely R346T, K417N/T, L452R, N460K E484A/K/Q, and N501Y found in the previous emerging SARS-CoV-2 variants, including Omicron and its subvariants in high frequency and their role in antibody evasion and immune evasion. The review also describes the different classes of nAb responsible for antibody escape in SARS-CoV-2 variants and the molecular perspective of the mutation in nAb escape. It will help the future researchers to develop efficient vaccines which can finally prevent the pandemic.
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Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Srijan Chatterjee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata 700126, West Bengal, India.
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148
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Hannon WW, Bloom JD. dms-viz: Structure-informed visualizations for deep mutational scanning and other mutation-based datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.29.564578. [PMID: 37961289 PMCID: PMC10634933 DOI: 10.1101/2023.10.29.564578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Understanding how mutations impact a protein's functions is valuable for many types of biological questions. High-throughput techniques such as deep-mutational scanning (DMS) have greatly expanded the number of mutation-function datasets. For instance, DMS has been used to determine how mutations to viral proteins affect antibody escape (Dadonaite et al. 2023), receptor affinity (Starr et al. 2020), and essential functions such as viral genome transcription and replication (Li et al. 2023). With the growth of sequence databases, in some cases the effects of mutations can also be inferred from phylogenies of natural sequences (Bloom and Neher 2023) (Figure 1). The mutation-based data generated by these approaches is often best understood in the context of a protein's 3D structure; for instance, to assess questions like how mutations that affect antibody escape relate to the physical antibody binding epitope on the protein. However, current approaches for visualizing mutation data in the context of a protein's structure are often cumbersome and require multiple steps and softwares. To streamline the visualization of mutation-associated data in the context of a protein structure, we developed a web-based tool, dms-viz. With dms-viz, users can straightforwardly visualize mutation-based data such as those from DMS experiments in the context of a 3D protein model in an interactive format. See https://dms-viz.github.io/ to use dms-viz.
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Affiliation(s)
- William W Hannon
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98109
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Jesse D Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Department of Genome Sciences, University of Washington, Seattle, WA 98109
- Howard Hughes Medical Institute, Seattle, WA 98109
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149
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Sun J, Liu X, Zhang S, Li M, Zhang Q, Chen J. Molecular insights and optimization strategies for the competitive binding of engineered ACE2 proteins: a multiple replica molecular dynamics study. Phys Chem Chem Phys 2023; 25:28479-28496. [PMID: 37846774 DOI: 10.1039/d3cp03392a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to spread globally, and rapid viral evolution and the emergence of new variants pose challenges to pandemic control. During infection, the spike protein of SARS-CoV-2 interacts with the human ACE2 protein via its receptor binding domain (RBD), and it is known that engineered forms of ACE2 can compete with wild-type (WT) ACE2 for binding to inhibit infection. Here, we conducted multiple replica molecular dynamics (MRMD) simulations to study the mechanisms of the engineered ACE2 variants 3N39 and 3N94 and provide directions for optimization. Our findings reveal that engineered ACE2 is notably more efficacious in systems that show weaker binding to WT ACE2 (i.e., WT and BA.1 RBD), but also faces immune escape as the virus evolves. Moreover, by modifying residue types near the binding interface, engineered ACE2 alters the electrostatic potential distribution and reconfigures the hydrogen bonding network, which results in modified binding to the RBD. However, this structural rearrangement does not occur in all RBD variants. In addition, we identified potentially engineerable beneficial residues and potentially engineerable detrimental residues in both ACE2 and RBD. Functional conservation can thus enable the optimization of these residues and improve the binding competitiveness of engineered ACE2, which therefore provides additional immune escape prevention. Finally, we conclude that these findings have implications for understanding the mechanisms responsible for engineered ACE2 and can help us to develop engineered ACE2 proteins that show superior performance.
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Affiliation(s)
- Jiahao Sun
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Meng Li
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250357, China.
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150
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Focosi D, Spezia PG, Maggi F. SARS-CoV-2 BA.2.86 ("Pirola"): Is it Pi or Just Another Omicron Sublineage? Vaccines (Basel) 2023; 11:1634. [PMID: 38005966 PMCID: PMC10674951 DOI: 10.3390/vaccines11111634] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 11/26/2023] Open
Abstract
The SARS-CoV-2 sublineage BA [...].
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy
| | - Pietro Giorgio Spezia
- National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (P.G.S.); (F.M.)
| | - Fabrizio Maggi
- National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (P.G.S.); (F.M.)
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