101
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Ogbunugafor CB, Guerrero RF, Shakhnovich EI, Shoulders MD. Epistasis meets pleiotropy in shaping biophysical protein subspaces associated with antimicrobial resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.09.535490. [PMID: 37066177 PMCID: PMC10104174 DOI: 10.1101/2023.04.09.535490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
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 framings of protein space consider how higher-level protein phenotypes can be described in terms of their biophysical dimensions, nor do they rigorously interrogate how forces like epistasis-describing the nonlinear interaction between mutations and their phenotypic consequences-manifest across these dimensions. 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 [(kcat, KM, Ki, and Tm (melting temperature)]. We then examine how three mutations (eight alleles in total) display pleiotropy in their interactions across these subspaces. We extend this approach to 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 the process of protein evolution and engineering 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, CT
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA
- Santa Fe Institute, Santa Fe, NM
| | - Rafael F. Guerrero
- Department of Biological Sciences, North Carolina State University, Raleigh, NC
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102
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Wei X, Chen J, Guo-Wei W. Persistent topological Laplacian analysis of SARS-CoV-2 variants. ARXIV 2023:arXiv:2301.10865v2. [PMID: 36748007 PMCID: PMC9900960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Topological data analysis (TDA) is an emerging field in mathematics and data science. Its central technique, persistent homology, has had tremendous success in many science and engineering disciplines. However, persistent homology has limitations, including its inability to handle heterogeneous information, such as multiple types of geometric objects; being qualitative rather than quantitative, e.g., counting a 5-member ring the same as a 6-member ring, and a failure to describe non-topological changes, such as homotopic changes in protein-protein binding. Persistent topological Laplacians (PTLs), such as persistent Laplacian and persistent sheaf Laplacian, were proposed to overcome the limitations of persistent homology. In this work, we examine the modeling and analysis power of PTLs in the study of the protein structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike receptor binding domain (RBD). First, we employ PTLs to study how the RBD mutation-induced structural changes of RBD-angiotensin-converting enzyme 2 (ACE2) binding complexes are captured in the changes of spectra of the PTLs among SARS-CoV-2 variants. Additionally, we use PTLs to analyze the binding of RBD and ACE2-induced structural changes of various SARS-CoV-2 variants. Finally, we explore the impacts of computationally generated RBD structures on a topological deep learning paradigm and predictions of deep mutational scanning datasets for the SARS-CoV-2 Omicron BA.2 variant. Our results indicate that PTLs have advantages over persistent homology in analyzing protein structural changes and provide a powerful new TDA tool for data science.
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Affiliation(s)
- Xiaoqi Wei
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Jiahui Chen
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Wei Guo-Wei
- Department of Mathematics, Michigan State University, MI 48824, USA
- Department of Electrical and Computer Engineering, Michigan State University, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, MI 48824, USA
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103
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Alves RPDS, Wang YT, Mikulski Z, McArdle S, Shafee N, Valentine KM, Miller R, Verma SK, Batiz FAS, Maule E, Nguyen MN, Timis J, Mann C, Zandonatti M, Alarcon S, Rowe J, Kronenberg M, Weiskopf D, Sette A, Hastie K, Saphire EO, Festin S, Kim K, Shresta S. SARS-CoV-2 Omicron (B.1.1.529) shows minimal neurotropism in a double-humanized mouse model. Antiviral Res 2023; 212:105580. [PMID: 36940916 PMCID: PMC10027296 DOI: 10.1016/j.antiviral.2023.105580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/23/2023]
Abstract
Although severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) initially infects the respiratory tract, it also directly or indirectly affects other organs, including the brain. However, little is known about the relative neurotropism of SARS-CoV-2 variants of concern (VOCs), including Omicron (B.1.1.529), which emerged in November 2021 and has remained the dominant pathogenic lineage since then. To address this gap, we examined the relative ability of Omicron, Beta (B.1.351), and Delta (B.1.617.2) to infect the brain in the context of a functional human immune system by using human angiotensin-converting enzyme 2 (hACE2) knock-in triple-immunodeficient NGC mice with or without reconstitution with human CD34+ stem cells. Intranasal inoculation of huCD34+-hACE2-NCG mice with Beta and Delta resulted in productive infection of the nasal cavity, lungs, and brain on day 3 post-infection, but Omicron was surprisingly unique in its failure to infect either the nasal tissue or brain. Moreover, the same infection pattern was observed in hACE2-NCG mice, indicating that antiviral immunity was not responsible for the lack of Omicron neurotropism. In independent experiments, we demonstrate that nasal inoculation with Beta or with D614G, an ancestral SARS-CoV-2 with undetectable replication in huCD34+-hACE2-NCG mice, resulted in a robust response by human innate immune cells, T cells, and B cells, confirming that exposure to SARS-CoV-2, even without detectable infection, is sufficient to induce an antiviral immune response. Collectively, these results suggest that modeling of the neurologic and immunologic sequelae of SARS-CoV-2 infection requires careful selection of the appropriate SARS-CoV-2 strain in the context of a specific mouse model.
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Affiliation(s)
| | - Ying-Ting Wang
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Zbigniew Mikulski
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sara McArdle
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Norazizah Shafee
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kristen M Valentine
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Robyn Miller
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Shailendra Kumar Verma
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Fernanda Ana Sosa Batiz
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Erin Maule
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Michael N Nguyen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Julia Timis
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Colin Mann
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Michelle Zandonatti
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Suzie Alarcon
- Sequencing Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jenny Rowe
- Charles River Laboratories Research Models and Services Inc., Wilmington, MA, USA
| | - Mitchell Kronenberg
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Kathryn Hastie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Stephen Festin
- Charles River Laboratories Research Models and Services Inc., Wilmington, MA, USA
| | - Kenneth Kim
- Histopathology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA.
| | - Sujan Shresta
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
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104
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Hoffmann M, Arora P, Nehlmeier I, Kempf A, Cossmann A, Schulz SR, Morillas Ramos G, Manthey LA, Jäck HM, Behrens GMN, Pöhlmann S. Profound neutralization evasion and augmented host cell entry are hallmarks of the fast-spreading SARS-CoV-2 lineage XBB.1.5. Cell Mol Immunol 2023; 20:419-422. [PMID: 36869193 PMCID: PMC9982771 DOI: 10.1038/s41423-023-00988-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 02/18/2023] [Indexed: 03/05/2023] Open
Affiliation(s)
- Markus Hoffmann
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany.
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany.
| | - Prerna Arora
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany
| | - Anne Cossmann
- Department for Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Sebastian R Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Glückstraße 6, 91054, Erlangen, Germany
| | - Gema Morillas Ramos
- Department for Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Luis A Manthey
- Department for Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Glückstraße 6, 91054, Erlangen, Germany
| | - Georg M N Behrens
- Department for Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
- Centre for Individualized Infection Medicine (CiiM), Feodor-Lynen-Straße 7, 30625, Hannover, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany
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105
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Yue C, Song W, Wang L, Jian F, Chen X, Gao F, Shen Z, Wang Y, Wang X, Cao Y. ACE2 binding and antibody evasion in enhanced transmissibility of XBB.1.5. THE LANCET. INFECTIOUS DISEASES 2023; 23:278-280. [PMID: 36746173 PMCID: PMC9897732 DOI: 10.1016/s1473-3099(23)00010-5] [Citation(s) in RCA: 178] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 02/05/2023]
Affiliation(s)
- Can Yue
- Chinese Academy of Sciences Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Changping Laboratory, Beijing 100871, China
| | - Weiliang Song
- Changping Laboratory, Beijing 100871, China; Biomedical Pioneering Innovation Center, Peking University, Beijing, China; School of Life Sciences, Peking University, Beijing, China
| | - Lei Wang
- Chinese Academy of Sciences Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fanchong Jian
- Chinese Academy of Sciences Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Changping Laboratory, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xiaosu Chen
- Chinese Academy of Sciences Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fei Gao
- Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin, China; Department of Pulmonary and Critical Care Medicine, The Fourth Hospital of Inner Mongolia, Hohhot, China
| | - Zhongyang Shen
- Organ Transplant Center, National Health Commission Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, China
| | - Youchun Wang
- Changping Laboratory, Beijing 100871, China; Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control, Beijing, China
| | - Xiangxi Wang
- Chinese Academy of Sciences Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Changping Laboratory, Beijing 100871, China.
| | - Yunlong Cao
- Changping Laboratory, Beijing 100871, China; Biomedical Pioneering Innovation Center, Peking University, Beijing, China.
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106
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Addetia A, Piccoli L, Case JB, Park YJ, Beltramello M, Guarino B, Dang H, Pinto D, Scheaffer S, Sprouse K, Bassi J, Silacci-Fregni C, Muoio F, Dini M, Vincenzetti L, Acosta R, Johnson D, Subramanian S, Saliba C, Giurdanella M, Lombardo G, Leoni G, Culap K, McAlister C, Rajesh A, Dellota E, Zhou J, Farhat N, Bohan D, Noack J, Lempp FA, Cameroni E, Whitener B, Giannini O, Ceschi A, Ferrari P, Franzetti-Pellanda A, Biggiogero M, Garzoni C, Zappi S, Bernasconi L, Kim MJ, Schnell G, Czudnochowski N, Franko N, Logue JK, Yoshiyama C, Stewart C, Chu H, Schmid MA, Purcell LIA, Snell G, Lanzavecchia A, Diamond M, Corti D, Veesler D. Therapeutic and vaccine-induced cross-reactive antibodies with effector function against emerging Omicron variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.17.523798. [PMID: 36711984 PMCID: PMC9882201 DOI: 10.1101/2023.01.17.523798] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Currently circulating SARS-CoV-2 variants acquired convergent mutations at receptor-binding domain (RBD) hot spots. Their impact on viral infection, transmission, and efficacy of vaccines and therapeutics remains poorly understood. Here, we demonstrate that recently emerged BQ.1.1. and XBB.1 variants bind ACE2 with high affinity and promote membrane fusion more efficiently than earlier Omicron variants. Structures of the BQ.1.1 and XBB.1 RBDs bound to human ACE2 and S309 Fab (sotrovimab parent) explain the altered ACE2 recognition and preserved antibody binding through conformational selection. We show that sotrovimab binds avidly to all Omicron variants, promotes Fc-dependent effector functions and protects mice challenged with BQ.1.1, the variant displaying the greatest loss of neutralization. Moreover, in several donors vaccine-elicited plasma antibodies cross-react with and trigger effector functions against Omicron variants despite reduced neutralizing activity. Cross-reactive RBD-directed human memory B cells remained dominant even after two exposures to Omicron spikes, underscoring persistent immune imprinting. Our findings suggest that this previously overlooked class of cross-reactive antibodies, exemplified by S309, may contribute to protection against disease caused by emerging variants through elicitation of effector functions.
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107
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Wang X, Yang Y, Song Z, Wang Y, Yang P, Li X, Wang F, Wang M, Shao L, Wang S. Concerns on Bebtelovimab (LY-CoV1404) used to neutralize Omicron subvariants. J Med Virol 2023; 95:e28565. [PMID: 36756927 DOI: 10.1002/jmv.28565] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/24/2022] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Affiliation(s)
- Xuejun Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yang Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,Youcare Pharmaceutical Group Co., Ltd., Beijing, China
| | - Zhifei Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yiming Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Peng Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,Youcare Pharmaceutical Group Co., Ltd., Beijing, China
| | - Xinyu Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fei Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,Youcare Pharmaceutical Group Co., Ltd., Beijing, China
| | - Mingming Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Liting Shao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shengqi Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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108
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Alexopoulos H, Trougakos IP, Dimopoulos MA, Terpos E. Serological testing for SARS-CoV-2: Advancements and future challenges. Eur J Intern Med 2023; 108:104-105. [PMID: 36586739 PMCID: PMC9792420 DOI: 10.1016/j.ejim.2022.12.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 12/26/2022] [Indexed: 12/28/2022]
Affiliation(s)
- Harry Alexopoulos
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Athens 15784, Greece
| | - Ioannis P Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Athens 15784, Greece
| | - Meletios-Athanasios Dimopoulos
- Department of Clinical Therapeutics, School of Medicine, Alexandra General Hospital, National and Kapodistrian University of Athens, Athens 11528, Greece
| | - Evangelos Terpos
- Department of Clinical Therapeutics, School of Medicine, Alexandra General Hospital, National and Kapodistrian University of Athens, Athens 11528, Greece.
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109
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Cao Y, Jian F, Wang J, Yu Y, Song W, Yisimayi A, Wang J, An R, Chen X, Zhang N, Wang Y, Wang P, Zhao L, Sun H, Yu L, Yang S, Niu X, Xiao T, Gu Q, Shao F, Hao X, Xu Y, Jin R, Shen Z, Wang Y, Xie XS. Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution. Nature 2023; 614:521-529. [PMID: 36535326 PMCID: PMC9931576 DOI: 10.1038/s41586-022-05644-7] [Citation(s) in RCA: 266] [Impact Index Per Article: 133.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Continuous evolution of Omicron has led to a rapid and simultaneous emergence of numerous variants that display growth advantages over BA.5 (ref. 1). Despite their divergent evolutionary courses, mutations on their receptor-binding domain (RBD) converge on several hotspots. The driving force and destination of such sudden convergent evolution and its effect on humoral immunity remain unclear. Here we demonstrate that these convergent mutations can cause evasion of neutralizing antibody drugs and convalescent plasma, including those from BA.5 breakthrough infection, while maintaining sufficient ACE2-binding capability. BQ.1.1.10 (BQ.1.1 + Y144del), BA.4.6.3, XBB and CH.1.1 are the most antibody-evasive strains tested. To delineate the origin of the convergent evolution, we determined the escape mutation profiles and neutralization activity of monoclonal antibodies isolated from individuals who had BA.2 and BA.5 breakthrough infections2,3. Owing to humoral immune imprinting, BA.2 and especially BA.5 breakthrough infection reduced the diversity of the neutralizing antibody binding sites and increased proportions of non-neutralizing antibody clones, which, in turn, focused humoral immune pressure and promoted convergent evolution in the RBD. Moreover, we show that the convergent RBD mutations could be accurately inferred by deep mutational scanning profiles4,5, and the evolution trends of BA.2.75 and BA.5 subvariants could be well foreseen through constructed convergent pseudovirus mutants. These results suggest that current herd immunity and BA.5 vaccine boosters may not efficiently prevent the infection of Omicron convergent variants.
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Affiliation(s)
- Yunlong Cao
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China.
- Changping Laboratory, Beijing, P. R. China.
| | - Fanchong Jian
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P.R. China
| | - Jing Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- School of Life Sciences, Peking University, Beijing, P. R. China
| | | | - Weiliang Song
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- School of Life Sciences, Peking University, Beijing, P. R. China
| | - Ayijiang Yisimayi
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- School of Life Sciences, Peking University, Beijing, P. R. China
| | - Jing Wang
- Changping Laboratory, Beijing, P. R. China
| | - Ran An
- Changping Laboratory, Beijing, P. R. China
| | - Xiaosu Chen
- Institute for Immunology, College of Life Sciences, Nankai University, Tianjin, 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
| | | | - Haiyan Sun
- Changping Laboratory, Beijing, P. R. China
| | | | - Sijie Yang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, P. R. China
| | - Xiao Niu
- Biomedical Pioneering Innovation Center (BIOPIC), 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), Peking University, Beijing, P. R. China
- Joint Graduate Program of Peking-Tsinghua-NIBS, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | | | - Fei Shao
- Changping Laboratory, Beijing, P. R. China
| | - Xiaohua Hao
- Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
| | - Yanli Xu
- Beijing Ditan Hospital, Capital Medical University, 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
| | - Youchun Wang
- Changping Laboratory, Beijing, P. R. China.
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, P. R. China.
| | - Xiaoliang Sunney Xie
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China.
- Changping Laboratory, Beijing, P. R. China.
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110
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Nicot F, Trémeaux P, Latour J, Carcenac R, Demmou S, Jeanne N, Ranger N, De Smet C, Raymond S, Dimeglio C, Izopet J. Whole-genome single molecule real-time sequencing of SARS-CoV-2 Omicron. J Med Virol 2023; 95:e28564. [PMID: 36756931 DOI: 10.1002/jmv.28564] [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: 01/06/2023] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
New variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can only be identified using accurate sequencing methods. Single molecule real-time (SMRT) sequencing has been used to characterize Alpha and Delta variants, but not Omicron variants harboring numerous mutations in the SARS-CoV-2 genome. This study assesses the performance of a target capture SMRT sequencing protocol for whole genome sequencing (WGS) of SARS-CoV-2 Omicron variants and compared it to that of an amplicon SMRT sequencing protocol optimized for Omicron variants. The failure rate of the target capture protocol (6%) was lower than that of the amplicon protocol (34%, p < 0.001) on our data set, and the median genome coverage with the target capture protocol (98.6% [interquartile range (IQR): 86-99.4]) was greater than that with the amplicon protocol (76.6% [IQR: 66-89.6], [p < 0.001]). The percentages of samples with >95% whole genome coverage were 64% with the target capture protocol and 19% with the amplicon protocol (p < 0.05). The clades of 96 samples determined with both protocols were 93% concordant and the lineages of 59 samples were 100% concordant. Thus, target capture SMRT sequencing appears to be an efficient method for WGS, genotyping and detecting mutations of SARS-CoV-2 Omicron variants.
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Affiliation(s)
- Florence Nicot
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Pauline Trémeaux
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Justine Latour
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Romain Carcenac
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Sofia Demmou
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Nicolas Jeanne
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Noémie Ranger
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | | | - Stéphanie Raymond
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Chloé Dimeglio
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Jacques Izopet
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
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111
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Chen J, Wang R, Hozumi Y, Liu G, Qiu Y, Wei X, Wei GW. Emerging Dominant SARS-CoV-2 Variants. J Chem Inf Model 2023; 63:335-342. [PMID: 36577010 PMCID: PMC9843632 DOI: 10.1021/acs.jcim.2c01352] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Indexed: 12/29/2022]
Abstract
Accurate and reliable forecasting of emerging dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants enables policymakers and vaccine makers to get prepared for future waves of infections. The last three waves of SARS-CoV-2 infections caused by dominant variants, Omicron (BA.1), BA.2, and BA.4/BA.5, were accurately foretold by our artificial intelligence (AI) models built with biophysics, genotyping of viral genomes, experimental data, algebraic topology, and deep learning. On the basis of newly available experimental data, we analyzed the impacts of all possible viral spike (S) protein receptor-binding domain (RBD) mutations on the SARS-CoV-2 infectivity. Our analysis sheds light on viral evolutionary mechanisms, i.e., natural selection through infectivity strengthening and antibody resistance. We forecast that BP.1, BL*, BA.2.75*, BQ.1*, and particularly BN.1* have a high potential to become the new dominant variants to drive the next surge. Our key projection about these variants dominance made on Oct. 18, 2022 (see arXiv:2210.09485) became reality in late November 2022.
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Affiliation(s)
- Jiahui Chen
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Rui Wang
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Yuta Hozumi
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Gengzhuo Liu
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Yuchi Qiu
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Xiaoqi Wei
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, MI 48824, USA
- Department of Electrical and Computer Engineering, Michigan State University, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, MI 48824, USA
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112
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Moriyama S. [Neutralizing antibodies against SARS-CoV-2]. Uirusu 2023; 73:153-162. [PMID: 39343550 DOI: 10.2222/jsv.73.153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Severe acute respiratory syndrome (SARS) corona virus 2 (SARS-CoV-2) is a novel coronavirus that infects humans and causes respiratory symptoms, resulting in a global pandemic since its appearance in 2019. Neutralizing antibody production is an important immune response following SARS-CoV-2 infection, and a great deal of research has been performed regarding the immune response against SARS-CoV-2 infection. However, SARS-CoV-2 is constantly changing and multiple amino acid reconstitutions accumulated in the spike protein enabled viruses to escape from immune responses, especially from neutralizing antibodies. In this review, the antibody responses to SARS-CoV-2 and the emergence of escape variants, and the development of broadly neutralizing antibodies will be introduced.
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Affiliation(s)
- Saya Moriyama
- Research center for drug and vaccine development, National Institute of Infectious Diseases
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113
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Cao Y, Jian F, Zhang Z, Yisimayi A, Hao X, Bao L, Yuan F, Yu Y, Du S, Wang J, Xiao T, Song W, Zhang Y, Liu P, An R, Wang P, Wang Y, Yang S, Niu X, Zhang Y, Gu Q, Shao F, Hu Y, Yin W, Zheng A, Wang Y, Qin C, Jin R, Xiao J, Xie XS. Rational identification of potent and broad sarbecovirus-neutralizing antibody cocktails from SARS convalescents. Cell Rep 2022; 41:111845. [PMID: 36493787 PMCID: PMC9712074 DOI: 10.1016/j.celrep.2022.111845] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/13/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages have escaped most receptor-binding domain (RBD)-targeting therapeutic neutralizing antibodies (NAbs), which proves that previous NAb drug screening strategies are deficient against the fast-evolving SARS-CoV-2. Better broad NAb drug candidate selection methods are needed. Here, we describe a rational approach for identifying RBD-targeting broad SARS-CoV-2 NAb cocktails. Based on high-throughput epitope determination, we propose that broad NAb drugs should target non-immunodominant RBD epitopes to avoid herd-immunity-directed escape mutations. Also, their interacting antigen residues should focus on sarbecovirus conserved sites and associate with critical viral functions, making the antibody-escaping mutations less likely to appear. Following these criteria, a featured non-competing antibody cocktail, SA55+SA58, is identified from a large collection of broad sarbecovirus NAbs isolated from SARS-CoV-2-vaccinated SARS convalescents. SA55+SA58 potently neutralizes ACE2-utilizing sarbecoviruses, including circulating Omicron variants, and could serve as broad SARS-CoV-2 prophylactics to offer long-term protection, especially for individuals who are immunocompromised or with high-risk comorbidities.
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Affiliation(s)
- Yunlong Cao
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China,Changping Laboratory, Beijing, P.R. China,Corresponding author
| | - Fanchong Jian
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China,College of Chemistry and Molecular Engineering, Peking University, Beijing, P.R. China
| | - Zhiying Zhang
- School of Life Sciences, Peking University, Beijing, P.R. China
| | - Ayijiang Yisimayi
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China,School of Life Sciences, Peking University, Beijing, P.R. China
| | - Xiaohua Hao
- Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China
| | - Linlin Bao
- Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, P.R. China
| | - Fei Yuan
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, P.R. China
| | | | - Shuo Du
- School of Life Sciences, Peking University, Beijing, P.R. China
| | - Jing Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China,School of Life Sciences, Peking University, Beijing, P.R. China
| | - Tianhe Xiao
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China,Joint Graduate Program of Peking-Tsinghua-NIBS, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P.R. China
| | - Weiliang Song
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China,School of Life Sciences, Peking University, Beijing, P.R. China
| | - Ying Zhang
- School of Life Sciences, Peking University, Beijing, P.R. China
| | - Pulan Liu
- School of Life Sciences, Peking University, Beijing, P.R. China
| | - Ran An
- Changping Laboratory, Beijing, P.R. China
| | - Peng Wang
- Changping Laboratory, Beijing, P.R. China
| | - Yao Wang
- Changping Laboratory, Beijing, P.R. China
| | - Sijie Yang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P.R. China
| | - Xiao Niu
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China,College of Chemistry and Molecular Engineering, Peking University, Beijing, P.R. China
| | - Yuhang Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, P.R. China
| | | | - Fei Shao
- Changping Laboratory, Beijing, P.R. China
| | - Yaling Hu
- Sinovac Biotech, Ltd., Beijing, P.R. China
| | | | - Aihua Zheng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, P.R. China
| | - Youchun Wang
- Changping Laboratory, Beijing, P.R. China,Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, P.R. China
| | - Chuan Qin
- Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, P.R. China,Corresponding author
| | - Ronghua Jin
- Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China,Corresponding author
| | - Junyu Xiao
- Changping Laboratory, Beijing, P.R. China,School of Life Sciences, Peking University, Beijing, P.R. China,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P.R. China,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, P.R. China,Corresponding author
| | - Xiaoliang Sunney Xie
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China,Changping Laboratory, Beijing, P.R. China,Corresponding author
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114
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Guenthoer J, Lilly M, Starr TN, Dadonaite B, Lovendahl KN, Croft JT, Stoddard CI, Chohan V, Ding S, Ruiz F, Kopp MS, Finzi A, Bloom JD, Chu HY, Lee KK, Overbaugh J. Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.15.520606. [PMID: 36561191 PMCID: PMC9774213 DOI: 10.1101/2022.12.15.520606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The antiviral benefit of antibodies can be compromised by viral escape especially for rapidly evolving viruses. Therefore, durable, effective antibodies must be both broad and potent to counter newly emerging, diverse strains. Discovery of such antibodies is critically important for SARS-CoV-2 as the global emergence of new variants of concern (VOC) has compromised the efficacy of therapeutic antibodies and vaccines. We describe a collection of broad and potent neutralizing monoclonal antibodies (mAbs) isolated from an individual who experienced a breakthrough infection with the Delta VOC. Four mAbs potently neutralize the Wuhan-Hu-1 vaccine strain, the Delta VOC, and also retain potency against the Omicron VOCs, including recently circulating BA.4/BA.5, in both pseudovirus-based and live virus assays, and one also potently neutralizes SARS-CoV-1. The potency of these mAbs was greater against Omicron VOCs than all but one of the mAbs that had been approved for therapeutic applications. The mAbs target distinct epitopes on the spike glycoprotein, three in the receptor binding domain (RBD) and one in an invariant region downstream of the RBD in subdomain 1 (SD1). The escape pathways we defined at single amino acid resolution with deep mutational scanning show they target conserved, functionally constrained regions of the glycoprotein, suggesting escape could incur a fitness cost. Overall, these mAbs are novel in their breadth across VOCs, their epitope specificity, and include a highly potent mAb targeting a rare epitope outside of the RBD in SD1.
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115
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Boer JC, Pan Q, Holien JK, Nguyen TB, Ascher DB, Plebanski M. A bias of Asparagine to Lysine mutations in SARS-CoV-2 outside the receptor binding domain affects protein flexibility. Front Immunol 2022; 13:954435. [PMID: 36569921 PMCID: PMC9788125 DOI: 10.3389/fimmu.2022.954435] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/14/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction COVID-19 pandemic has been threatening public health and economic development worldwide for over two years. Compared with the original SARS-CoV-2 strain reported in 2019, the Omicron variant (B.1.1.529.1) is more transmissible. This variant has 34 mutations in its Spike protein, 15 of which are present in the Receptor Binding Domain (RBD), facilitating viral internalization via binding to the angiotensin-converting enzyme 2 (ACE2) receptor on endothelial cells as well as promoting increased immune evasion capacity. Methods Herein we compared SARS-CoV-2 proteins (including ORF3a, ORF7, ORF8, Nucleoprotein (N), membrane protein (M) and Spike (S) proteins) from multiple ancestral strains. We included the currently designated original Variant of Concern (VOC) Omicron, its subsequent emerged variants BA.1, BA2, BA3, BA.4, BA.5, the two currently emerging variants BQ.1 and BBX.1, and compared these with the previously circulating VOCs Alpha, Beta, Gamma, and Delta, to better understand the nature and potential impact of Omicron specific mutations. Results Only in Omicron and its subvariants, a bias toward an Asparagine to Lysine (N to K) mutation was evident within the Spike protein, including regions outside the RBD domain, while none of the regions outside the Spike protein domain were characterized by this mutational bias. Computational structural analysis revealed that three of these specific mutations located in the central core region, contribute to a preference for the alteration of conformations of the Spike protein. Several mutations in the RBD which have circulated across most Omicron subvariants were also analysed, and these showed more potential for immune escape. Conclusion This study emphasizes the importance of understanding how specific N to K mutations outside of the RBD region affect SARS-CoV-2 conformational changes and the need for neutralizing antibodies for Omicron to target a subset of conformationally dependent B cell epitopes.
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Affiliation(s)
- Jennifer C. Boer
- School of Health and Biomedical Science, Royal Melbourne Institute of Technology, Melbourne, VIC, Australia
| | - Qisheng Pan
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Jessica K. Holien
- School of Science, Royal Melbourne Institute of Technology (RMIT) University, Melbourne, VIC, Australia
| | - Thanh-Binh Nguyen
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - David B. Ascher
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Magdalena Plebanski
- School of Health and Biomedical Science, Royal Melbourne Institute of Technology, Melbourne, VIC, Australia,*Correspondence: Magdalena Plebanski,
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