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Ramasamy R. Overview of immunological & virological factors driving the evolution & global spread of SARS-CoV-2 variants. Indian J Med Res 2023; 158:257-268. [PMID: 37815068 PMCID: PMC10720969 DOI: 10.4103/ijmr.ijmr_2591_22] [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: 12/21/2022] [Indexed: 10/11/2023] Open
Abstract
The SARS-CoV-2, a highly infectious positive strand RNA virus first identified in December 2019, has produced multiple genetic variants that have rapidly and sequentially spread worldwide during the coronavirus disease 2019 (COVID-19) pandemic. Genetic changes in SARS-CoV-2 for greater infectivity, replication and transmission were selected during the early stages of the pandemic. More recently, after widespread infection and vaccination, SARS-CoV-2 variants that evade antigen-specific adaptive immunity, have begun to be selected. This article provides an overview of the molecular immunological and virological factors underlying the origin and global spread of important SARS-CoV-2 variant lineages.
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Xiao S, Alshahrani M, Gupta G, Tao P, Verkhivker G. Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. J Chem Inf Model 2023; 63:5272-5296. [PMID: 37549201 PMCID: PMC11162552 DOI: 10.1021/acs.jcim.3c00778] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
The new generation of SARS-CoV-2 Omicron variants displayed a significant growth advantage and increased viral fitness by acquiring convergent mutations, suggesting that the immune pressure can promote convergent evolution leading to the sudden acceleration of SARS-CoV-2 evolution. In the current study, we combined structural modeling, microsecond molecular dynamics simulations, and Markov state models to characterize conformational landscapes and identify specific dynamic signatures of the SARS-CoV-2 spike complexes with the host receptor ACE2 for the recently emerged highly transmissible XBB.1, XBB.1.5, BQ.1, and BQ.1.1 Omicron variants. Microsecond simulations and Markovian modeling provided a detailed characterization of the functional conformational states and revealed the increased thermodynamic stabilization of the XBB.1.5 subvariant, which can be contrasted to more dynamic BQ.1 and BQ.1.1 subvariants. Despite considerable structural similarities, Omicron mutations can induce unique dynamic signatures and specific distributions of the conformational states. The results suggested that variant-specific changes of the conformational mobility in the functional interfacial loops of the receptor-binding domain in the SARS-CoV-2 spike protein can be fine-tuned through crosstalk between convergent mutations which could provide an evolutionary path for modulation of immune escape. By combining atomistic simulations and Markovian modeling analysis with perturbation-based approaches, we determined important complementary roles of convergent mutation sites as effectors and receivers of allosteric signaling involved in modulation of conformational plasticity and regulation of allosteric communications. This study also revealed hidden allosteric pockets and suggested that convergent mutation sites could control evolution and distribution of allosteric pockets through modulation of conformational plasticity in the flexible adaptable regions.
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Affiliation(s)
- Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Grace Gupta
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
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53
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Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation-based profiling approaches: hidden role of omicron mutations as modulators of allosteric signaling and epistatic relationships. Phys Chem Chem Phys 2023; 25:21245-21266. [PMID: 37548589 PMCID: PMC10536792 DOI: 10.1039/d3cp02042h] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
In this study, we systematically examine the conformational dynamics, binding and allosteric communications in the Omicron BA.1, BA.2, BA.3 and BA.4/BA.5 spike protein complexes with the ACE2 host receptor using molecular dynamics simulations and perturbation-based network profiling approaches. Microsecond atomistic simulations provided a detailed characterization of the conformational landscapes and revealed the increased thermodynamic stabilization of the BA.2 variant which can be contrasted with the BA.4/BA.5 variants inducing a significant mobility of the complexes. Using the dynamics-based mutational scanning of spike residues, we identified structural stability and binding affinity hotspots in the Omicron complexes. Perturbation response scanning and network-based mutational profiling approaches probed the effect of the Omicron mutations on allosteric interactions and communications in the complexes. The results of this analysis revealed specific roles of Omicron mutations as conformationally plastic and evolutionary adaptable modulators of binding and allostery which are coupled to the major regulatory positions through interaction networks. Through perturbation network scanning of allosteric residue potentials in the Omicron variant complexes performed in the background of the original strain, we characterized regions of epistatic couplings that are centered around the binding affinity hotspots N501Y and Q498R. Our results dissected the vital role of these epistatic centers in regulating protein stability, efficient ACE2 binding and allostery which allows for accumulation of multiple Omicron immune escape mutations at other sites. Through integrative computational approaches, this study provides a systematic analysis of the effects of Omicron mutations on thermodynamics, binding and allosteric signaling in the complexes with ACE2 receptor.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA.
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Grace Gupta
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75275, USA.
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75275, USA.
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54
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Wang H, Yuan Y, Wu B, Xiao M, Wang Z, Diao T, Zeng R, Chen L, Lei Y, Long P, Guo Y, Lai X, Wen Y, Li W, Cai H, Song L, Ni W, Zhao Y, Ouyang K, Wang J, Wang Q, Liu L, Wang C, Pan A, Li X, Gong R, Wu T. Neutralization against SARS-CoV-2 Delta/Omicron variants and B cell response after inactivated vaccination among COVID-19 convalescents. Front Med 2023; 17:747-757. [PMID: 36738428 PMCID: PMC9898702 DOI: 10.1007/s11684-022-0954-x] [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: 05/01/2022] [Accepted: 07/20/2022] [Indexed: 02/05/2023]
Abstract
Emerging SARS-CoV-2 variants have made COVID-19 convalescents susceptible to re-infection and have raised concern about the efficacy of inactivated vaccination in neutralization against emerging variants and antigen-specific B cell response. To this end, a study on a long-term cohort of 208 participants who have recovered from COVID-19 was conducted, and the participants were followed up at 3.3 (Visit 1), 9.2 (Visit 2), and 18.5 (Visit 3) months after SARS-CoV-2 infection. They were classified into three groups (no-vaccination (n = 54), one-dose (n = 62), and two-dose (n = 92) groups) on the basis of the administration of inactivated vaccination. The neutralizing antibody (NAb) titers against the wild-type virus continued to decrease in the no-vaccination group, but they rose significantly in the one-dose and two-dose groups, with the highest NAb titers being observed in the two-dose group at Visit 3. The NAb titers against the Delta variant for the no-vaccination, one-dose, and two-dose groups decreased by 3.3, 1.9, and 2.3 folds relative to the wild-type virus, respectively, and those against the Omicron variant decreased by 7.0, 4.0, and 3.8 folds, respectively. Similarly, the responses of SARS-CoV-2 RBD-specific B cells and memory B cells were boosted by the second vaccine dose. Results showed that the convalescents benefited from the administration of the inactivated vaccine (one or two doses), which enhanced neutralization against highly mutated SARS-CoV-2 variants and memory B cell responses. Two doses of inactivated vaccine among COVID-19 convalescents are therefore recommended for the prevention of the COVID-19 pandemic, and vaccination guidelines and policies need to be updated.
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Affiliation(s)
- Hao Wang
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yu Yuan
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Bihao Wu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingzhong Xiao
- Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, 430061, China
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China
| | - Zhen Wang
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Tingyue Diao
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Rui Zeng
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Li Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanshou Lei
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Pinpin Long
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yi Guo
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xuefeng Lai
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuying Wen
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wenhui Li
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hao Cai
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Lulu Song
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei Ni
- Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, 430061, China
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China
| | - Youyun Zhao
- Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, 430061, China
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China
| | - Kani Ouyang
- Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, 430061, China
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China
| | - Jingzhi Wang
- Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, 430061, China
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China
| | - Qi Wang
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Li Liu
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Chaolong Wang
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - An Pan
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaodong Li
- Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, 430061, China.
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China.
| | - Rui Gong
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Tangchun Wu
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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55
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Sergeeva AP, Katsamba PS, Liao J, Sampson JM, Bahna F, Mannepalli S, Morano NC, Shapiro L, Friesner RA, Honig B. Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity. J Mol Biol 2023; 435:168187. [PMID: 37355034 PMCID: PMC10286572 DOI: 10.1016/j.jmb.2023.168187] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/26/2023]
Abstract
The strength of binding between human angiotensin converting enzyme 2 (ACE2) and the receptor binding domain (RBD) of viral spike protein plays a role in the transmissibility of the SARS-CoV-2 virus. In this study we focus on a subset of RBD mutations that have been frequently observed in infected individuals and probe binding affinity changes to ACE2 using surface plasmon resonance (SPR) measurements and free energy perturbation (FEP) calculations. Our SPR results are largely in accord with previous studies but discrepancies do arise due to differences in experimental methods and to protocol differences even when a single method is used. Overall, we find that FEP performance is superior to that of other computational approaches examined as determined by agreement with experiment and, in particular, by its ability to identify stabilizing mutations. Moreover, the calculations successfully predict the observed cooperative stabilization of binding by the Q498R N501Y double mutant present in Omicron variants and offer a physical explanation for the underlying mechanism. Overall, our results suggest that despite the significant computational cost, FEP calculations may offer an effective strategy to understand the effects of interfacial mutations on protein-protein binding affinities and, hence, in a variety of practical applications such as the optimization of neutralizing antibodies.
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Affiliation(s)
- Alina P Sergeeva
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA. https://twitter.com/AlinaSergeeva
| | - Phinikoula S Katsamba
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Junzhuo Liao
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Jared M Sampson
- Department of Chemistry, Columbia University, New York, NY 10027, USA; Schrödinger, Inc., New York, NY 10036, USA
| | - Fabiana Bahna
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Seetha Mannepalli
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Nicholas C Morano
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Lawrence Shapiro
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| | | | - Barry Honig
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA; Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA.
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56
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Dokainish HM, Sugita Y. Structural effects of spike protein D614G mutation in SARS-CoV-2. Biophys J 2023; 122:2910-2920. [PMID: 36397671 PMCID: PMC9671695 DOI: 10.1016/j.bpj.2022.11.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 09/02/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022] Open
Abstract
A single mutation from aspartate to glycine at position 614 has dominated all circulating variants of the severe acute respiratory syndrome coronavirus 2. D614G mutation induces structural changes in the spike (S) protein that strengthen the virus infectivity. Here, we use molecular dynamics simulations to dissect the effects of mutation and 630-loop rigidification on S-protein structure. The introduction of the mutation orders the 630-loop structure and thereby induces global structural changes toward the cryoelectron microscopy structure of the D614G S-protein. The ordered 630-loop weakens local interactions between the 614th residue and others in contrast to disordered structures in the wild-type protein. The mutation allosterically alters global interactions between receptor-binding domains, forming an asymmetric and mobile down conformation and facilitating transitions toward up conformation. The loss of salt bridge between D614 and K854 upon the mutation generally stabilizes S-protein protomer, including the fusion peptide proximal region that mediates membrane fusion. Understanding the molecular basis of D614G mutation is crucial as it dominates in all variants of concern, including Delta and Omicron.
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Affiliation(s)
- Hisham M Dokainish
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan; Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan; Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan.
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57
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Reuter N, Chen X, Kropff B, Peter AS, Britt WJ, Mach M, Überla K, Thomas M. SARS-CoV-2 Spike Protein Is Capable of Inducing Cell-Cell Fusions Independent from Its Receptor ACE2 and This Activity Can Be Impaired by Furin Inhibitors or a Subset of Monoclonal Antibodies. Viruses 2023; 15:1500. [PMID: 37515187 PMCID: PMC10384293 DOI: 10.3390/v15071500] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which was responsible for the COVID-19 pandemic, efficiently spreads cell-to-cell through mechanisms facilitated by its membrane glycoprotein spike. We established a dual split protein (DSP) assay based on the complementation of GFP and luciferase to quantify the fusogenic activity of the SARS-CoV-2 spike protein. We provide several lines of evidence that the spike protein of SARS-CoV-2, but not SARS-CoV-1, induced cell-cell fusion even in the absence of its receptor, angiotensin-converting enzyme 2 (ACE2). This poorly described ACE2-independent cell fusion activity of the spike protein was strictly dependent on the proteasomal cleavage of the spike by furin while TMPRSS2 was dispensable. Previous and current variants of concern (VOCs) differed significantly in their fusogenicity. The Delta spike was extremely potent compared to Alpha, Beta, Gamma and Kappa, while the Omicron spike was almost devoid of receptor-independent fusion activity. Nonetheless, for all analyzed variants, cell fusion was dependent on furin cleavage and could be pharmacologically inhibited with CMK. Mapping studies revealed that amino acids 652-1273 conferred the ACE2-independent fusion activity of the spike. Unexpectedly, residues proximal to the furin cleavage site were not of major relevance, whereas residue 655 critically regulated fusion. Finally, we found that the spike's fusion activity in the absence of ACE2 could be inhibited by antibodies directed against its N-terminal domain (NTD) but not by antibodies targeting its receptor-binding domain (RBD). In conclusion, our BSL-1-compatible DSP assay allowed us to screen for inhibitors or antibodies that interfere with the spike's fusogenic activity and may therefore contribute to both rational vaccine design and development of novel treatment options against SARS-CoV-2.
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Affiliation(s)
- Nina Reuter
- Virologisches Institut, Klinische und Molekulare Virologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Xiaohan Chen
- Virologisches Institut, Klinische und Molekulare Virologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Barbara Kropff
- Virologisches Institut, Klinische und Molekulare Virologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Antonia Sophia Peter
- Virologisches Institut, Klinische und Molekulare Virologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - William J Britt
- Departments of Pediatrics, Microbiology and Neurobiology, Children's Hospital of Alabama, School of Medicine, University of Alabama, Birmingham, AL 35233-1771, USA
| | - Michael Mach
- Virologisches Institut, Klinische und Molekulare Virologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Klaus Überla
- Virologisches Institut, Klinische und Molekulare Virologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Marco Thomas
- Virologisches Institut, Klinische und Molekulare Virologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
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58
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Zhang J, Tang W, Gao H, Lavine CL, Shi W, Peng H, Zhu H, Anand K, Kosikova M, Kwon HJ, Tong P, Gautam A, Rits-Volloch S, Wang S, Mayer ML, Wesemann DR, Seaman MS, Lu J, Xiao T, Xie H, Chen B. Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein. Nat Struct Mol Biol 2023; 30:980-990. [PMID: 37430064 DOI: 10.1038/s41594-023-01023-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/17/2023] [Indexed: 07/12/2023]
Abstract
The Omicron subvariant BA.2 has become the dominant circulating strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in many countries. Here, we have characterized structural, functional and antigenic properties of the full-length BA.2 spike (S) protein and compared replication of the authentic virus in cell culture and an animal model with previously prevalent variants. BA.2 S can fuse membranes slightly more efficiently than Omicron BA.1, but still less efficiently than other previous variants. Both BA.1 and BA.2 viruses replicated substantially faster in animal lungs than the early G614 (B.1) strain in the absence of pre-existing immunity, possibly explaining the increased transmissibility despite their functionally compromised spikes. As in BA.1, mutations in the BA.2 S remodel its antigenic surfaces, leading to strong resistance to neutralizing antibodies. These results suggest that both immune evasion and replicative advantage may contribute to the heightened transmissibility of the Omicron subvariants.
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Affiliation(s)
- Jun Zhang
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Weichun Tang
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Hailong Gao
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Christy L Lavine
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Wei Shi
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Hanqin Peng
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Haisun Zhu
- Institute for Protein Innovation, Harvard Institutes of Medicine, Boston, MA, USA
| | - Krishna Anand
- Institute for Protein Innovation, Harvard Institutes of Medicine, Boston, MA, USA
| | - Matina Kosikova
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Hyung Joon Kwon
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Pei Tong
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital; Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - Avneesh Gautam
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital; Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | | | | | - Megan L Mayer
- The Harvard Cryo-EM Center for Structural Biology, Boston, MA, USA
| | - Duane R Wesemann
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital; Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jianming Lu
- Codex BioSolutions, Inc., Rockville, MD, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA
| | - Tianshu Xiao
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Hang Xie
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA.
| | - Bing Chen
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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59
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Wu CY, Yang YH, Lin YS, Shu LH, Cheng YC, Liu HT, Lin YY, Lee IY, Shih WT, Yang PR, Tsai YY, Chang GH, Hsu CM, Yeh RA, Wu YH, Wu YH, Shen RC, Tsai MS. The anti-SARS-CoV-2 effect and mechanism of Chiehyuan herbal oral protection solution. Heliyon 2023; 9:e17701. [PMID: 37483781 PMCID: PMC10359827 DOI: 10.1016/j.heliyon.2023.e17701] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 06/07/2023] [Accepted: 06/26/2023] [Indexed: 07/25/2023] Open
Abstract
The Chiehyuan herbal oral protection solution (GB-2) is a herbal mixture commonly utilized in Taiwan for combating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as per traditional Chinese medicine practices. This study assessed the clinical impact of GB-2 through prospective clinical trials. With twice-daily use for a week, GB-2 was shown to diminish the expression of angiotensin-converting enzyme 2 (ACE2) in oral mucosal cells. Moreover, after two weeks of use, it could reduce transmembrane protease, serine 2 (TMRPSS2) expression in these cells. Additionally, in vitro experiments demonstrated that GB-2 lessened the entry efficiency of the Omicron, L452R-D614G, T478K-D614G, and L452R-T478K-D614G variants of the SARS-CoV-2 pseudotyped lentivirus. It also impeded the interaction between ACE2 and the receptor-binding domain (RBD) presenting N501Y-K417N-E484A-G339D-Q493R-G496S-Q498R and L452R-T478K mutations. Glycyrrhizic acid, a major compound in GB-2, also hindered the entry of the Omicron variant (BA.1) of the SARS-CoV-2 pseudotyped lentivirus by obstructing the binding between ACE2 and the RBD presenting the N501Y-K417N-E484A-G339D-Q493R-G496S-Q498R mutation. To sum up, these findings suggest that GB-2 can decrease ACE2 and TMPRSS2 expression in oral mucosal cells. Both glycyrrhizic acid and GB-2 were found to reduce the entry efficiency of the Omicron variant (BA.1) of the SARS-CoV-2 pseudotyped lentivirus and block the binding between ACE2 and the RBD with the N501Y-K417N-E484A-G339D-Q493R-G496S-Q498R mutation. This evidence implies that GB-2 might be a potential candidate for further study as a preventative measure against SARS-CoV-2 infection.
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Affiliation(s)
- Ching-Yuan Wu
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
- School of Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Yao-Hsu Yang
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
- School of Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Shih Lin
- Department of Pharmacy, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Li-Hsin Shu
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Yu-Ching Cheng
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
- Department of Otolaryngology, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Hung-Te Liu
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Yin-Yin Lin
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - I-Yun Lee
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Wei-Tai Shih
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Pei-Rung Yang
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Ying-Ying Tsai
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Geng-He Chang
- Department of Otolaryngology, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
- Faculty of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Health Information and Epidemiology Laboratory, Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Cheng-Ming Hsu
- Department of Otolaryngology, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
- Faculty of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Reming-Albert Yeh
- Department of Otolaryngology, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Yu-Huei Wu
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Heng Wu
- Department of Electrical Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Rou-Chen Shen
- Department of Otolaryngology, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Ming-Shao Tsai
- Department of Otolaryngology, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
- Faculty of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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60
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Giron CC, Laaksonen A, Barroso da Silva FL. Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies. J Biomol Struct Dyn 2023; 41:5707-5727. [PMID: 35815535 DOI: 10.1080/07391102.2022.2095305] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/23/2022] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 remains a health threat with the continuous emergence of new variants. This work aims to expand the knowledge about the SARS-CoV-2 receptor-binding domain (RBD) interactions with cell receptors and monoclonal antibodies (mAbs). By using constant-pH Monte Carlo simulations, the free energy of interactions between the RBD from different variants and several partners (Angiotensin-Converting Enzyme-2 (ACE2) polymorphisms and various mAbs) were predicted. Computed RBD-ACE2-binding affinities were higher for two ACE2 polymorphisms (rs142984500 and rs4646116) typically found in Europeans which indicates a genetic susceptibility. This is amplified for Omicron (BA.1) and its sublineages BA.2 and BA.3. The antibody landscape was computationally investigated with the largest set of mAbs so far in the literature. From the 32 studied binders, groups of mAbs were identified from weak to strong binding affinities (e.g. S2K146). These mAbs with strong binding capacity and especially their combination are amenable to experimentation and clinical trials because of their high predicted binding affinities and possible neutralization potential for current known virus mutations and a universal coronavirus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Carolina Corrêa Giron
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Universidade Federal do Triângulo Mineiro, Hospital de Clínicas, Uberaba, MG, Brazil
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, PR China
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, Romania
- Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, Luleå, Sweden
- Department of Chemical and Geological Sciences, University of Cagliari, Monserrato, Italy
| | - Fernando Luís Barroso da Silva
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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61
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Hu S, Wang N, Chen S, Zhang H, Wang C, Ma W, Zhang X, Wu Y, Lv Y, Xue Z, Bai H, Ge S, He H, Lu W, Zhang T, Ding Y, Liu R, Han S, Zhan Y, Zhan G, Guo Z, Zhang Y, Lu J, Gao J, Jia Q, Wang Y, Wang H, Lu S, Jin T, Chiu S, He L. Harringtonine: A more effective antagonist for Omicron variant. Biochem Pharmacol 2023; 213:115617. [PMID: 37211174 PMCID: PMC10195862 DOI: 10.1016/j.bcp.2023.115617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/23/2023]
Abstract
Fusion with host cell membrane is the main mechanism of infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we propose that a new strategy to screen small-molecule antagonists blocking SARS-CoV-2 membrane fusion. Using cell membrane chromatography (CMC), we found that harringtonine (HT) simultaneously targeted SARS-CoV-2 S protein and host cell surface TMPRSS2 expressed by the host cell, and subsequently confirmed that HT can inhibit membrane fusion. HT effectively blocked SARS-CoV-2 original strain entry with the IC50 of 0.217 μM, while the IC50 in delta variant decreased to 0.101 μM, the IC50 in Omicron BA.1 variant was 0.042 μM. Due to high transmissibility and immune escape, Omicron subvariant BA.5 has become the dominant strain of the SARS-CoV-2 virus and led to escalating COVID-19 cases, however, against BA.5, HT showed a surprising effectiveness. The IC50 in Omicron BA.5 was even lower than 0.0019 μM. The above results revealed the effect of HT on Omicron is very significant. In summary, we characterize HT as a small-molecule antagonist by direct targeting on the Spike protein and TMPRSS2.
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Affiliation(s)
- Shiling Hu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Nan Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Shaohong Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Huajun Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Cheng Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Weina Ma
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Xinghai Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yan Wu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yanni Lv
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Zhuoyin Xue
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Haoyun Bai
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Shuai Ge
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Huaizhen He
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Wen Lu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Tao Zhang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Yuanyuan Ding
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Rui Liu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Shengli Han
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Yingzhuan Zhan
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Guanqun Zhan
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Zengjun Guo
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Yongjing Zhang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Jiayu Lu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Jiapan Gao
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Qianqian Jia
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Yuejin Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Hongliang Wang
- Department of pathogen biology and immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Shemin Lu
- School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Tengchuan Jin
- Division of Life Sciences and Medicine, University of Sciences and Technology of China, Hefei, China
| | - Sandra Chiu
- Division of Life Sciences and Medicine, University of Sciences and Technology of China, Hefei, China.
| | - Langchong He
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China.
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Gao J, Cao C, Shi M, Hong S, Guo S, Li J, Liang T, Song P, Xu R, Li N. Kaempferol inhibits SARS-CoV-2 invasion by impairing heptad repeats-mediated viral fusion. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 118:154942. [PMID: 37421767 PMCID: PMC10289257 DOI: 10.1016/j.phymed.2023.154942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/17/2023] [Accepted: 06/22/2023] [Indexed: 07/10/2023]
Abstract
BACKGROUND The continuous evolution of SARS-CoV-2 has underscored the development of broad-spectrum prophylaxis. Antivirals targeting the membrane fusion process represent promising paradigms. Kaempferol (Kae), an ubiquitous plant flavonol, has been shown efficacy against various enveloped viruses. However, its potential in anti-SARS-CoV-2 invasion remains obscure. PURPOSE To evaluate capabilities and mechanisms of Kae in preventing SARS-CoV-2 invasion. METHODS To avoid interference of viral replication, virus-like particles (VLPs) constructed with luciferase reporter were applied. To investigate the antiviral potency of Kae, human induced pluripotent stem cells (hiPSC)-derived alveolar epithelial cells type II (AECII) and human ACE2 (hACE2) transgenic mice were utilized as in vitro and in vivo models, respectively. Using dual split protein (DSP) assays, inhibitory activities of Kae in viral fusion were determined in Alpha, Delta and Omicron variants of SARS-CoV-2, as well as in SARS-CoV and MERS-CoV. To further reveal molecular determinants of Kae in restricting viral fusion, synthetic peptides corresponding to the conserved heptad repeat (HR) 1 and 2, involved in viral fusion, and the mutant form of HR2 were explored by circular dichroism and native polyacrylamide gel electrophoresis. RESULTS Kae inhibited SARS-CoV-2 invasion both in vitro and in vivo, which was mainly attributed to its suppressive effects on viral fusion, but not endocytosis, two pathways that mediate viral invasion. In accordance with the proposed model of anti-fusion prophylaxis, Kae functioned as a pan-inhibitor of viral fusion, including three emerged highly pathogenic coronaviruses, and the currently circulating Omicron BQ.1.1 and XBB.1 variants of SARS-CoV-2. Consistent with the typical target of viral fusion inhibitors, Kae interacted with HR regions of SARS-CoV-2 S2 subunits. Distinct from previous inhibitory fusion peptides which prevent the formation of six-helix bundle (6-HB) by competitively interacting with HRs, Kae deformed HR1 and directly reacted with lysine residues within HR2 region, the latter of which was considered critical for the preservation of stabilized S2 during SARS-CoV-2 invasion. CONCLUSIONS Kae prevents SARS-CoV-2 infection by blocking membrane fusion and possesses a broad-spectrum anti-fusion ability. These findings provide valuable insights into potential benefits of Kae-containing botanical products as a complementary prophylaxis, especially during the waves of breakthrough infections and re-infections.
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Affiliation(s)
- Junwei Gao
- Department of Biomedical Engineering and Technology, Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Can Cao
- Department of Biomedical Engineering and Technology, Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Mingfei Shi
- Department of Biomedical Engineering and Technology, Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Shihao Hong
- Department of Biomedical Engineering and Technology, Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Shijie Guo
- Department of Biomedical Engineering and Technology, Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jing Li
- Department of Nephropathy, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
| | - Tengxiao Liang
- Department of Emergency, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
| | - Ping Song
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China..
| | - Ruodan Xu
- Department of Biomedical Engineering and Technology, Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China..
| | - Ning Li
- Department of Biomedical Engineering and Technology, Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China..
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63
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Kuzmina A, Korovin D, Cohen Lass I, Atari N, Ottolenghi A, Hu P, Mandelboim M, Rosental B, Rosenberg E, Diaz-Griffero F, Taube R. Changes within the P681 residue of spike dictate cell fusion and syncytia formation of Delta and Omicron variants of SARS-CoV-2 with no effects on neutralization or infectivity. Heliyon 2023; 9:e16750. [PMID: 37292300 PMCID: PMC10238279 DOI: 10.1016/j.heliyon.2023.e16750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 04/13/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
The rapid spread and dominance of the Omicron SARS-CoV-2 lineages have posed severe health challenges worldwide. While extensive research on the role of the Receptor Binding Domain (RBD) in promoting viral infectivity and vaccine sensitivity has been well documented, the functional significance of the 681PRRAR/SV687 polybasic motif of the viral spike is less clear. In this work, we monitored the infectivity levels and neutralization potential of the wild-type human coronavirus 2019 (hCoV-19), Delta, and Omicron SARS-CoV-2 pseudoviruses against sera samples drawn four months post administration of a third dose of the BNT162b2 mRNA vaccine. Our findings show that in comparison to hCoV-19 and Delta SARS-CoV-2, Omicron lineages BA.1 and BA.2 exhibit enhanced infectivity and a sharp decline in their sensitivity to vaccine-induced neutralizing antibodies. Interestingly, P681 mutations within the viral spike do not play a role in the neutralization potential or infectivity of SARS Cov-2 pseudoviruses carrying mutations in this position. The P681 residue however, dictates the ability of the spike protein to promote fusion and syncytia formation between infected cells. While spike from hCoV-19 (P681) and Omicron (H681) promote only modest cell fusion and formation of syncytia between cells that express the spike-protein, Delta spike (R681) displays enhanced fusogenic activity and promotes syncytia formation. Additional analysis shows that a single P681R mutation within the hCoV-19 spike, or H681R within the Omicron spike, restores fusion potential to similar levels observed for the Delta R681 spike. Conversely, R681P point mutation within the spike of Delta pseudovirus abolishes efficient fusion and syncytia formation. Our investigation also demonstrates that spike proteins from hCoV-19 and Delta SARS-CoV-2 are efficiently incorporated into viral particles relative to the spike of Omicron lineages. We conclude that the third dose of the Pfizer-BNT162b2 provides appreciable protection against the newly emerged Omicron sub-lineages. However, the neutralization sensitivity of these new variants is diminished relative to that of the hCoV-19 or Delta SARS-CoV-2. We further show that the P681 residue within spike dictates cell fusion and syncytia formation with no effects on the infectivity of the specific viral variant and on its sensitivity to vaccine-mediated neutralization.
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Affiliation(s)
- Alona Kuzmina
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
| | - Dina Korovin
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
| | - Ido Cohen Lass
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
| | - Nofar Atari
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
| | - Aner Ottolenghi
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
- Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Israel
| | - Pan Hu
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv, Israel
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
- Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Israel
| | | | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
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64
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Haddrell A, Otero-Fernandez M, Oswin H, Cogan T, Bazire J, Tian J, Alexander R, Mann JFS, Hill D, Finn A, Davidson AD, Reid JP. Differences in airborne stability of SARS-CoV-2 variants of concern is impacted by alkalinity of surrogates of respiratory aerosol. J R Soc Interface 2023; 20:20230062. [PMID: 37340783 PMCID: PMC10282576 DOI: 10.1098/rsif.2023.0062] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/30/2023] [Indexed: 06/22/2023] Open
Abstract
The mechanistic factors hypothesized to be key drivers for the loss of infectivity of viruses in the aerosol phase often remain speculative. Using a next-generation bioaerosol technology, we report measurements of the aero-stability of several SARS-CoV-2 variants of concern in aerosol droplets of well-defined size and composition at high (90%) and low (40%) relative humidity (RH) upwards of 40 min. When compared with the ancestral virus, the infectivity of the Delta variant displayed different decay profiles. At low RH, a loss of viral infectivity of approximately 55% was observed over the initial 5 s for both variants. Regardless of RH and variant, greater than 95% of the viral infectivity was lost after 40 min of being aerosolized. Aero-stability of the variants correlate with their sensitivities to alkaline pH. Removal of all acidic vapours dramatically increased the rate of infectivity decay, with 90% loss after 2 min, while the addition of nitric acid vapour improved aero-stability. Similar aero-stability in droplets of artificial saliva and growth medium was observed. A model to predict loss of viral infectivity is proposed: at high RH, the high pH of exhaled aerosol drives viral infectivity loss; at low RH, high salt content limits the loss of viral infectivity.
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Affiliation(s)
- Allen Haddrell
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, UK
| | | | - Henry Oswin
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, UK
| | - Tristan Cogan
- Bristol Veterinary School, University of Bristol, Langford House, Langford, Bristol, UK
| | - James Bazire
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Jianghan Tian
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, UK
| | - Robert Alexander
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Jamie F. S. Mann
- Bristol Veterinary School, University of Bristol, Langford House, Langford, Bristol, UK
| | - Darryl Hill
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Adam Finn
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- School of Population Health Sciences, University of Bristol, Bristol, UK
| | - Andrew D. Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Jonathan P. Reid
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, UK
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65
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Yi Y, Li W, Liu K, Xue H, Yu R, Zhang M, Bao YO, Lai X, Fan J, Huang Y, Wang J, Shi X, Li J, Wei H, Xiang K, Li L, Zhang R, Zhao X, Qiao X, Yang H, Ye M. Licorice-saponin A3 is a broad-spectrum inhibitor for COVID-19 by targeting viral spike and anti-inflammation. J Pharm Anal 2023:S2095-1779(23)00099-0. [PMID: 37363744 PMCID: PMC10201890 DOI: 10.1016/j.jpha.2023.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/28/2023] Open
Abstract
Currently, human health due to corona virus disease 2019 (COVID-19) pandemic has been seriously threatened. The coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein plays a crucial role in virus transmission and several S-based therapeutic approaches have been approved for the treatment of COVID-19. However, the efficacy is compromised by the SARS-CoV-2 evolvement and mutation. Here we report the SARS-CoV-2 S protein receptor-binding domain (RBD) inhibitor licorice-saponin A3 (A3) could widely inhibit RBD of SARS-CoV-2 variants, including Beta, Delta, and Omicron BA.1, XBB and BQ1.1. Furthermore, A3 could potently inhibit SARS-CoV-2 Omicron virus in Vero E6 cells, with EC50 of 1.016 μM. The mechanism was related with binding with Y453 of RBD determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) analysis combined with quantum mechanics/molecular mechanics (QM/MM) simulations. Interestingly, phosphoproteomics analysis and multi fluorescent immunohistochemistry (mIHC) respectively indicated that A3 also inhibits host inflammation by directly modulating the JNK and p38 MAPK pathways and rebalancing the corresponding immune dysregulation. This work supports A3 as a promising broad-spectrum small molecule drug candidate for COVID-19.
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Affiliation(s)
- Yang Yi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Wenzhe Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shenzhen Children's Hospital, 7019 Yitian Road, Shenzhen 518036, China
| | - Heng Xue
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Meng Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Yang-Oujie Bao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Xinyuan Lai
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Jingjing Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Yuxi Huang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Xiaomeng Shi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Junhua Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuanhui Xiang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Linjie Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue Qiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Hang Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Hubei Jiangxia Laboratory, Wuhan 430000, China
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
- Yunnan Baiyao International Medical Research Center, Peking University, 38 Xueyuan Road, Beijing 100191, China
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Xiao S, Alshahrani M, Gupta G, Tao P, Verkhivker G. Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variants Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.20.541592. [PMID: 37292827 PMCID: PMC10245745 DOI: 10.1101/2023.05.20.541592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The new generation of SARS-CoV-2 Omicron variants displayed a significant growth advantage and the increased viral fitness by acquiring convergent mutations, suggesting that the immune pressure can promote convergent evolution leading to the sudden acceleration of SARS-CoV-2 evolution. In the current study, we combined structural modeling, extensive microsecond MD simulations and Markov state models to characterize conformational landscapes and identify specific dynamic signatures of the SARS-CoV-2 spike complexes with the host receptor ACE2 for the recently emerged highly transmissible XBB.1, XBB.1.5, BQ.1, and BQ.1.1 Omicron variants. Microsecond simulations and Markovian modeling provided a detailed characterization of the conformational landscapes and revealed the increased thermodynamic stabilization of the XBB.1.5 subvariant which is contrasted to more dynamic BQ.1 and BQ.1.1 subvariants. Despite considerable structural similarities, Omicron mutations can induce unique dynamic signatures and specific distributions of conformational states. The results suggested that variant-specific changes of conformational mobility in the functional interfacial loops of the spike receptor binding domain can be fine-tuned through cross-talk between convergent mutations thereby providing an evolutionary path for modulation of immune escape. By combining atomistic simulations and Markovian modeling analysis with perturbation-based approaches, we determined important complementary roles of convergent mutation sites as effectors and receivers of allosteric signaling involved in modulating conformational plasticity at the binding interface and regulating allosteric responses. This study also characterized the dynamics-induced evolution of allosteric pockets in the Omicron complexes that revealed hidden allosteric pockets and suggested that convergent mutation sites could control evolution and distribution of allosteric pockets through modulation of conformational plasticity in the flexible adaptable regions. Through integrative computational approaches, this investigation provides a systematic analysis and comparison of the effects of Omicron subvariants on conformational dynamics and allosteric signaling in the complexes with the ACE2 receptor. For Table of Contents Use Only
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Verkhivker G, Alshahrani M, Gupta G. Balancing Functional Tradeoffs between Protein Stability and ACE2 Binding in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic and Energetic Changes. Viruses 2023; 15:1143. [PMID: 37243229 PMCID: PMC10221141 DOI: 10.3390/v15051143] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Evolutionary and functional studies suggested that the emergence of the Omicron variants can be determined by multiple fitness trade-offs including the immune escape, binding affinity for ACE2, conformational plasticity, protein stability and allosteric modulation. In this study, we systematically characterize conformational dynamics, structural stability and binding affinities of the SARS-CoV-2 Spike Omicron complexes with the host receptor ACE2 for BA.2, BA.2.75, XBB.1 and XBB.1.5 variants. We combined multiscale molecular simulations and dynamic analysis of allosteric interactions together with the ensemble-based mutational scanning of the protein residues and network modeling of epistatic interactions. This multifaceted computational study characterized molecular mechanisms and identified energetic hotspots that can mediate the predicted increased stability and the enhanced binding affinity of the BA.2.75 and XBB.1.5 complexes. The results suggested a mechanism driven by the stability hotspots and a spatially localized group of the Omicron binding affinity centers, while allowing for functionally beneficial neutral Omicron mutations in other binding interface positions. A network-based community model for the analysis of epistatic contributions in the Omicron complexes is proposed revealing the key role of the binding hotspots R498 and Y501 in mediating community-based epistatic couplings with other Omicron sites and allowing for compensatory dynamics and binding energetic changes. The results also showed that mutations in the convergent evolutionary hotspot F486 can modulate not only local interactions but also rewire the global network of local communities in this region allowing the F486P mutation to restore both the stability and binding affinity of the XBB.1.5 variant which may explain the growth advantages over the XBB.1 variant. The results of this study are consistent with a broad range of functional studies rationalizing functional roles of the Omicron mutation sites that form a coordinated network of hotspots enabling a balance of multiple fitness tradeoffs and shaping up a complex functional landscape of virus transmissibility.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
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Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. Probing Conformational Landscapes of Binding and Allostery in the SARS-CoV-2 Omicron Variant Complexes Using Microsecond Atomistic Simulations and Perturbation-Based Profiling Approaches: Hidden Role of Omicron Mutations as Modulators of Allosteric Signaling and Epistatic Relationships. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539337. [PMID: 37205479 PMCID: PMC10187228 DOI: 10.1101/2023.05.03.539337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In this study, we systematically examine the conformational dynamics, binding and allosteric communications in the Omicron BA.1, BA.2, BA.3 and BA.4/BA.5 complexes with the ACE2 host receptor using molecular dynamics simulations and perturbation-based network profiling approaches. Microsecond atomistic simulations provided a detailed characterization of the conformational landscapes and revealed the increased thermodynamic stabilization of the BA.2 variant which is contrasted with the BA.4/BA.5 variants inducing a significant mobility of the complexes. Using ensemble-based mutational scanning of binding interactions, we identified binding affinity and structural stability hotspots in the Omicron complexes. Perturbation response scanning and network-based mutational profiling approaches probed the effect of the Omicron variants on allosteric communications. The results of this analysis revealed specific roles of Omicron mutations as "plastic and evolutionary adaptable" modulators of binding and allostery which are coupled to the major regulatory positions through interaction networks. Through perturbation network scanning of allosteric residue potentials in the Omicron variant complexes, which is performed in the background of the original strain, we identified that the key Omicron binding affinity hotspots N501Y and Q498R could mediate allosteric interactions and epistatic couplings. Our results suggested that the synergistic role of these hotspots in controlling stability, binding and allostery can enable for compensatory balance of fitness tradeoffs with conformationally and evolutionary adaptable immune-escape Omicron mutations. Through integrative computational approaches, this study provides a systematic analysis of the effects of Omicron mutations on thermodynamics, binding and allosteric signaling in the complexes with ACE2 receptor. The findings support a mechanism in which Omicron mutations can evolve to balance thermodynamic stability and conformational adaptability in order to ensure proper tradeoff between stability, binding and immune escape.
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Yurkovetskiy L, Egri S, Kurhade C, Diaz-Salinas MA, Jaimes JA, Nyalile T, Xie X, Choudhary MC, Dauphin A, Li JZ, Munro JB, Shi PY, Shen K, Luban J. S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.535005. [PMID: 37034621 PMCID: PMC10081308 DOI: 10.1101/2023.03.30.535005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
SARS-CoV-2 variants bearing complex combinations of mutations that confer increased transmissibility, COVID-19 severity, and immune escape, were first detected after S:D614G had gone to fixation, and likely originated during persistent infection of immunocompromised hosts. To test the hypothesis that S:D614G facilitated emergence of such variants, S:D614G was reverted to the ancestral sequence in the context of sequential Spike sequences from an immunocompromised individual, and within each of the major SARS-CoV-2 variants of concern. In all cases, infectivity of the S:D614G revertants was severely compromised. The infectivity of atypical SARS-CoV-2 lineages that propagated in the absence of S:D614G was found to be dependent upon either S:Q613H or S:H655Y. Notably, Gamma and Omicron variants possess both S:D614G and S:H655Y, each of which contributed to infectivity of these variants. Among sarbecoviruses, S:Q613H, S:D614G, and S:H655Y are only detected in SARS-CoV-2, which is also distinguished by a polybasic S1/S2 cleavage site. Genetic and biochemical experiments here showed that S:Q613H, S:D614G, and S:H655Y each stabilize Spike on virions, and that they are dispensable in the absence of S1/S2 cleavage, consistent with selection of these mutations by the S1/S2 cleavage site. CryoEM revealed that either S:D614G or S:H655Y shift the Spike receptor binding domain (RBD) towards the open conformation required for ACE2-binding and therefore on pathway for infection. Consistent with this, an smFRET reporter for RBD conformation showed that both S:D614G and S:H655Y spontaneously adopt the conformation that ACE2 induces in the parental Spike. Data from these orthogonal experiments demonstrate that S:D614G and S:H655Y are convergent adaptations to the polybasic S1/S2 cleavage site which stabilize S1 on the virion in the open RBD conformation and act epistatically to promote the fitness of variants bearing complex combinations of clinically significant mutations.
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Affiliation(s)
- Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- These authors contributed equally
| | - Shawn Egri
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- These authors contributed equally
| | - Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
- These authors contributed equally
| | - Marco A. Diaz-Salinas
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- These authors contributed equally
| | - Javier A. Jaimes
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- These authors contributed equally
| | - Thomas Nyalile
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Manish C. Choudhary
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ann Dauphin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Jonathan Z. Li
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - James B. Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kuang Shen
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
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Deng S, Liu Y, Tam RCY, Chen P, Zhang AJ, Mok BWY, Long T, Kukic A, Zhou R, Xu H, Song W, Chan JFW, To KKW, Chen Z, Yuen KY, Wang P, Chen H. An intranasal influenza virus-vectored vaccine prevents SARS-CoV-2 replication in respiratory tissues of mice and hamsters. Nat Commun 2023; 14:2081. [PMID: 37045873 PMCID: PMC10092940 DOI: 10.1038/s41467-023-37697-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/23/2023] [Indexed: 04/14/2023] Open
Abstract
Current available vaccines for COVID-19 are effective in reducing severe diseases and deaths caused by SARS-CoV-2 infection but less optimal in preventing infection. Next-generation vaccines which are able to induce mucosal immunity in the upper respiratory to prevent or reduce infections caused by highly transmissible variants of SARS-CoV-2 are urgently needed. We have developed an intranasal vaccine candidate based on a live attenuated influenza virus (LAIV) with a deleted NS1 gene that encodes cell surface expression of the receptor-binding-domain (RBD) of the SARS-CoV-2 spike protein, designated DelNS1-RBD4N-DAF. Immune responses and protection against virus challenge following intranasal administration of DelNS1-RBD4N-DAF vaccines were analyzed in mice and compared with intramuscular injection of the BioNTech BNT162b2 mRNA vaccine in hamsters. DelNS1-RBD4N-DAF LAIVs induced high levels of neutralizing antibodies against various SARS-CoV-2 variants in mice and hamsters and stimulated robust T cell responses in mice. Notably, vaccination with DelNS1-RBD4N-DAF LAIVs, but not BNT162b2 mRNA, prevented replication of SARS-CoV-2 variants, including Delta and Omicron BA.2, in the respiratory tissues of animals. The DelNS1-RBD4N-DAF LAIV system warrants further evaluation in humans for the control of SARS-CoV-2 transmission and, more significantly, for creating dual function vaccines against both influenza and COVID-19 for use in annual vaccination strategies.
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Affiliation(s)
- Shaofeng Deng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Ying Liu
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Rachel Chun-Yee Tam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Pin Chen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Anna Jinxia Zhang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics Limited, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Bobo Wing-Yee Mok
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics Limited, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Teng Long
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics Limited, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Anja Kukic
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Runhong Zhou
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Haoran Xu
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Wenjun Song
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Jasper Fuk-Woo Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics Limited, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Kelvin Kai-Wang To
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics Limited, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Zhiwei Chen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics Limited, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics Limited, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Pui Wang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.
- Centre for Virology, Vaccinology and Therapeutics Limited, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.
| | - Honglin Chen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.
- State Key Laboratory for Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.
- Centre for Virology, Vaccinology and Therapeutics Limited, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.
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Gili R, Burioni R. SARS-CoV-2 before and after Omicron: two different viruses and two different diseases? J Transl Med 2023; 21:251. [PMID: 37038133 PMCID: PMC10088248 DOI: 10.1186/s12967-023-04095-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/28/2023] [Indexed: 04/12/2023] Open
Abstract
For the first time in the history of medicine, it has been possible to describe-after a spillover-the evolution of a new human virus spreading in a non-immune population. This allowed not only to observe the subsequent emersion of variants endowed with features providing the virus with an evolutionary advantage, but also the shift of the pathways of virus replication and the acquisition of immunoevasive features. These characteristics had a remarkable influence on the diffusion of the SARS-CoV-2 and on the clinical presentation and prognosis of COVID-19, aspects that are described and commented in this review.
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Affiliation(s)
- Renata Gili
- Università Vita Salute San Raffaele Medical School, via Olgettina 58, 20132, Milan, Italy
| | - Roberto Burioni
- Università Vita Salute San Raffaele Medical School, via Olgettina 58, 20132, Milan, Italy.
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Furusawa Y, Kiso M, Iida S, Uraki R, Hirata Y, Imai M, Suzuki T, Yamayoshi S, Kawaoka Y. In SARS-CoV-2 delta variants, Spike-P681R and D950N promote membrane fusion, Spike-P681R enhances spike cleavage, but neither substitution affects pathogenicity in hamsters. EBioMedicine 2023; 91:104561. [PMID: 37043872 PMCID: PMC10083686 DOI: 10.1016/j.ebiom.2023.104561] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/18/2023] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 delta (B.1.617.2 lineage) variant was first identified at the end of 2020 and possessed two unique amino acid substitutions in its spike protein: S-P681R, at the S1/S2 cleavage site, and S-D950N, in the HR1 of the S2 subunit. However, the roles of these substitutions in virus phenotypes have not been fully characterized. METHODS We used reverse genetics to generate Wuhan-D614G viruses with these substitutions and delta viruses lacking these substitutions and explored how these changes affected their viral characteristics in vitro and in vivo. FINDINGS S-P681R enhanced spike cleavage and membrane fusion, whereas S-D950N slightly promoted membrane fusion. Although S-681R reduced the virus replicative ability especially in VeroE6 cells, neither substitution affected virus replication in Calu-3 cells and hamsters. The pathogenicity of all recombinant viruses tested in hamsters was slightly but not significantly affected. INTERPRETATION Our observations suggest that the S-P681R and S-D950N substitutions alone do not increase virus pathogenicity, despite of their enhancement of spike cleavage or fusogenicity. FUNDING A full list of funding bodies that contributed to this study can be found under Acknowledgments.
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Affiliation(s)
- Yuri Furusawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Maki Kiso
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ryuta Uraki
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Yuichiro Hirata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masaki Imai
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan; International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Seiya Yamayoshi
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan; International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan; Pandemic Preparedness, Infection, and Advanced Research Center, The University of Tokyo, Tokyo, Japan; Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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Dual mechanism: Epigenetic inhibitor apabetalone reduces SARS-CoV-2 Delta and Omicron variant spike binding and attenuates SARS-CoV-2 RNA induced inflammation. Int Immunopharmacol 2023; 117:109929. [PMID: 36857935 PMCID: PMC9946890 DOI: 10.1016/j.intimp.2023.109929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/03/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023]
Abstract
The SARS-CoV-2 virus initiates infection via interactions between the viral spike protein and the ACE2 receptors on host cells. Variants of concern have mutations in the spike protein that enhance ACE2 binding affinity, leading to increased virulence and transmission. Viral RNAs released after entry into host cells trigger interferon-I (IFN-I) mediated inflammatory responses for viral clearance and resolution of infection. However, overreactive host IFN-I responses and pro-inflammatory signals drive COVID-19 pathophysiology and disease severity during acute infection. These immune abnormalities also lead to the development of post-COVID syndrome if persistent. Novel therapeutics are urgently required to reduce short- and long-term pathologic consequences associated with SARS-CoV-2 infection. Apabetalone, an inhibitor of epigenetic regulators of the BET protein family, is a candidate for COVID-19 treatment via a dual mechanism of action. In vitro, apabetalone downregulates ACE2 gene expression to limit SARS-CoV-2 entry and propagation. In pre-clinical models and patients treated for cardiovascular disease, apabetalone inhibits expression of inflammatory mediators involved in the pathologic cytokine storm (CS) stimulated by various cytokines. Here we show apabetalone treatment of human lung epithelial cells reduces binding of viral spike protein regardless of mutations found in the highly contagious Delta variant and heavily mutated Omicron. Additionally, we demonstrate that apabetalone counters expression of pro-inflammatory factors with roles in CS and IFN-I signaling in lung cells stimulated with SARS-CoV-2 RNA. Our results support clinical evaluation of apabetalone to treat COVID-19 and post-COVID syndrome regardless of the SARS-CoV-2 variant.
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74
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Haque S, Mathkor DM, Alkhanani MF, Bantun F, Momenah AM, Faidah H, Jalal NA, Kumar V. Comprehensive deep mutational scanning reveals the pH induced stability and binding differences between SARS-CoV-2 spike RBD and human ACE2. J Biomol Struct Dyn 2023; 41:15207-15218. [PMID: 36995177 DOI: 10.1080/07391102.2023.2194007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/25/2023] [Indexed: 03/31/2023]
Abstract
The SARS-CoV-2 spike (S) glycoprotein with its mobile receptor-binding domain (RBD), binds to the human ACE2 receptor and thus facilitates virus entry through low-pH-endosomal pathways. The high degree of SARS-CoV-2 mutability has raised concern among scientists and medical professionals because it created doubt about the effectiveness of drugs and vaccinations designed specifically for COVID-19. In this study, we used computational saturation mutagenesis approach, including structure-based free energy calculations to analyse the effects of the missense mutations on the SARS-CoV-2 S-RBD stability and the S-RBD binding affinity with ACE2 at three different pH (pH 4.5, pH 6.5, and pH 7.4). A total of 3705 mutations in the S-RBD protein were analyzed, and we discovered that most of these mutations destabilize the RBD protein. Specifically, residues G404, G431, G447, A475, and G526 were important for RBD protein stability. In addition, RBD residues Y449, Y489, Y495, Q498, and N487 were critical for the RBD-ACE2 interaction. Next, we found that the distribution of the mean stability changes and mean binding energy changes of RBD due to mutations at both serological and endosomal pH correlated well, indicating the similar effects of mutations. Overall, this computational analysis is useful for understanding the effects of missense mutations in SARS-CoV-2 pathogenesis at different pH.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan-45142, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Darin Mansor Mathkor
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan-45142, Saudi Arabia
| | - Mustfa Faisal Alkhanani
- Biology Department, College of Sciences, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Farkad Bantun
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Aiman M Momenah
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Hani Faidah
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Naif A Jalal
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, Uttar Pradesh, India
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75
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Zhang Q, Tang WC, Stancanelli E, Jung E, Syed Z, Pagadala V, Saidi L, Chen CZ, Gao P, Xu M, Pavlinov I, Li B, Huang W, Chen L, Liu J, Xie H, Zheng W, Ye Y. Heparan sulfate promotes ACE2 super-cluster assembly to enhance SARS-CoV-2-associated syncytium formation. RESEARCH SQUARE 2023:rs.3.rs-2693563. [PMID: 37034606 PMCID: PMC10081376 DOI: 10.21203/rs.3.rs-2693563/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
The mechanism of syncytium formation, caused by spike-induced cell-cell fusion in severe COVID-19, is largely unclear. Here we combine chemical genetics with 4D confocal imaging to establish the cell surface heparan sulfate (HS) as a critical host factor exploited by SARS-CoV-2 to enhance spike’s fusogenic activity. HS binds spike to facilitate ACE2 clustering, generating synapse-like cell-cell contacts to promote fusion pore formation. ACE2 clustering, and thus, syncytium formation is significantly mitigated by chemical or genetic elimination of cell surface HS, while in a cell-free system consisting of purified HS, spike, and lipid-anchored ACE2, HS directly induces ACE2 clustering. Importantly, the interaction of HS with spike allosterically enables a conserved ACE2 linker in receptor clustering, which concentrates spike at the fusion site to overcome fusion-associated activity loss. This fusion-boosting mechanism can be effectively targeted by an investigational HS-binding drug, which reduces syncytium formation in vitro and viral infection in mice.
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Affiliation(s)
- Qi Zhang
- The National Center for Advancing Translational Sciences
| | - Wei-Chun Tang
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research & Review, Center for Biologics Evaluation & Research, US Food & Drug Administration
| | | | | | | | | | - Layla Saidi
- National Institute of Diabetes and Digestive and Kidney Diseases
| | | | - Peng Gao
- National Center for Advancing Translational Sciences
| | - Miao Xu
- National Center for Advancing Translational Sciences
| | - Ivan Pavlinov
- National Center for Advancing Translational Sciences
| | - Bing Li
- National Center for Advancing Translational Sciences
| | - Wenwei Huang
- National Center for Advancing Translational Sciences
| | | | | | - Hang Xie
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research & Review, Center for Biologics Evaluation & Research, US Food & Drug Administration
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76
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He X, He C, Hong W, Yang J, Wei X. Research progress in spike mutations of SARS-CoV-2 variants and vaccine development. Med Res Rev 2023. [PMID: 36929527 DOI: 10.1002/med.21941] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 09/27/2022] [Accepted: 02/26/2023] [Indexed: 03/18/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic can hardly end with the emergence of different variants over time. In the past 2 years, several variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), such as the Delta and Omicron variants, have emerged with higher transmissibility, immune evasion and drug resistance, leading to higher morbidity and mortality in the population. The prevalent variants of concern (VOCs) share several mutations on the spike that can affect virus characteristics, including transmissibility, antigenicity, and immune evasion. Increasing evidence has demonstrated that the neutralization capacity of sera from COVID-19 convalescent or vaccinated individuals is decreased against SARS-CoV-2 variants. Moreover, the vaccine effectiveness of current COVID-19 vaccines against SARS-CoV-2 VOCs is not as high as that against wild-type SARS-CoV-2. Therefore, more attention might be paid to how the mutations impact vaccine effectiveness. In this review, we summarized the current studies on the mutations of the SARS-CoV-2 spike, particularly of the receptor binding domain, to elaborate on how the mutations impact the infectivity, transmissibility and immune evasion of the virus. The effects of mutations in the SARS-CoV-2 spike on the current therapeutics were highlighted, and potential strategies for future vaccine development were suggested.
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Affiliation(s)
- Xuemei He
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Cai He
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Weiqi Hong
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jingyun Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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77
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Triveri A, Casali E, Frasnetti E, Doria F, Frigerio F, Cinquini F, Pavoni S, Moroni E, Marchetti F, Serapian SA, Colombo G. Conformational Behavior of SARS-Cov-2 Spike Protein Variants: Evolutionary Jumps in Sequence Reverberate in Structural Dynamic Differences. J Chem Theory Comput 2023; 19:2120-2134. [PMID: 36926878 PMCID: PMC10029694 DOI: 10.1021/acs.jctc.3c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
SARS-CoV-2 has evolved rapidly in the first 3 years of pandemic diffusion. The initial evolution of the virus appeared to proceed through big jumps in sequence changes rather than through the stepwise accumulation of point mutations on already established variants. Here, we examine whether this nonlinear mutational process reverberates in variations of the conformational dynamics of the SARS-CoV-2 Spike protein (S-protein), the first point of contact between the virus and the human host. We run extensive microsecond-scale molecular dynamics simulations of seven distinct variants of the protein in their fully glycosylated state and set out to elucidate possible links between the mutational spectrum of the S-protein and the structural dynamics of the respective variant, at global and local levels. The results reveal that mutation-dependent structural and dynamic modulations mostly consist of increased coordinated motions in variants that acquire stability and in an increased internal flexibility in variants that are less stable. Importantly, a limited number of functionally important substructures (the receptor binding domain, in particular) share the same time of movements in all variants, indicating efficient preorganization for functional regions dedicated to host interactions. Our results support a model in which the internal dynamics of the S-proteins from different strains varies in a way that reflects the observed random and non-stepwise jumps in sequence evolution, while conserving the functionally oriented traits of conformational dynamics necessary to support productive interactions with host receptors.
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Affiliation(s)
- Alice Triveri
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Emanuele Casali
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Elena Frasnetti
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Filippo Doria
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Francesco Frigerio
- Department of Physical Chemistry, R&D
Eni SpA, via Maritano 27, 20097 San Donato Milanese (Mi),
Italy
| | - Fabrizio Cinquini
- Upstream & Technical
Services—TECS/STES—Eni Spa, via Emilia 1, 20097 San Donato
Milanese (Mi), Italy
| | - Silvia Pavoni
- Department of Physical Chemistry, R&D
Eni SpA, via Maritano 27, 20097 San Donato Milanese (Mi),
Italy
| | | | - Filippo Marchetti
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Stefano A. Serapian
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Giorgio Colombo
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
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78
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Calvaresi V, Wrobel AG, Toporowska J, Hammerschmid D, Doores KJ, Bradshaw RT, Parsons RB, Benton DJ, Roustan C, Reading E, Malim MH, Gamblin SJ, Politis A. Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein. Nat Commun 2023; 14:1421. [PMID: 36918534 PMCID: PMC10013288 DOI: 10.1038/s41467-023-36745-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/15/2023] [Indexed: 03/15/2023] Open
Abstract
SARS-CoV-2 spike glycoprotein mediates receptor binding and subsequent membrane fusion. It exists in a range of conformations, including a closed state unable to bind the ACE2 receptor, and an open state that does so but displays more exposed antigenic surface. Spikes of variants of concern (VOCs) acquired amino acid changes linked to increased virulence and immune evasion. Here, using HDX-MS, we identified changes in spike dynamics that we associate with the transition from closed to open conformations, to ACE2 binding, and to specific mutations in VOCs. We show that the RBD-associated subdomain plays a role in spike opening, whereas the NTD acts as a hotspot of conformational divergence of VOC spikes driving immune evasion. Alpha, beta and delta spikes assume predominantly open conformations and ACE2 binding increases the dynamics of their core helices, priming spikes for fusion. Conversely, substitutions in omicron spike lead to predominantly closed conformations, presumably enabling it to escape antibodies. At the same time, its core helices show characteristics of being pre-primed for fusion even in the absence of ACE2. These data inform on SARS-CoV-2 evolution and omicron variant emergence.
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Affiliation(s)
- Valeria Calvaresi
- Department of Chemistry, King's College London, SE1 1DB, London, UK.
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, NW1 1AT, London, UK.
| | | | | | - Katie J Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, SE1 9RT, London, UK
| | | | | | - Donald J Benton
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Chloë Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT, London, UK
| | - Eamonn Reading
- Department of Chemistry, King's College London, SE1 1DB, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, SE1 9RT, London, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Argyris Politis
- Department of Chemistry, King's College London, SE1 1DB, London, UK.
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, M13 9PT, Manchester, UK.
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN, Manchester, UK.
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79
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Ramos-Guzmán CA, Andjelkovic M, Zinovjev K, Ruiz-Pernía JJ, Tuñón I. The impact of SARS-CoV-2 3CL protease mutations on nirmatrelvir inhibitory efficiency. Computational insights into potential resistance mechanisms. Chem Sci 2023; 14:2686-2697. [PMID: 36908962 PMCID: PMC9993853 DOI: 10.1039/d2sc06584c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/13/2023] [Indexed: 02/16/2023] Open
Abstract
The use of antiviral drugs can promote the appearance of mutations in the target protein that increase the resistance of the virus to the treatment. This is also the case of nirmatrelvir, a covalent inhibitor of the 3CL protease, or main protease, of SARS-CoV-2. In this work we show how the by-residue decomposition of noncovalent interactions established between the drug and the enzyme, in combination with an analysis of naturally occurring mutations, can be used to detect potential mutations in the 3CL protease conferring resistance to nirmatrelvir. We also investigate the consequences of these mutations on the reaction mechanism to form the covalent enzyme-inhibitor complex using QM/MM methods. In particular, we show that the E166V variant of the protease displays smaller binding affinity to nirmatrelvir and larger activation free energy for the formation of the covalent complex, both factors contributing to the observed resistance to the treatment with this drug. The conclusions derived from our work can be used to anticipate the consequences of the introduction of nirmatrelvir in the fitness landscape of the virus and to design new inhibitors adapted to some of the possible resistance mechanisms.
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Affiliation(s)
- Carlos A Ramos-Guzmán
- Departamento de Química Física, Universidad de Valencia 46100 Burjassot Spain
- Instituto de Materiales Avanzados, Universidad Jaume I 12071 Castelló Spain
| | - Milorad Andjelkovic
- Departamento de Química Física, Universidad de Valencia 46100 Burjassot Spain
| | - Kirill Zinovjev
- Departamento de Química Física, Universidad de Valencia 46100 Burjassot Spain
| | | | - Iñaki Tuñón
- Departamento de Química Física, Universidad de Valencia 46100 Burjassot Spain
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80
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Zhu Y, Li M, Liu N, Wu T, Han X, Zhao G, He Y. Development of highly effective LCB1-based lipopeptides targeting the spike receptor-binding motif of SARS-CoV-2. Antiviral Res 2023; 211:105541. [PMID: 36682464 PMCID: PMC9851916 DOI: 10.1016/j.antiviral.2023.105541] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/07/2023] [Accepted: 01/12/2023] [Indexed: 01/21/2023]
Abstract
LCB1 is a computationally designed 56-mer miniprotein targeting the spike (S) receptor-binding motif of SARS-CoV- 2 with high potent activity (Science, 2020; Cell host microbe, 2021); however, recent studies have demonstrated that emerging SARS-CoV-2 variants are highly resistant to LCB1's inhibition. In this study, we first identified a truncated peptide termed LCB1v8, which maintained the high antiviral potency. Then, a group of lipopeptides were generated by modifying LCB1v8 with diverse lipids, and of two lipopeptides, the C-terminally stearicacid-conjugtaed LCB1v17 and cholesterol-conjugated LCB1v18, were highly effective in inhibiting both S protein-pseudovirus and authentic SARS-CoV-2 infections. We further showed that LCB1-based inhibitors had similar α-helicity and thermostability in structure and bound to the target-mimic RBD protein with high affinity, and the lipopeptides exhibited greatly enhanced binding with the viral and cellular membranes, improved inhibitory activities against emerging SARS-CoV-2 variants. Moreover, LCB1v18 was validated with high preventive and therapeutic efficacies in K18-hACE2 transgenic mice against lethal SARS-CoV-2 challenge. In conclusion, our studies have provided important information for understanding the structure and activity relationship (SAR) of LCB1 inhibitor and would guide the future development of novel antivirals.
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Affiliation(s)
- Yuanmei Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Min Li
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Nian Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Tong Wu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xuelian Han
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Guangyu Zhao
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China.
| | - Yuxian He
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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81
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Beahm DR, Deng Y, DeAngelo TM, Sarpeshkar R. Drug Cocktail Formulation via Circuit Design. IEEE TRANSACTIONS ON MOLECULAR, BIOLOGICAL, AND MULTI-SCALE COMMUNICATIONS 2023; 9:28-48. [PMID: 37397625 PMCID: PMC10312325 DOI: 10.1109/tmbmc.2023.3246928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Electronic circuits intuitively visualize and quantitatively simulate biological systems with nonlinear differential equations that exhibit complicated dynamics. Drug cocktail therapies are a powerful tool against diseases that exhibit such dynamics. We show that just six key states, which are represented in a feedback circuit, enable drug-cocktail formulation: 1) healthy cell number; 2) infected cell number; 3) extracellular pathogen number; 4) intracellular pathogenic molecule number; 5) innate immune system strength; and 6) adaptive immune system strength. To enable drug cocktail formulation, the model represents the effects of the drugs in the circuit. For example, a nonlinear feedback circuit model fits measured clinical data, represents cytokine storm and adaptive autoimmune behavior, and accounts for age, sex, and variant effects for SARS-CoV-2 with few free parameters. The latter circuit model provided three quantitative insights on the optimal timing and dosage of drug components in a cocktail: 1) antipathogenic drugs should be given early in the infection, but immunosuppressant timing involves a tradeoff between controlling pathogen load and mitigating inflammation; 2) both within and across-class combinations of drugs have synergistic effects; 3) if they are administered sufficiently early in the infection, anti-pathogenic drugs are more effective at mitigating autoimmune behavior than immunosuppressant drugs.
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Affiliation(s)
| | - Yijie Deng
- Thayer School or Engineering, Dartmouth College, Hanover, NH 03755 USA
| | - Thomas M DeAngelo
- Thayer School or Engineering, Dartmouth College, Hanover, NH 03755 USA
| | - Rahul Sarpeshkar
- Departments of Engineering, Physics, Microbiology & Immunobiology, and Molecular & Systems Biology, Dartmouth College, Hanover, NH 03755 USA
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82
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Kwon HJ, Zhang J, Kosikova M, Tang W, Ortega-Rodriguez U, Peng H, Meseda CA, Pedro CL, Schmeisser F, Lu J, Kang I, Zhou B, Davis CT, Wentworth DE, Chen WH, Shriver MC, Barnes RS, Pasetti MF, Weir JP, Chen B, Xie H. Distinct in vitro and in vivo neutralization profiles of monoclonal antibodies elicited by the receptor binding domain of the ancestral SARS-CoV-2. J Med Virol 2023; 95:e28673. [PMID: 36916782 PMCID: PMC10189799 DOI: 10.1002/jmv.28673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023]
Abstract
Broadly neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are sought to curb coronavirus disease 2019 (COVID-19) infections. Here we produced and characterized a set of mouse monoclonal antibodies (mAbs) specific for the ancestral SARS-CoV-2 receptor binding domain (RBD). Two of them, 17A7 and 17B10, were highly potent in microneutralization assay with 50% inhibitory concentration (IC50 ) ≤135 ng/mL against infectious SARS-CoV-2 variants, including G614, Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Kappa, Lambda, B.1.1.298, B.1.222, B.1.5, and R.1. Both mAbs (especially 17A7) also exhibited strong in vivo efficacy in protecting K18-hACE2 transgenic mice from the lethal infection with G614, Alpha, Beta, Gamma, and Delta viruses. Structural analysis indicated that 17A7 and 17B10 target the tip of the receptor binding motif in the RBD-up conformation. A third RBD-reactive mAb (3A6) although escaped by Beta and Gamma, was highly effective in cross-neutralizing Delta and Omicron BA.1 variants in vitro and in vivo. In competition experiments, antibodies targeting epitopes similar to these 3 mAbs were rarely enriched in human COVID-19 convalescent sera or postvaccination sera. These results are helpful to inform new antibody/vaccine design and these mAbs can be useful tools for characterizing SARS-CoV-2 variants and elicited antibody responses.
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Affiliation(s)
- Hyung Joon Kwon
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Jun Zhang
- Division of Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Matina Kosikova
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Weichun Tang
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Uriel Ortega-Rodriguez
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Hanqin Peng
- Division of Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Clement A. Meseda
- Laboratory of DNA viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Cyntia L. Pedro
- Laboratory of DNA viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Falko Schmeisser
- Laboratory of DNA viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Jianming Lu
- Codex BioSolutions, Inc.,12358 Parklawn Drive, Suite 250A, Rockville, MD 20852, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University School of Medicine, 3900 Reservoir Road, N.W., Washington, D.C. 20057, USA
| | - Insung Kang
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Bin Zhou
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Charles T. Davis
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - David E. Wentworth
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Wilbur H. Chen
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Mallory C. Shriver
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Robin S. Barnes
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marcela F. Pasetti
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jerry P. Weir
- Laboratory of DNA viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Bing Chen
- Division of Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Hang Xie
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
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83
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Newby ML, Fogarty CA, Allen JD, Butler J, Fadda E, Crispin M. Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics. J Mol Biol 2023; 435:167928. [PMID: 36565991 PMCID: PMC9769069 DOI: 10.1016/j.jmb.2022.167928] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/25/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
The emergence of SARS-CoV-2 variants alters the efficacy of existing immunity, whether arisen naturally or through vaccination. Understanding the structure of the viral spike assists in determining the impact of mutations on the antigenic surface. One class of mutation impacts glycosylation attachment sites, which have the capacity to influence the antigenic structure beyond the immediate site of attachment. Here, we compare the site-specific glycosylation of recombinant viral spike mimetics of B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta), B.1.1.529 (Omicron). The P.1 strain exhibits two additional N-linked glycan sites compared to the other variants analyzed and we investigate the impact of these glycans by molecular dynamics. The acquired N188 site is shown to exhibit very limited glycan maturation, consistent with limited enzyme accessibility. Structural modeling and molecular dynamics reveal that N188 is located within a cavity by the receptor binding domain, which influences the dynamics of these attachment domains. These observations suggest a mechanism whereby mutations affecting viral glycosylation sites have a structural impact across the protein surface.
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Affiliation(s)
- Maddy L Newby
- School of Biological Sciences, University of Southampton, Southampton, UK. https://twitter.com/Maddy_Newby
| | - Carl A Fogarty
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland. https://twitter.com/2016Carl
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK. https://twitter.com/JoelDalllen
| | - John Butler
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland.
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK.
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84
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Kuo HC, Kuo KC, Du PX, Keskin BB, Su WY, Ho TS, Tsai PS, Pau CH, Shih HC, Huang YH, Weng KP, Syu GD. Profiling humoral immunity after mixing and matching COVID-19 vaccines using SARS-CoV-2 variant protein microarrays. Mol Cell Proteomics 2023; 22:100507. [PMID: 36787877 PMCID: PMC9922205 DOI: 10.1016/j.mcpro.2023.100507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
In November 2022, 68% of the population received at least one dose of COVID-19 vaccines. Due to the ongoing mutations, especially for the variants of concern (VOCs), it is important to monitor the humoral immune responses after different vaccination strategies. In this study, we developed a SARS-CoV-2 variant protein microarray that contained the spike proteins from the VOCs, e.g., alpha, beta, gamma, delta, and omicron, to quantify the binding antibody and surrogate neutralizing antibody. Plasmas were collected after two doses of matching AZD1222 (AZx2), two doses of matching mRNA-1273 (Mx2), or mixing AZD1222 and mRNA-1273 (AZ+M). The results showed a significant decrease of surrogate neutralizing antibodies against the receptor-binding domain in all VOCs in AZx2 and Mx2 but not AZ+M. A similar but minor reduction pattern of surrogate neutralizing antibodies against the extracellular domain was observed. While Mx2 exhibited a higher surrogate neutralizing level against all VOCs compared to AZx2, AZ+M showed an even higher surrogate neutralizing level in gamma and omicron compared to Mx2. It is worth noting that the binding antibody displayed a low correlation to the surrogate neutralizing antibody (R-square 0.130-0.382). This study delivers insights into humoral immunities, SARS-CoV-2 mutations, and mixing and matching vaccine strategies, which may provide a more effective vaccine strategy especially in preventing omicron.
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Affiliation(s)
- Ho-Chang Kuo
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan,Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan,College of Medicine, Chang Gung University, Taoyuan, Taiwan 33302
| | - Kuang-Che Kuo
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
| | - Pin-Xian Du
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Batuhan Birol Keskin
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Wen-Yu Su
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Tzong-Shiann Ho
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan R.O.C.,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan R.O.C.,Department of Pediatrics, Tainan Hospital, Ministry of Health and Welfare, Tainan 700, Taiwan R.O.C
| | - Pei-Shan Tsai
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Chi Ho Pau
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Hsi-Chang Shih
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ying-Hsien Huang
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan,Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan,College of Medicine, Chang Gung University, Taoyuan, Taiwan 33302
| | - Ken-Pen Weng
- Congenital Structural Heart Disease Center, Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung 813414, Taiwan,School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Guan-Da Syu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan; International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan 701, Taiwan; Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan.
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85
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Ching WY, Adhikari P, Jawad B, Podgornik R. Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory. Biomedicines 2023; 11:517. [PMID: 36831053 PMCID: PMC9953097 DOI: 10.3390/biomedicines11020517] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
The spike protein (S-protein) is a crucial part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with its many domains responsible for binding, fusion, and host cell entry. In this review we use the density functional theory (DFT) calculations to analyze the atomic-scale interactions and investigate the consequences of mutations in S-protein domains. We specifically describe the key amino acids and functions of each domain, which are essential for structural stability as well as recognition and fusion processes with the host cell; in addition, we speculate on how mutations affect these properties. Such unprecedented large-scale ab initio calculations, with up to 5000 atoms in the system, are based on the novel concept of amino acid-amino acid-bond pair unit (AABPU) that allows for an alternative description of proteins, providing valuable information on partial charge, interatomic bonding and hydrogen bond (HB) formation. In general, our results show that the S-protein mutations for different variants foster an increased positive partial charge, alter the interatomic interactions, and disrupt the HB networks. We conclude by outlining a roadmap for future computational research of biomolecular virus-related systems.
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Affiliation(s)
- Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
- Department of Applied Sciences, University of Technology, Baghdad 10066, Iraq
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
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86
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Characterization of a Vesicular Stomatitis Virus-Vectored Recombinant Virus Bearing Spike Protein of SARS-CoV-2 Delta Variant. Microorganisms 2023; 11:microorganisms11020431. [PMID: 36838396 PMCID: PMC9960918 DOI: 10.3390/microorganisms11020431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
The frequent emergence of SARS-CoV-2 variants thwarts the prophylactic and therapeutic countermeasures confronting COVID-19. Among them, the Delta variant attracts widespread attention due to its high pathogenicity and fatality rate compared with other variants. However, with the emergence of new variants, studies on Delta variants have been gradually weakened and ignored. In this study, a replication-competent recombinant virus carrying the S protein of the SARS-CoV-2 Delta variant was established based on the vesicular stomatitis virus (VSV), which presented a safe alternative model for studying the Delta variant. The recombinant virus showed a replication advantage in Vero E6 cells, and the viral titers reach 107.3 TCID50/mL at 36 h post-inoculation. In the VSV-vectored recombinant platform, the spike proteins of the Delta variant mediated higher fusion activity and syncytium formation than the wild-type strain. Notably, the recombinant virus was avirulent in BALB/c mice, Syrian hamsters, 3-day ICR suckling mice, and IFNAR/GR-/- mice. It induced protective neutralizing antibodies in rodents, and protected the Syrian hamsters against the SARS-CoV-2 Delta variant infection. Meanwhile, the eGFP reporter of recombinant virus enabled the visual assay of neutralizing antibodies. Therefore, the recombinant virus could be a safe and convenient surrogate tool for authentic SARS-CoV-2. This efficient and reliable model has significant potential for research on viral-host interactions, epidemiological investigation of serum-neutralizing antibodies, and vaccine development.
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87
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Jiang H, Liu R, Wang L, Wang X, Zhang M, Lin S, Cao Z, Wu F, Liu Y, Liu J. Chiral-Selective Antigen-Presentation by Supramolecular Chiral Polymer Micelles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2208157. [PMID: 36398497 DOI: 10.1002/adma.202208157] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Chirality is ubiquitous in biological systems, which is closely related to biological functions, life processes, and even the pathogenesis of diseases. However, the interface between the chirality of synthetic materials and organisms, particularly the immune system, remains poorly understood. Here, supramolecular chiral polymer micelles (SCPMs) are prepared by complexing antigenic proteins with chiral amino acid-modified polyethyleneimine. The introduction of chirality not only reduces the toxicity of cationic polymer, but also benefits cell uptake and antigen presentation. Especially, D-chirality presents the lowest cytotoxicity, while promoting the highest expression level of costimulatory molecules on dendritic cells compared to L-chirality and achirality. The superiority of D-chirality to stimulate dendritic cell maturation is supported by immunization with D-SCPMs, which achieves significant antigen-specific proliferation of T cells in the spleen, lymph nodes, and tumor of mice. Chirality-mediated antigen processing and presentation are demonstrated by D-SCPMs self-assembled from chiral alkaline histidine or neutral phenylalanine modified polyethyleneimine and tumor associated ovalbumin or severe acute respiratory syndrome coronavirus 2 spike 1 antigenic protein. Immunoactivation enabled by D-chirality opens a window to prepare potent nanotherapeutics for disease prevention and treatment.
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Affiliation(s)
- Hejin Jiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Rui Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Lu Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xinyue Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Mengmeng Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Sisi Lin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Zhenping Cao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Feng Wu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yingbin Liu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jinyao Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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88
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Bhattacharya M, Chatterjee S, Sharma AR, Lee SS, Chakraborty C. Delta variant (B.1.617.2) of SARS-CoV-2: current understanding of infection, transmission, immune escape, and mutational landscape. Folia Microbiol (Praha) 2023; 68:17-28. [PMID: 35962276 PMCID: PMC9374302 DOI: 10.1007/s12223-022-01001-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/07/2022] [Indexed: 12/01/2022]
Abstract
The Delta variant is one of the alarming variants of the SARS-CoV-2 virus that have been immensely detrimental and a significant cause of the prolonged pandemic (B.1.617.2). During the SARS-CoV-2 pandemic from December 2020 to October 2021, the Delta variant showed global dominance, and afterwards, the Omicron variant showed global dominance. Delta shows high infectivity rate which accounted for nearly 70% of the cases after December 2020. This review discusses the additional attributes that make the Delta variant so infectious and transmissible. The study also focuses on the significant mutations, namely the L452R and T478K present on the receptor-binding domain of spike (S)-glycoprotein, which confers specific alterations to the Delta variant. Considerably, we have also highlighted other notable factors such as the immune escape, infectivity and re-infectivity, vaccine escape, Ro number, S-glycoprotein stability, cleavage pattern, and its binding affinity with the host cell receptor protein. We have also emphasized clinical manifestations, symptomatology, morbidity, and mortality for the Delta variant compared with other significant SARS-CoV-2 variants. This review will help the researchers to get an elucidative view of the Delta variant to adopt some practical strategies to minimize the escalating spread of the SARS-CoV-2 Delta variant.
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Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore-756020, Odisha, India
| | - Srijan Chatterjee
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, 700126, India
| | - Ashish Ranjan Sharma
- 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
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, 700126, India.
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89
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Saville JW, Mannar D, Zhu X, Berezuk AM, Cholak S, Tuttle KS, Vahdatihassani F, Subramaniam S. Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein. Cell Rep 2023; 42:111964. [PMID: 36640338 PMCID: PMC9812370 DOI: 10.1016/j.celrep.2022.111964] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/10/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
The BA.2 sub-lineage of the Omicron (B.1.1.529) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant rapidly supplanted the original BA.1 sub-lineage in early 2022. Both lineages threatened the efficacy of vaccine-elicited antibodies and acquired increased binding to several mammalian ACE2 receptors. Cryoelectron microscopy (cryo-EM) analysis of the BA.2 spike (S) glycoprotein in complex with mouse ACE2 (mACE2) identifies BA.1- and BA.2-mutated residues Q493R, N501Y, and Y505H as complementing non-conserved residues between human and mouse ACE2, rationalizing the enhanced S protein-mACE2 interaction for Omicron variants. Cryo-EM structures of the BA.2 S-human ACE2 complex and of the extensively mutated BA.2 amino-terminal domain (NTD) reveal a dramatic reorganization of the highly antigenic N1 loop into a β-strand, providing an explanation for decreased binding of the BA.2 S protein to antibodies isolated from BA.1-convalescent patients. Our analysis reveals structural mechanisms underlying the antigenic drift in the rapidly evolving Omicron variant landscape.
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Affiliation(s)
- James W Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Dhiraj Mannar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Xing Zhu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Alison M Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Spencer Cholak
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Katharine S Tuttle
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Faezeh Vahdatihassani
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Gandeeva Therapeutics, Inc., Burnaby, BC V5C 6N5, Canada.
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90
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Almendro-Vázquez P, Laguna-Goya R, Paz-Artal E. Defending against SARS-CoV-2: The T cell perspective. Front Immunol 2023; 14:1107803. [PMID: 36776863 PMCID: PMC9911802 DOI: 10.3389/fimmu.2023.1107803] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/16/2023] [Indexed: 01/28/2023] Open
Abstract
SARS-CoV-2-specific T cell response has been proven essential for viral clearance, COVID-19 outcome and long-term memory. Impaired early T cell-driven immunity leads to a severe form of the disease associated with lymphopenia, hyperinflammation and imbalanced humoral response. Analyses of acute SARS-CoV-2 infection have revealed that mild COVID-19 course is characterized by an early induction of specific T cells within the first 7 days of symptoms, coordinately followed by antibody production for an effective control of viral infection. In contrast, patients who do not develop an early specific cellular response and initiate a humoral immune response with subsequent production of high levels of antibodies, develop severe symptoms. Yet, delayed and persistent bystander CD8+ T cell activation has been also reported in hospitalized patients and could be a driver of lung pathology. Literature supports that long-term maintenance of T cell response appears more stable than antibody titters. Up to date, virus-specific T cell memory has been detected 22 months post-symptom onset, with a predominant IL-2 memory response compared to IFN-γ. Furthermore, T cell responses are conserved against the emerging variants of concern (VoCs) while these variants are mostly able to evade humoral responses. This could be partly explained by the high HLA polymorphism whereby the viral epitope repertoire recognized could differ among individuals, greatly decreasing the likelihood of immune escape. Current COVID-19-vaccination has been shown to elicit Th1-driven spike-specific T cell response, as does natural infection, which provides substantial protection against severe COVID-19 and death. In addition, mucosal vaccination has been reported to induce strong adaptive responses both locally and systemically and to protect against VoCs in animal models. The optimization of vaccine formulations by including a variety of viral regions, innovative adjuvants or diverse administration routes could result in a desirable enhanced cellular response and memory, and help to prevent breakthrough infections. In summary, the increasing evidence highlights the relevance of monitoring SARS-CoV-2-specific cellular immune response, and not only antibody levels, as a correlate for protection after infection and/or vaccination. Moreover, it may help to better identify target populations that could benefit most from booster doses and to personalize vaccination strategies.
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Affiliation(s)
- Patricia Almendro-Vázquez
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Rocío Laguna-Goya
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Estela Paz-Artal
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, Madrid, Spain
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91
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Arruda HR, Lima TM, Alvim RG, Victorio FB, Abreu DP, Marsili FF, Cruz KD, Marques MA, Sosa-Acosta P, Quinones-Vega M, de S. Guedes J, Nogueira FC, Silva JL, Castilho LR, de Oliveira GA. Conformational stability of SARS-CoV-2 glycoprotein spike variants. iScience 2023; 26:105696. [PMID: 36465857 PMCID: PMC9710096 DOI: 10.1016/j.isci.2022.105696] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/18/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
The severe acute respiratory syndrome spread worldwide, causing a pandemic. SARS-CoV-2 mutations have arisen in the spike, a glycoprotein at the viral envelope and an antigenic candidate for vaccines against COVID-19. Here, we present comparative data of the glycosylated full-length ancestral and D614G spike together with three other transmissible strains classified by the World Health Organization as variants of concern: beta, gamma, and delta. By showing that D614G has less hydrophobic surface exposure and trimer persistence, we place D614G with features that support a model of temporary fitness advantage for virus spillover. Furthermore, during the SARS-CoV-2 adaptation, the spike accumulates alterations leading to less structural stability for some variants. The decreased trimer stability of the ancestral and gamma and the presence of D614G uncoupled conformations mean higher ACE-2 affinities compared to the beta and delta strains. Mapping the energetics and flexibility of variants is necessary to improve vaccine development.
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Affiliation(s)
- Hiam R.S. Arruda
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Tulio M. Lima
- Cell Culture Engineering Laboratory, COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-598, Brazil
- EPQB Program, School of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-598 Brazil
| | - Renata G.F. Alvim
- Cell Culture Engineering Laboratory, COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-598, Brazil
| | - Fernanda B.A. Victorio
- Cell Culture Engineering Laboratory, COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-598, Brazil
| | - Daniel P.B. Abreu
- Cell Culture Engineering Laboratory, COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-598, Brazil
| | - Federico F. Marsili
- Cell Culture Engineering Laboratory, COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-598, Brazil
- Biochemistry Program, Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-909, Brazil
| | - Karen D. Cruz
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Mayra A. Marques
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Patricia Sosa-Acosta
- Biochemistry Program, Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-909, Brazil
- Laboratory of Proteomics (LabProt), LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-598, Brazil
| | - Mauricio Quinones-Vega
- Biochemistry Program, Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-909, Brazil
- Laboratory of Proteomics (LabProt), LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-598, Brazil
| | - Jéssica de S. Guedes
- Biochemistry Program, Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-909, Brazil
- Laboratory of Proteomics (LabProt), LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-598, Brazil
| | - Fábio C.S. Nogueira
- Biochemistry Program, Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-909, Brazil
- Laboratory of Proteomics (LabProt), LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-598, Brazil
| | - Jerson L. Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Leda R. Castilho
- Cell Culture Engineering Laboratory, COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-598, Brazil
- Biochemistry Program, Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-909, Brazil
| | - Guilherme A.P. de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
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92
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Ma R, Zhang Y, Zhang Y, Li X, Ji Z. The Relationship between the Transmission of Different SARS-CoV-2 Strains and Air Quality: A Case Study in China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20031943. [PMID: 36767307 PMCID: PMC9916065 DOI: 10.3390/ijerph20031943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/07/2023] [Accepted: 01/17/2023] [Indexed: 06/11/2023]
Abstract
Coronavirus Disease 2019 (COVID-19) has been a global public health concern for almost three years, and the transmission characteristics vary among different virus variants. Previous studies have investigated the relationship between air pollutants and COVID-19 infection caused by the original strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, it is unclear whether individuals might be more susceptible to COVID-19 due to exposure to air pollutants, with the SARS-CoV-2 mutating faster and faster. This study aimed to explore the relationship between air pollutants and COVID-19 infection caused by three major SARS-CoV-2 strains (the original strain, Delta variant, and Omicron variant) in China. A generalized additive model was applied to investigate the associations of COVID-19 infection with six air pollutants (PM2.5, PM10, SO2, CO, NO2, and O3). A positive correlation might be indicated between air pollutants (PM2.5, PM10, and NO2) and confirmed cases of COVID-19 caused by different SARS-CoV-2 strains. It also suggested that the mutant variants appear to be more closely associated with air pollutants than the original strain. This study could provide valuable insight into control strategies that limit the concentration of air pollutants at lower levels and would better control the spread of COVID-19 even as the virus continues to mutate.
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Affiliation(s)
- Ruiqing Ma
- School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
- International Joint Research Centre of Shaanxi Province for Pollutants Exposure and Eco-Environmental Health, Xi’an 710119, China
| | - Yeyue Zhang
- School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
- International Joint Research Centre of Shaanxi Province for Pollutants Exposure and Eco-Environmental Health, Xi’an 710119, China
| | - Yini Zhang
- School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
- International Joint Research Centre of Shaanxi Province for Pollutants Exposure and Eco-Environmental Health, Xi’an 710119, China
| | - Xi Li
- School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
- International Joint Research Centre of Shaanxi Province for Pollutants Exposure and Eco-Environmental Health, Xi’an 710119, China
| | - Zheng Ji
- School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
- International Joint Research Centre of Shaanxi Province for Pollutants Exposure and Eco-Environmental Health, Xi’an 710119, China
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93
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Bendall EE, Callear AP, Getz A, Goforth K, Edwards D, Monto AS, Martin ET, Lauring AS. Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants. Nat Commun 2023; 14:272. [PMID: 36650162 PMCID: PMC9844183 DOI: 10.1038/s41467-023-36001-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Transmission bottlenecks limit the spread of novel mutations and reduce the efficiency of selection along a transmission chain. While increased force of infection, receptor binding, or immune evasion may influence bottleneck size, the relationship between transmissibility and the transmission bottleneck is unclear. Here we compare the transmission bottleneck of non-VOC SARS-CoV-2 lineages to those of Alpha, Delta, and Omicron. We sequenced viruses from 168 individuals in 65 households. Most virus populations had 0-1 single nucleotide variants (iSNV). From 64 transmission pairs with detectable iSNV, we identify a per clade bottleneck of 1 (95% CI 1-1) for Alpha, Delta, and Omicron and 2 (95% CI 2-2) for non-VOC. These tight bottlenecks reflect the low diversity at the time of transmission, which may be more pronounced in rapidly transmissible variants. Tight bottlenecks will limit the development of highly mutated VOC in transmission chains, adding to the evidence that selection over prolonged infections may drive their evolution.
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Affiliation(s)
- Emily E Bendall
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Amy P Callear
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Amy Getz
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Kendra Goforth
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Drew Edwards
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Arnold S Monto
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Emily T Martin
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Adam S Lauring
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
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Haddad-Boubaker S, Arbi M, Souiai O, Chouikha A, Fares W, Edington K, Sims S, Camma C, Lorusso A, Diagne MM, Diallo A, Boubaker IBB, Ferjani S, Mastouri M, Mhalla S, Karray H, Gargouri S, Bahri O, Trabelsi A, Kallala O, Hannachi N, Chaabouni Y, Smaoui H, Meftah K, Bouhalila SB, Foughali S, Zribi M, Lamari A, Touzi H, Safer M, Alaya NB, Kahla AB, Gdoura M, Triki H. The Delta variant wave in Tunisia: Genetic diversity, spatio-temporal distribution and evidence of the spread of a divergent AY.122 sub-lineage. Front Public Health 2023; 10:990832. [PMID: 36684874 PMCID: PMC9846204 DOI: 10.3389/fpubh.2022.990832] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 12/09/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction The Delta variant posed an increased risk to global public health and rapidly replaced the pre-existent variants worldwide. In this study, the genetic diversity and the spatio-temporal dynamics of 662 SARS-CoV2 genomes obtained during the Delta wave across Tunisia were investigated. Methods Viral whole genome and partial S-segment sequencing was performed using Illumina and Sanger platforms, respectively and lineage assignemnt was assessed using Pangolin version 1.2.4 and scorpio version 3.4.X. Phylogenetic and phylogeographic analyses were achieved using IQ-Tree and Beast programs. Results The age distribution of the infected cases showed a large peak between 25 to 50 years. Twelve Delta sub-lineages were detected nation-wide with AY.122 being the predominant variant representing 94.6% of sequences. AY.122 sequences were highly related and shared the amino-acid change ORF1a:A498V, the synonymous mutations 2746T>C, 3037C>T, 8986C>T, 11332A>G in ORF1a and 23683C>T in the S gene with respect to the Wuhan reference genome (NC_045512.2). Spatio-temporal analysis indicates that the larger cities of Nabeul, Tunis and Kairouan constituted epicenters for the AY.122 sub-lineage and subsequent dispersion to the rest of the country. Discussion This study adds more knowledge about the Delta variant and sub-variants distribution worldwide by documenting genomic and epidemiological data from Tunisia, a North African region. Such results may be helpful to the understanding of future COVID-19 waves and variants.
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Affiliation(s)
- Sondes Haddad-Boubaker
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Marwa Arbi
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Anissa Chouikha
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Wasfi Fares
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Kate Edington
- New Variant Assessment Platform (NVAP), UK Health Security Agency, London, United Kingdom
| | - Sam Sims
- New Variant Assessment Platform (NVAP), UK Health Security Agency, London, United Kingdom
| | - Cesare Camma
- Department of Virology, Instituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale (IZSAM), Teramo, Italy
| | - Alessio Lorusso
- Department of Virology, Instituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale (IZSAM), Teramo, Italy
| | | | - Amadou Diallo
- Department of Virology, Pasteur Institute of Dakar, Dakar, Senegal
| | - Ilhem Boutiba Ben Boubaker
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
- Laboratory Research Antimicrobial Resistance, Faculty of Medicine of Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Sana Ferjani
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
- Laboratory Research Antimicrobial Resistance, Faculty of Medicine of Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Maha Mastouri
- Laboratory of Microbiology, Fattouma Bourguiba Hospital, Monastir, Tunisia
- Laboratory Research Laboratoire des Maladies Transmissibles et Substances Biologiquement Actives, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Salma Mhalla
- Laboratory of Microbiology, Fattouma Bourguiba Hospital, Monastir, Tunisia
- Laboratory Research Laboratoire des Maladies Transmissibles et Substances Biologiquement Actives, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Hela Karray
- Laboratory of Microbiology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - Saba Gargouri
- Laboratory of Microbiology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - Olfa Bahri
- Laboratory of Microbiology and Biochemistry, Aziza Othmana Hospital, Tunis, Tunisia
| | | | - Ouafa Kallala
- Laboratory of Virology, Sahloul Hospital of Sousse, Sousse, Tunisia
| | - Naila Hannachi
- Laboratory of Microbiology, Farhat Hached Hospital of Sousse, Sousse, Tunisia
| | - Yassine Chaabouni
- Laboratory of Medical Biology, Ibn El Jazzar Hospital, Kairouan, Tunisia
- Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hanen Smaoui
- Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Microbiology of Children and Immunocompromised, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Bechir Hamza Children's Hospital, Tunis, Tunisia
| | - Khaoula Meftah
- Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Microbiology of Children and Immunocompromised, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Bechir Hamza Children's Hospital, Tunis, Tunisia
| | - Sophia Besbes Bouhalila
- Laboratory of Medical Biology and Blood Bank, Institute Mohamed Kassab d'orthopédie, Manouba, Tunisia
| | - Soumaya Foughali
- Laboratory of Medical Biology, Menzel Bourguiba Hospital, Bizerte, Tunisia
| | - Mariem Zribi
- Laboratory of Microbiology, La Rabta Hospital, Tunis, Tunisia
| | - Asma Lamari
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Henda Touzi
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Mouna Safer
- National Observatory of New and Emergent Diseases, Tunis, Tunisia
| | - Nissaf Ben Alaya
- Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- National Observatory of New and Emergent Diseases, Tunis, Tunisia
| | - Alia Ben Kahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Mariem Gdoura
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Virology, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
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Jin X, Sun X, Chai Y, Bai Y, Li Y, Hao T, Qi J, Song H, Wong CCL, Gao GF. Structural characterization of SARS-CoV-2 dimeric ORF9b reveals potential fold-switching trigger mechanism. SCIENCE CHINA. LIFE SCIENCES 2023; 66:152-164. [PMID: 36184694 PMCID: PMC9527070 DOI: 10.1007/s11427-022-2168-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/20/2022] [Indexed: 11/06/2022]
Abstract
The constant emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants indicates the evolution and adaptation of the virus. Enhanced innate immune evasion through increased expression of viral antagonist proteins, including ORF9b, contributes to the improved transmission of the Alpha variant; hence, more attention should be paid to these viral proteins. ORF9b is an accessory protein that suppresses innate immunity via a monomer conformation by binding to Tom70. Here, we solved the dimeric structure of SARS-CoV-2 ORF9b with a long hydrophobic tunnel containing a lipid molecule that is crucial for the dimeric conformation and determined the specific lipid ligands as monoglycerides by conducting a liquid chromatography with tandem mass spectrometry analysis, suggesting an important role in the viral life cycle. Notably, a long intertwined loop accessible for host factor binding was observed in the structure. Eight phosphorylated residues in ORF9b were identified, and residues S50 and S53 were found to contribute to the stabilization of dimeric ORF9b. Additionally, we proposed a model of multifunctional ORF9b with a distinct conformation, suggesting that ORF9b is a fold-switching protein, while both lipids and phosphorylation contribute to the switching. Specifically, the ORF9b monomer interacts with Tom70 to suppress the innate immune response, whereas the ORF9b dimer binds to the membrane involving mature virion assembly. Our results provide a better understanding of the multiple functions of ORF9b.
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Affiliation(s)
- Xiyue Jin
- grid.59053.3a0000000121679639School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027 China ,grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xue Sun
- grid.11135.370000 0001 2256 9319Peking University First Hospital, Peking University, Beijing, 100034 China ,grid.11135.370000 0001 2256 9319Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing, 100191 China
| | - Yan Chai
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yu Bai
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ying Li
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Tianjiao Hao
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jianxun Qi
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Hao Song
- grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
| | - Catherine C. L. Wong
- grid.11135.370000 0001 2256 9319Peking University First Hospital, Peking University, Beijing, 100034 China ,grid.11135.370000 0001 2256 9319Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing, 100191 China ,grid.11135.370000 0001 2256 9319Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China ,grid.11135.370000 0001 2256 9319School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, 100191 China
| | - George F. Gao
- grid.59053.3a0000000121679639School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027 China ,grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
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96
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Neamtu A, Mocci F, Laaksonen A, Barroso da Silva FL. Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants. Colloids Surf B Biointerfaces 2023; 221:112986. [PMID: 36375294 PMCID: PMC9617679 DOI: 10.1016/j.colsurfb.2022.112986] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/13/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022]
Abstract
A highly efficient and robust multiple scales in silico protocol, consisting of atomistic Molecular Dynamics (MD), coarse-grain (CG) MD, and constant-pH CG Monte Carlo (MC), has been developed and used to study the binding affinities of selected antigen-binding fragments of the monoclonal antibody (mAbs) CR3022 and several of its here optimized versions against 11 SARS-CoV-2 variants including the wild type. Totally 235,000 mAbs structures were initially generated using the RosettaAntibodyDesign software, resulting in top 10 scored CR3022-like-RBD complexes with critical mutations and compared to the native one, all having the potential to block virus-host cell interaction. Of these 10 finalists, two candidates were further identified in the CG simulations to be the best against all SARS-CoV-2 variants. Surprisingly, all 10 candidates and the native CR3022 exhibited a higher affinity for the Omicron variant despite its highest number of mutations. The multiscale protocol gives us a powerful rational tool to design efficient mAbs. The electrostatic interactions play a crucial role and appear to be controlling the affinity and complex building. Studied mAbs carrying a more negative total net charge show a higher affinity. Structural determinants could be identified in atomistic simulations and their roles are discussed in detail to further hint at a strategy for designing the best RBD binder. Although the SARS-CoV-2 was specifically targeted in this work, our approach is generally suitable for many diseases and viral and bacterial pathogens, leukemia, cancer, multiple sclerosis, rheumatoid, arthritis, lupus, and more.
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Affiliation(s)
- Andrei Neamtu
- Department of Physiology, "Grigore T. Popa" University of Medicine and Pharmacy of Iasi, Str. Universitatii nr. 16, 700051 Iasi, România; TRANSCEND Centre - Regional Institute of Oncology (IRO) Iasi, Str. General Henri Mathias Berthelot, Nr. 2-4 Iași, România
| | - Francesca Mocci
- University of Cagliari, Department of Chemical and Geological Sciences, Campus Monserrato, SS 554 bivio per Sestu, 09042 Monserrato, Italy
| | - Aatto Laaksonen
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, PetruPoni Institute of Macromolecular Chemistry Aleea Grigore Ghica-Voda, 41 A, 700487 Iasi, Romania; University of Cagliari, Department of Chemical and Geological Sciences, Campus Monserrato, SS 554 bivio per Sestu, 09042 Monserrato, Italy; Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden; State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing 210009, PR China; Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - Fernando L Barroso da Silva
- Universidade de São Paulo, Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. café, s/no - campus da USP, BR-14040-903 Ribeirão Preto, SP, Brazil; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA.
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97
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Li Y, Xu S, Ye Q, Chi H, Guo Z, Chen J, Wu M, Fan B, Li B, Qin C, Liu Z. Rational Development of Hypervalent Glycan Shield-Binding Nanoparticles with Broad-Spectrum Inhibition against Fatal Viruses Including SARS-CoV-2 Variants. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2202689. [PMID: 36377484 PMCID: PMC9839850 DOI: 10.1002/advs.202202689] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 09/22/2022] [Indexed: 05/31/2023]
Abstract
Infectious virus diseases, particularly coronavirus disease 2019, have posed a severe threat to public health, whereas the developed therapeutic and prophylactic strategies are seriously challenged by viral evolution and mutation. Therefore, broad-spectrum inhibitors of viruses are highly demanded. Herein, an unprecedented antiviral strategy is reported, targeting the viral glycan shields with hypervalent mannose-binding nanoparticles. The nanoparticles exhibit a unique double-punch mechanism, being capable of not only blocking the virus-receptor interaction but also inducing viral aggregation, thereby allowing for inhibiting the virus entry and facilitating the phagocytosis of viruses. The nanoparticles exhibit potent and broad-spectrum antiviral efficacy to multiple pseudoviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its major variants (D614G, N501Y, N439K, Δ69-70, Delta, and Omicron; lentiviruses expressing only the spike proteins), as well as other vital viruses (human immunodeficiency virus 1 and Lassa virus), with apparent EC50 values around the 10-9 m level. Significantly, the broad-spectrum inhibition of authentic viruses of both wild-type SARS-CoV-2 and Delta variants is confirmed. Therefore, this hypervalent glycan-shield targeting strategy opens new access to broad-spectrum viral inhibition.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023P. R. China
| | - Shuxin Xu
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023P. R. China
| | - Qing Ye
- Department of VirologyState Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071P. R. China
| | - Hang Chi
- Department of VirologyState Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071P. R. China
| | - Zhanchen Guo
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023P. R. China
| | - Jingran Chen
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023P. R. China
| | - Mei Wu
- Department of VirologyState Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071P. R. China
| | - Baochao Fan
- Institute of Veterinary MedicineJiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of AgricultureNanjing210014P. R. China
| | - Bin Li
- Institute of Veterinary MedicineJiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of AgricultureNanjing210014P. R. China
| | - Cheng‐Feng Qin
- Department of VirologyState Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071P. R. China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023P. R. China
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98
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Li M, Ren Y, Aw ZQ, Chen B, Yang Z, Lei Y, Cheng L, Liang Q, Hong J, Yang Y, Chen J, Wong YH, Wei J, Shan S, Zhang S, Ge J, Wang R, Dong JZ, Chen Y, Shi X, Zhang Q, Zhang Z, Chu JJH, Wang X, Zhang L. Broadly neutralizing and protective nanobodies against SARS-CoV-2 Omicron subvariants BA.1, BA.2, and BA.4/5 and diverse sarbecoviruses. Nat Commun 2022; 13:7957. [PMID: 36575191 PMCID: PMC9792944 DOI: 10.1038/s41467-022-35642-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022] Open
Abstract
As SARS-CoV-2 Omicron and other variants of concern (VOCs) continue spreading worldwide, development of antibodies and vaccines to confer broad and protective activity is a global priority. Here, we report on the identification of a special group of nanobodies from immunized alpaca with potency against diverse VOCs including Omicron subvariants BA.1, BA.2 and BA.4/5, SARS-CoV-1, and major sarbecoviruses. Crystal structure analysis of one representative nanobody, 3-2A2-4, discovers a highly conserved epitope located between the cryptic and the outer face of the receptor binding domain (RBD), distinctive from the receptor ACE2 binding site. Cryo-EM and biochemical evaluation reveal that 3-2A2-4 interferes structural alteration of RBD required for ACE2 binding. Passive delivery of 3-2A2-4 protects K18-hACE2 mice from infection of authentic SARS-CoV-2 Delta and Omicron. Identification of these unique nanobodies will inform the development of next generation antibody therapies and design of pan-sarbecovirus vaccines.
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Affiliation(s)
- Mingxi Li
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Yifei Ren
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhen Qin Aw
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
- Infectious Disease Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
| | - Bo Chen
- NB BIOLAB Co., Ltd, Chengdu, 611137, China
| | - Ziqing Yang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Yuqing Lei
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Lin Cheng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, 518112, China
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Qingtai Liang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Junxian Hong
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Yiling Yang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Jing Chen
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yi Hao Wong
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
- Infectious Disease Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
| | - Jing Wei
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Sisi Shan
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Senyan Zhang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jiwan Ge
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ruoke Wang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | | | | | - Xuanling Shi
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Qi Zhang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, 518112, China
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Justin Jang Hann Chu
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore.
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore.
- Infectious Disease Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore.
- Collaborative and Translation Unit for HFMD, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 138673, Singapore.
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Linqi Zhang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China.
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
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99
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Zhu R, Canena D, Sikora M, Klausberger M, Seferovic H, Mehdipour AR, Hain L, Laurent E, Monteil V, Wirnsberger G, Wieneke R, Tampé R, Kienzl NF, Mach L, Mirazimi A, Oh YJ, Penninger JM, Hummer G, Hinterdorfer P. Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level. Nat Commun 2022; 13:7926. [PMID: 36566234 PMCID: PMC9789309 DOI: 10.1038/s41467-022-35641-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/14/2022] [Indexed: 12/25/2022] Open
Abstract
Recent waves of COVID-19 correlate with the emergence of the Delta and the Omicron variant. We report that the Spike trimer acts as a highly dynamic molecular caliper, thereby forming up to three tight bonds through its RBDs with ACE2 expressed on the cell surface. The Spike of both Delta and Omicron (B.1.1.529) Variant enhance and markedly prolong viral attachment to the host cell receptor ACE2, as opposed to the early Wuhan-1 isolate. Delta Spike shows rapid binding of all three Spike RBDs to three different ACE2 molecules with considerably increased bond lifetime when compared to the reference strain, thereby significantly amplifying avidity. Intriguingly, Omicron (B.1.1.529) Spike displays less multivalent bindings to ACE2 molecules, yet with a ten time longer bond lifetime than Delta. Delta and Omicron (B.1.1.529) Spike variants enhance and prolong viral attachment to the host, which likely not only increases the rate of viral uptake, but also enhances the resistance of the variants against host-cell detachment by shear forces such as airflow, mucus or blood flow. We uncover distinct binding mechanisms and strategies at single-molecule resolution, employed by circulating SARS-CoV-2 variants to enhance infectivity and viral transmission.
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Affiliation(s)
- Rong Zhu
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Daniel Canena
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Mateusz Sikora
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Faculty of Physics, University of Vienna, Vienna, Austria
- Malopolska Centre of Biotechnology, Gronostajowa 7A, 30-387, Kraków, Poland
| | - Miriam Klausberger
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Hannah Seferovic
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Ahmad Reza Mehdipour
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Center for Molecular Modeling, University of Ghent, Ghent, Belgium
| | - Lisa Hain
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Elisabeth Laurent
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
- Core Facility Biomolecular & Cellular Analysis, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Vanessa Monteil
- Department of Laboratory Medicine, Unit of Clinical Microbiology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | | | - Ralph Wieneke
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Nikolaus F Kienzl
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Lukas Mach
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Ali Mirazimi
- Department of Laboratory Medicine, Unit of Clinical Microbiology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
- National Veterinary Institute, Uppsala, Sweden
| | - Yoo Jin Oh
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Peter Hinterdorfer
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria.
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100
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Kwon HJ, Kosikova M, Tang W, Ortega-Rodriguez U, Radvak P, Xiang R, Mercer KE, Muskhelishvili L, Davis K, Ward JM, Kosik I, Holly J, Kang I, Yewdell JW, Plant EP, Chen WH, Shriver MC, Barnes RS, Pasetti MF, Zhou B, Wentworth DE, Xie H. Enhanced virulence and waning vaccine-elicited antibodies account for breakthrough infections caused by SARS-CoV-2 delta and beyond. iScience 2022; 25:105507. [PMID: 36373096 PMCID: PMC9635945 DOI: 10.1016/j.isci.2022.105507] [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: 08/14/2022] [Revised: 10/05/2022] [Accepted: 11/01/2022] [Indexed: 11/08/2022] Open
Abstract
Here we interrogate the factors responsible for SARS-CoV-2 breakthrough infections in a K18-hACE2 transgenic mouse model. We show that Delta and the closely related Kappa variant cause viral pneumonia and severe lung lesions in K18-hACE2 mice. Human COVID-19 mRNA post-vaccination sera after the 2nd dose are significantly less efficient in neutralizing Delta/Kappa than early 614G virus in vitro and in vivo. By 5 months post-vaccination, ≥50% of donors lack detectable neutralizing antibodies against Delta and Kappa and all mice receiving 5-month post-vaccination sera die after the lethal challenges. Although a 3rd vaccine dose can boost antibody neutralization against Delta in vitro and in vivo, the mean log neutralization titers against the latest Omicron subvariants are 1/3-1/2 of those against the original 614D virus. Our results suggest that enhanced virulence, greater immune evasion, and waning of vaccine-elicited protection account for SARS-CoV-2 variants caused breakthrough infections.
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Affiliation(s)
- Hyung-Joon Kwon
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Martina Kosikova
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Weichun Tang
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Uriel Ortega-Rodriguez
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Peter Radvak
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Ruoxuan Xiang
- Division of Biostatistics, Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Kelly E. Mercer
- Biomarkers and Alternative Models Branch, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, AR, USA
| | | | - Kelly Davis
- Toxicologic Pathology Associates, Jefferson, AR, USA
| | | | - Ivan Kosik
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jaroslav Holly
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Insung Kang
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Jonathan W. Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ewan P. Plant
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Wilbur H. Chen
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mallory C. Shriver
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Robin S. Barnes
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Marcela F. Pasetti
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bin Zhou
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - David E. Wentworth
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Hang Xie
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
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