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Estrada M, Zhu C, Bzami A, White JA, Lal M. Development of a quantitative ELISA for SARS-CoV-2 vaccine candidate, NDV-HXP-S, with CpG 1018® adjuvant. Hum Vaccin Immunother 2024; 20:2315709. [PMID: 38372198 PMCID: PMC10877971 DOI: 10.1080/21645515.2024.2315709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/05/2024] [Indexed: 02/20/2024] Open
Abstract
NDV-HXP-S is a Newcastle disease virus (NDV) vectored vaccine candidate which expresses the S-antigen of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This vaccine candidate is under evaluation in human clinical studies with and without cytosine phosphate guanine (CpG) 1018® adjuvant. Existing potency methods for NDV-HXP-S do not allow for quantification of the S-antigen when the adjuvant is present. To support evaluation of NDV-HXP-S with CpG 1018® adjuvant, an inhibition enzyme-linked immunosorbent assay (ELISA) was developed to allow for quantification and stability assessments of the vaccine. A pilot 6-month stability study was conducted on NDV-HXP-S vaccine with and without CpG 1018® adjuvant under refrigerated conditions (2°C to 8°C) and accelerated stability testing conditions (40°C). The vaccine was mixed with and without CpG 1018® adjuvant in saline and maintained S-antigen content at 2°C to 8°C for the entire 6-month period. Additionally, a pilot controlled temperature chain (CTC) stability study was conducted at the completion of the 6-month study and demonstrated the possibility for this vaccine candidate to attain CTC stability labeling.
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Affiliation(s)
- Marcus Estrada
- Medical Devices and Health Technologies, PATH, Seattle, WA, USA
| | - Changcheng Zhu
- Medical Devices and Health Technologies, PATH, Seattle, WA, USA
| | - Anan Bzami
- Medical Devices and Health Technologies, PATH, Seattle, WA, USA
| | | | - Manjari Lal
- Medical Devices and Health Technologies, PATH, Seattle, WA, USA
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Torgauten HM, Onyango TB, Ljostveit S, Hallin EI, Serkland TT, Skrede S, Langeland N, Cox RJ, Wergeland S, Myhr KM, Torkildsen Ø. Hospitalisations and humoral COVID-19 vaccine response in vaccinated rituximab-treated multiple sclerosis patients. Mult Scler Relat Disord 2024; 89:105770. [PMID: 39029342 DOI: 10.1016/j.msard.2024.105770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 06/07/2024] [Accepted: 07/13/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND Patients with multiple sclerosis (MS) treated with anti-CD20 therapies such as rituximab may have increased risk of severe COVID-19 disease. Vaccination induces protective immunity, but humoral vaccine response is known to be attenuated in rituximab-treated MS-patients-patients, which has indicated a need for real world data on severe morbidity and mortality from COVID-19 after vaccination. METHODS Rituximab-treated patients treated at Haukeland University Hospital were identified through the National MS Registry and invited to participate in the study by giving a consent and providing a blood sample 3 weeks or later after ordinary COVID-19- vaccination, i.e. 2 doses given with a standard interval of 3 weeks. Blood samples were analysed with Enzyme-Linked Immunosorbent assay (ELISA) to evaluate humoral vaccine response with screening test against receptor-binding domain (RBD) and confirmatory Spike IgG-specific ELISA. A haemagglutination test (HAT) was performed as a marker of neutralizing antibodies. Patient serum concentration of rituximab were quantified using liquid chromatography tandem mass spectrometry (LC-MS/MS). Registry data from the Norwegian MS registry and information on hospitalization from patient records were collected and linked to laboratory results. RESULTS 111 patients were included in the study. A total of 7 (6.3%) were hospitalized due to COVID-19 disease during the observation period. No patient was admitted to ICU and there were no deaths. 34.2% did not have detectable titre of SARS CoV-2 Spike IgG antibodies, 72.1% did not have a detectable titre of SARS CoV-2 RBD antibodies, and 88.2% did not have a detectable HAT titre. There was a correlation between hospitalisation and the absence of SARS CoV-2 Spike IgG antibody titre, and between hospitalisation and MS disease duration, as well as between spike IgG antibody titre and CD19 B-cell count, time since last rituximab infusion, cumulative rituximab treatment time and total IgG level in the patients. CONCLUSION A substantial proportion of rituximab-treated MS-patients-patients did not have detectable humoral vaccine responses after 2 doses of COVID-19 vaccination. Despite this, the cumulative percentage of patients hospitalized with COVID-19 disease throughout the observation period of 22 months was low, and no patients required ICU treatment. The results support that vaccinated MS-patients treated with rituximab have a protective effect against serious Covid-19 infection.
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Affiliation(s)
- Hilde M Torgauten
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway; Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | | | - Sonja Ljostveit
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Erik I Hallin
- Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, Bergen, Norway
| | - Trond T Serkland
- Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, Bergen, Norway; Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Silje Skrede
- Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, Bergen, Norway; Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Norway; National Advisory Unit for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Rebecca Jane Cox
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Stig Wergeland
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway; Department of Clinical Medicine, University of Bergen, Bergen, Norway; Norwegian MS Registry, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Kjell-Morten Myhr
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway; Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Øivind Torkildsen
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway; Department of Clinical Medicine, University of Bergen, Bergen, Norway.
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3
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Voss WN, Mallory MA, Byrne PO, Marchioni JM, Knudson SA, Powers JM, Leist SR, Dadonaite B, Townsend DR, Kain J, Huang Y, Satterwhite E, Castillo IN, Mattocks M, Paresi C, Munt JE, Scobey T, Seeger A, Premkumar L, Bloom JD, Georgiou G, McLellan JS, Baric RS, Lavinder JJ, Ippolito GC. Hybrid immunity to SARS-CoV-2 arises from serological recall of IgG antibodies distinctly imprinted by infection or vaccination. Cell Rep Med 2024; 5:101668. [PMID: 39094579 DOI: 10.1016/j.xcrm.2024.101668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/15/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
We describe the molecular-level composition of polyclonal immunoglobulin G (IgG) anti-spike antibodies from ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, vaccination, or their combination ("hybrid immunity") at monoclonal resolution. Infection primarily triggers S2/N-terminal domain (NTD)-reactive antibodies, whereas vaccination mainly induces anti-receptor-binding domain (RBD) antibodies. This imprint persists after secondary exposures wherein >60% of ensuing hybrid immunity derives from the original IgG pool. Monoclonal constituents of the original IgG pool can increase breadth, affinity, and prevalence upon secondary exposures, as exemplified by the plasma antibody SC27. Following a breakthrough infection, vaccine-induced SC27 gained neutralization breadth and potency against SARS-CoV-2 variants and zoonotic viruses (half-maximal inhibitory concentration [IC50] ∼0.1-1.75 nM) and increased its binding affinity to the protective RBD class 1/4 epitope (dissociation constant [KD] < 5 pM). According to polyclonal escape analysis, SC27-like binding patterns are common in SARS-CoV-2 hybrid immunity. Our findings provide a detailed molecular definition of immunological imprinting and show that vaccination can produce class 1/4 (SC27-like) IgG antibodies circulating in the blood.
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Affiliation(s)
- William N Voss
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Michael A Mallory
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Patrick O Byrne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jeffrey M Marchioni
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Sean A Knudson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - John M Powers
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah R Leist
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Douglas R Townsend
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jessica Kain
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Yimin Huang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ed Satterwhite
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Izabella N Castillo
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melissa Mattocks
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chelsea Paresi
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Jennifer E Munt
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Trevor Scobey
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Allison Seeger
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA
| | - George Georgiou
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ralph S Baric
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason J Lavinder
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
| | - Gregory C Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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4
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Pierzynowska K, Morcinek-Orłowska J, Gaffke L, Jaroszewicz W, Skowron PM, Węgrzyn G. Applications of the phage display technology in molecular biology, biotechnology and medicine. Crit Rev Microbiol 2024; 50:450-490. [PMID: 37270791 DOI: 10.1080/1040841x.2023.2219741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 10/17/2022] [Accepted: 05/25/2023] [Indexed: 06/06/2023]
Abstract
The phage display technology is based on the presentation of peptide sequences on the surface of virions of bacteriophages. Its development led to creation of sophisticated systems based on the possibility of the presentation of a huge variability of peptides, attached to one of proteins of bacteriophage capsids. The use of such systems allowed for achieving enormous advantages in the processes of selection of bioactive molecules. In fact, the phage display technology has been employed in numerous fields of biotechnology, as diverse as immunological and biomedical applications (in both diagnostics and therapy), the formation of novel materials, and many others. In this paper, contrary to many other review articles which were focussed on either specific display systems or the use of phage display in selected fields, we present a comprehensive overview of various possibilities of applications of this technology. We discuss an usefulness of the phage display technology in various fields of science, medicine and the broad sense of biotechnology. This overview indicates the spread and importance of applications of microbial systems (exemplified by the phage display technology), pointing to the possibility of developing such sophisticated tools when advanced molecular methods are used in microbiological studies, accompanied with understanding of details of structures and functions of microbial entities (bacteriophages in this case).
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Affiliation(s)
- Karolina Pierzynowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | | | - Lidia Gaffke
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Weronika Jaroszewicz
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdańsk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
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5
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Zhang T, Yang D, Tang L, Hu Y. Current development of severe acute respiratory syndrome coronavirus 2 neutralizing antibodies (Review). Mol Med Rep 2024; 30:148. [PMID: 38940338 PMCID: PMC11228696 DOI: 10.3892/mmr.2024.13272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/21/2024] [Indexed: 06/29/2024] Open
Abstract
The coronavirus disease 2019 pandemic due to severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) seriously affected global public health security. Studies on vaccines, neutralizing antibodies (NAbs) and small molecule antiviral drugs are currently ongoing. In particular, NAbs have emerged as promising therapeutic agents due to their well‑defined mechanism, high specificity, superior safety profile, ease of large‑scale production and simultaneous application for both prevention and treatment of viral infection. Numerous NAb therapeutics have entered the clinical research stages, demonstrating promising therapeutic and preventive effects. These agents have been used for outbreak prevention and control under urgent authorization processes. The present review summarizes the molecular targets of SARS‑CoV‑2‑associated NAbs and screening and identification techniques for NAb development. Moreover, the current shortcomings and challenges that persist with the use of NAbs are discussed. The aim of the present review is to offer a reference for the development of NAbs for any future emergent infectious diseases, including SARS‑CoV‑2.
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Affiliation(s)
- Tong Zhang
- Department of Hematology, Wuhan Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Di Yang
- Department of Hematology, Wuhan Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Liang Tang
- Department of Hematology, Wuhan Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Yu Hu
- Department of Hematology, Wuhan Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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6
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Xu J, Gong J, Bo X, Tong Y, Ren Z, Ni M. A benchmark for evaluation of structure-based online tools for antibody-antigen binding affinity. Biophys Chem 2024; 311:107253. [PMID: 38768531 DOI: 10.1016/j.bpc.2024.107253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/08/2024] [Accepted: 04/28/2024] [Indexed: 05/22/2024]
Abstract
The prediction of binding affinity changes caused by missense mutations can elucidate antigen-antibody interactions. A few accessible structure-based online computational tools have been proposed. However, selecting suitable software for particular research is challenging, especially research on the SARS-CoV-2 spike protein with antibodies. Therefore, benchmarking of the mutation-diverse SARS-CoV-2 datasets is critical. Here, we collected the datasets including 1216 variants about the changes in binding affinity of antigens from 22 complexes for SARS-CoV-2 S proteins and 22 monoclonal antibodies as well as applied them to evaluate the performance of seven binding affinity prediction tools. The tested tools' Pearson correlations between predicted and measured changes in binding affinity were between -0.158 and 0.657, while accuracy in classification tasks on predicting increasing or decreasing affinity ranged from 0.444 to 0.834. These tools performed relatively better on predicting single mutations, especially at epitope sites, whereas poor performance on extremely decreasing affinity. The tested tools were relatively insensitive to the experimental techniques used to obtain structures of complexes. In summary, we constructed a list of datasets and evaluated a range of structure-based online prediction tools that will explicate relevant processes of antigen-antibody interactions and enhance the computational design of therapeutic monoclonal antibodies.
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Affiliation(s)
- Jiayi Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jianting Gong
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Zilin Ren
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China.
| | - Ming Ni
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China.
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7
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Simmons HC, Finney J, Kotaki R, Adachi Y, Park Moseman A, Watanabe A, Song S, Robinson-McCarthy LR, Le Sage V, Kuraoka M, Moseman EA, Kelsoe G, Takahashi Y, McCarthy KR. A protective and broadly binding antibody class engages the influenza virus hemagglutinin head at its stem interface. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.13.571543. [PMID: 38168412 PMCID: PMC10760138 DOI: 10.1101/2023.12.13.571543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Influenza infection and vaccination impart strain-specific immunity that protects against neither seasonal antigenic variants nor the next pandemic. However, antibodies directed to conserved sites can confer broad protection. Here we identify and characterize a class of human antibodies that engage a previously undescribed, conserved epitope on the influenza hemagglutinin (HA) protein. Prototype antibody S8V1-157 binds at the normally occluded interface between the HA head and stem. Antibodies to this HA head-stem interface epitope are non-neutralizing in vitro but protect against lethal influenza infection in mice. Antibody isotypes that direct clearance of infected cells enhance this protection. Head-stem interface antibodies bind to most influenza A serotypes and seasonal human variants, and are present at low frequencies in the memory B cell populations of multiple human donors. Vaccines designed to elicit these antibodies might contribute to "universal" influenza immunity.
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Affiliation(s)
- Holly C. Simmons
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Joel Finney
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Ryutaro Kotaki
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Yu Adachi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Annie Park Moseman
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Akiko Watanabe
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Shengli Song
- Department of Surgery, Duke University, Durham, North Carolina 27710, USA
| | - Lindsey R. Robinson-McCarthy
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Valerie Le Sage
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Masayuki Kuraoka
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - E. Ashley Moseman
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Garnett Kelsoe
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Yoshimasa Takahashi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Kevin R. McCarthy
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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8
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Liang L, Wang B, Zhang Q, Zhang S, Zhang S. Antibody drugs targeting SARS-CoV-2: Time for a rethink? Biomed Pharmacother 2024; 176:116900. [PMID: 38861858 DOI: 10.1016/j.biopha.2024.116900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/20/2024] [Accepted: 06/06/2024] [Indexed: 06/13/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) heavily burdens human health. Multiple neutralizing antibodies (nAbs) have been issued for emergency use or tested for treating infected patients in the clinic. However, SARS-CoV-2 variants of concern (VOC) carrying mutations reduce the effectiveness of nAbs by preventing neutralization. Uncoding the mutation profile and immune evasion mechanism of SARS-CoV-2 can improve the outcome of Ab-mediated therapies. In this review, we first outline the development status of anti-SARS-CoV-2 Ab drugs and provide an overview of SARS-CoV-2 variants and their prevalence. We next focus on the failure causes of anti-SARS-CoV-2 Ab drugs and rethink the design strategy for developing new Ab drugs against COVID-19. This review provides updated information for the development of therapeutic Ab drugs against SARS-CoV-2 variants.
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Affiliation(s)
- Likeng Liang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Bo Wang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Qing Zhang
- Department of Laboratory Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Shiwu Zhang
- Department of Pathology, Tianjin Union Medical Center, Nankai University, Tianjin 300121, China
| | - Sihe Zhang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China.
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9
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Connor RI, Sakharkar M, Rappazzo CG, Kaku CI, Curtis NC, Shin S, Wieland-Alter WF, Wentworth J, Mielcarz DW, Weiner JA, Ackerman ME, Walker LM, Lee J, Wright PF. Characteristics and Functions of Infection-enhancing Antibodies to the N-terminal Domain of SARS-CoV-2. Pathog Immun 2024; 9:1-24. [PMID: 38933606 PMCID: PMC11197847 DOI: 10.20411/pai.v9i2.679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/08/2024] [Indexed: 06/28/2024] Open
Abstract
Background Fcγ-receptor (FcγR)-independent enhancement of SARS-CoV-2 infection mediated by N-terminal domain (NTD)-binding monoclonal antibodies (mAbs) has been observed in vitro, but the functional significance of these antibodies in vivo is less clear. Methods We characterized 1,213 SARS-CoV-2 spike (S)-binding mAbs derived from COVID-19 convalescent patients for binding specificity to the SARS-CoV-2 S protein, VH germ-line usage, and affinity maturation. Infection enhancement in a vesicular stomatitis virus (VSV)-SARS-CoV-2 S pseudovirus (PV) assay was characterized in respiratory and intestinal epithelial cell lines, and against SARS-CoV-2 variants of concern (VOC). Proteomic deconvolution of the serum antibody repertoire was used to determine functional attributes of secreted NTD-binding mAbs. Results We identified 72/1213 (5.9%) mAbs that enhanced SARS-CoV-2 infection in a PV assay. The majority (68%) of these mAbs recognized the NTD, were identified in patients with mild and severe disease, and persisted for at least 5 months post-infection. Infection enhancement by NTD-binding mAbs was not observed in intestinal and respiratory epithelial cell lines and was diminished or lost against SARS-CoV-2 VOC. Proteomic deconvolution of the serum antibody repertoire from 2 of the convalescent patients identified, for the first time, NTD-binding, infection-enhancing mAbs among the circulating immunoglobulins directly isolated from serum. Functional analysis of these mAbs demonstrated robust activation of FcγRIIIa associated with antibody binding to recombinant S proteins. Conclusions Functionally active NTD-specific mAbs arise frequently during natural infection and can last as major serum clonotypes during convalescence. These antibodies display functional attributes that include FcγR activation, and may be selected against by mutations in NTD associated with SARS-CoV-2 VOC.
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Affiliation(s)
- Ruth I. Connor
- Department of Pediatrics, Geisel School of Medicine, Dartmouth Health, Lebanon, New Hampshire
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
| | | | | | | | | | - Seungmin Shin
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire
| | - Wendy F. Wieland-Alter
- Department of Pediatrics, Geisel School of Medicine, Dartmouth Health, Lebanon, New Hampshire
| | - Jordan Wentworth
- DartLab, Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire
| | - Daniel W. Mielcarz
- DartLab, Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire
| | - Joshua A. Weiner
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire
| | - Margaret E. Ackerman
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire
| | | | - Jiwon Lee
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire
| | - Peter F. Wright
- Department of Pediatrics, Geisel School of Medicine, Dartmouth Health, Lebanon, New Hampshire
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10
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Hwang J, Kim BK, Moon S, Park W, Kim KW, Yoon JH, Oh H, Jung S, Park Y, Kim S, Kim M, Kim S, Jung Y, Park M, Kim JH, Jung ST, Kim SJ, Kim YS, Chung WJ, Song MS, Kweon DH. Conversion of Host Cell Receptor into Virus Destructor by Immunodisc to Neutralize Diverse SARS-CoV-2 Variants. Adv Healthc Mater 2024; 13:e2302803. [PMID: 38329411 DOI: 10.1002/adhm.202302803] [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: 09/22/2023] [Revised: 12/29/2023] [Indexed: 02/09/2024]
Abstract
The decreasing efficacy of antiviral drugs due to viral mutations highlights the challenge of developing a single agent targeting multiple strains. Using host cell viral receptors as competitive inhibitors is promising, but their low potency and membrane-bound nature have limited this strategy. In this study, the authors show that angiotensin-converting enzyme 2 (ACE2) in a planar membrane patch can effectively neutralize all tested severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that emerged during the COVID-19 pandemic. The ACE2-incorporated membrane patch implemented using nanodiscs replicated the spike-mediated membrane fusion process outside the host cell, resulting in virus lysis, extracellular RNA release, and potent antiviral activity. While neutralizing antibodies became ineffective as the SARS-CoV-2 evolved to better penetrate host cells the ACE2-incorporated nanodiscs became more potent, highlighting the advantages of using receptor-incorporated nanodiscs for antiviral purposes. ACE2-incorporated immunodisc, an Fc fusion nanodisc developed in this study, completely protected humanized mice infected with SARS-CoV-2 after prolonged retention in the airways. This study demonstrates that the incorporation of viral receptors into immunodisc transforms the entry gate into a potent virucide for all current and future variants, a concept that can be extended to different viruses.
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Affiliation(s)
- Jaehyeon Hwang
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Beom Kyu Kim
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Seokoh Moon
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Wonbeom Park
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Kyeong Won Kim
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jeong Hyeon Yoon
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hyunseok Oh
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- Research Center, Mvrix Inc., Anyang, 14058, Republic of Korea
| | - Sangwon Jung
- Research Center, Mvrix Inc., Anyang, 14058, Republic of Korea
| | - Youngseo Park
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Suhyun Kim
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Misoo Kim
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Soomin Kim
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Younghun Jung
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Myungseo Park
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jun-Ho Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea
| | - Sang Taek Jung
- Department of Biomedical Sciences, Graduate School, Korea University, Seoul, 02841, Republic of Korea
| | - Sang Jick Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Yong-Sung Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea
| | - Woo-Jae Chung
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Min-Suk Song
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Dae-Hyuk Kweon
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- Research Center, Mvrix Inc., Anyang, 14058, Republic of Korea
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11
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Tu TH, Grunbaum A, Santinon F, Kazanova A, Rozza N, Kremer R, Mihalcioiu C, Rudd CE. Decreased progenitor TCF1 + T-cells correlate with COVID-19 disease severity. Commun Biol 2024; 7:526. [PMID: 38702425 PMCID: PMC11068881 DOI: 10.1038/s42003-024-05922-2] [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: 09/19/2023] [Accepted: 02/16/2024] [Indexed: 05/06/2024] Open
Abstract
COVID-19, caused by SARS-CoV-2, can lead to a severe inflammatory disease characterized by significant lymphopenia. However, the underlying cause for the depletion of T-cells in COVID-19 patients remains incompletely understood. In this study, we assessed the presence of different T-cell subsets in the progression of COVID-19 from mild to severe disease, with a focus on TCF1 expressing progenitor T-cells that are needed to replenish peripheral T-cells during infection. Our results showed a preferential decline in TCF1+ progenitor CD4 and CD8+ T-cells with disease severity. This decline was seen in various TCF1+ subsets including naive, memory and effector-memory cells, and surprisingly, was accompanied by a loss in cell division as seen by a marked decline in Ki67 expression. In addition, TCF1+ T-cells showed a reduction in pro-survival regulator, BcL2, and the appearance of a new population of TCF1 negative caspase-3 expressing cells in peripheral blood from patients with severe disease. The decline in TCF1+ T-cells was also seen in a subgroup of severe patients with vitamin D deficiency. Lastly, we found that sera from severe patients inhibited TCF1 transcription ex vivo which was attenuated by a blocking antibody against the cytokine, interleukin-12 (IL12). Collectively, our findings underscore the potential significance of TCF1+ progenitor T-cells in accounting for the loss of immunity in severe COVID-19 and outline an array of markers that could be used to identify disease progression.
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Affiliation(s)
- Thai Hien Tu
- Départment of Medicine, Universite de Montreal, Montreal, QC, H3T 1J4, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC, H3T 1J4, Canada
- Division of Immunology-Oncology, Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, H1T 2M4, Canada
| | - Ami Grunbaum
- Division of Experimental Medicine, McGill University, Montreal, QC, H3A 0G4, Canada
- Department of Medicine, Research Institute of the McGill University Health Center, Montreal, H3A 0G4, Canada
- Division of Medical Biochemistry, McGill University Health Centre, Montréal, QC, Canada
| | - François Santinon
- Départment of Medicine, Universite de Montreal, Montreal, QC, H3T 1J4, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC, H3T 1J4, Canada
- Division of Immunology-Oncology, Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, H1T 2M4, Canada
| | - Alexandra Kazanova
- Départment of Medicine, Universite de Montreal, Montreal, QC, H3T 1J4, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC, H3T 1J4, Canada
- Division of Immunology-Oncology, Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, H1T 2M4, Canada
| | - Nicholas Rozza
- Division of Experimental Medicine, McGill University, Montreal, QC, H3A 0G4, Canada
- Department of Medicine, Research Institute of the McGill University Health Center, Montreal, H3A 0G4, Canada
| | - Richard Kremer
- Division of Experimental Medicine, McGill University, Montreal, QC, H3A 0G4, Canada
- Department of Medicine, Research Institute of the McGill University Health Center, Montreal, H3A 0G4, Canada
- Division of Medical Biochemistry, McGill University Health Centre, Montréal, QC, Canada
| | - Catalin Mihalcioiu
- Department of Medical Oncology, McGill University Health Center, Montreal, Quebec, Canada
| | - Christopher E Rudd
- Départment of Medicine, Universite de Montreal, Montreal, QC, H3T 1J4, Canada.
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC, H3T 1J4, Canada.
- Division of Immunology-Oncology, Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, H1T 2M4, Canada.
- Division of Experimental Medicine, McGill University, Montreal, QC, H3A 0G4, Canada.
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12
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Ng JCF, Montamat Garcia G, Stewart AT, Blair P, Mauri C, Dunn-Walters DK, Fraternali F. sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data. Nat Methods 2024; 21:823-834. [PMID: 37932398 PMCID: PMC11093741 DOI: 10.1038/s41592-023-02060-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/02/2023] [Indexed: 11/08/2023]
Abstract
Class-switch recombination (CSR) is an integral part of B cell maturation. Here we present sciCSR (pronounced 'scissor', single-cell inference of class-switch recombination), a computational pipeline that analyzes CSR events and dynamics of B cells from single-cell RNA sequencing (scRNA-seq) experiments. Validated on both simulated and real data, sciCSR re-analyzes scRNA-seq alignments to differentiate productive heavy-chain immunoglobulin transcripts from germline 'sterile' transcripts. From a snapshot of B cell scRNA-seq data, a Markov state model is built to infer the dynamics and direction of CSR. Applying sciCSR on severe acute respiratory syndrome coronavirus 2 vaccination time-course scRNA-seq data, we observe that sciCSR predicts, using data from an earlier time point in the collected time-course, the isotype distribution of B cell receptor repertoires of subsequent time points with high accuracy (cosine similarity ~0.9). Using processes specific to B cells, sciCSR identifies transitions that are often missed by conventional RNA velocity analyses and can reveal insights into the dynamics of B cell CSR during immune response.
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Affiliation(s)
- Joseph C F Ng
- Department of Structural and Molecular Biology, Division of Biosciences and Institute of Structural and Molecular Biology, University College London, London, UK.
| | - Guillem Montamat Garcia
- Division of Infection and Immunity and Institute of Immunity and Transplantation, Royal Free Hospital, University College London, London, UK
| | | | - Paul Blair
- Division of Infection and Immunity and Institute of Immunity and Transplantation, Royal Free Hospital, University College London, London, UK
| | - Claudia Mauri
- Division of Infection and Immunity and Institute of Immunity and Transplantation, Royal Free Hospital, University College London, London, UK
| | | | - Franca Fraternali
- Department of Structural and Molecular Biology, Division of Biosciences and Institute of Structural and Molecular Biology, University College London, London, UK.
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13
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Hills FR, Eruera AR, Hodgkinson-Bean J, Jorge F, Easingwood R, Brown SHJ, Bouwer JC, Li YP, Burga LN, Bostina M. Variation in structural motifs within SARS-related coronavirus spike proteins. PLoS Pathog 2024; 20:e1012158. [PMID: 38805567 PMCID: PMC11236199 DOI: 10.1371/journal.ppat.1012158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 07/10/2024] [Accepted: 03/28/2024] [Indexed: 05/30/2024] Open
Abstract
SARS-CoV-2 is the third known coronavirus (CoV) that has crossed the animal-human barrier in the last two decades. However, little structural information exists related to the close genetic species within the SARS-related coronaviruses. Here, we present three novel SARS-related CoV spike protein structures solved by single particle cryo-electron microscopy analysis derived from bat (bat SL-CoV WIV1) and civet (cCoV-SZ3, cCoV-007) hosts. We report complex glycan trees that decorate the glycoproteins and density for water molecules which facilitated modeling of the water molecule coordination networks within structurally important regions. We note structural conservation of the fatty acid binding pocket and presence of a linoleic acid molecule which are associated with stabilization of the receptor binding domains in the "down" conformation. Additionally, the N-terminal biliverdin binding pocket is occupied by a density in all the structures. Finally, we analyzed structural differences in a loop of the receptor binding motif between coronaviruses known to infect humans and the animal coronaviruses described in this study, which regulate binding to the human angiotensin converting enzyme 2 receptor. This study offers a structural framework to evaluate the close relatives of SARS-CoV-2, the ability to inform pandemic prevention, and aid in the development of pan-neutralizing treatments.
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Affiliation(s)
- Francesca R. Hills
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alice-Roza Eruera
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James Hodgkinson-Bean
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Fátima Jorge
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
| | - Richard Easingwood
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
| | - Simon H. J. Brown
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, New South Wales, Australia
| | - James C. Bouwer
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, New South Wales, Australia
| | - Yi-Ping Li
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Laura N. Burga
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
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14
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Garg P, Hsueh SCC, Plotkin SS. Testing the feasibility of targeting a conserved region on the S2 domain of the SARS-CoV-2 spike protein. Biophys J 2024; 123:992-1005. [PMID: 38491772 PMCID: PMC11052916 DOI: 10.1016/j.bpj.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/02/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
The efficacy of vaccines against the SARS-CoV-2 virus significantly declines with the emergence of mutant strains, prompting investigation into the feasibility of targeting highly conserved but often cryptic regions on the S2 domain of spike protein. Using tools from molecular dynamics, we find that exposure of a conserved S2 epitope located in the central helices below the receptor binding domains would require large-scale motion beyond receptor binding domain up-down motion, but, along the reaction coordinates we explored, it is unlikely to be exposed by such large-scale dynamic fluctuations of the S1 domain without any external facilitating factors, despite some previous computational evidence suggesting transient exposure of this region. Furthermore, glycans, particularly those on N165 and N234, hinder S2-exposing opening dynamics, and thus stabilize spike in addition to immunologically shielding the protein surface. Although the S2 epitope region examined here is central to large-scale conformational changes during viral entry, free energy landscape analysis obtained using the path coordinate formalism reveals no inherent "loaded spring" effect, suggesting that a vaccine immunogen would tend to present the epitope in a prefusion-like conformation and may be effective in neutralization. These findings contribute to a deeper understanding of the dynamic origins of the function of the spike protein, as well as further characterizing the feasibility of the S2 epitope as a therapeutic target.
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Affiliation(s)
- Pranav Garg
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shawn C C Hsueh
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada; Genome Sciences and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada.
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15
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Bhavsar D, Sano K, Singh G, Krammer F. An ELISA-Based Method to Measure Mucosal Antibody Responses Against SARS-CoV-2 in Human Saliva. Curr Protoc 2024; 4:e1024. [PMID: 38578049 DOI: 10.1002/cpz1.1024] [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] [Indexed: 04/06/2024]
Abstract
The primary mode of transmission for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is infection of the respiratory tract through droplets and/or aerosols. Therefore, immune responses at respiratory mucosal surfaces play a significant role in the prevention of infection. Greater emphasis is now being placed on mucosal immunity induced by exposure to SARS-CoV-2 antigens through infection or vaccination. In concert with cellular immunity, humoral responses at mucosal surfaces, especially the secretory version of immunoglobulin A (sIgA), can be instrumental in preventing respiratory infections. A better understanding of mucosal immune responses can further our knowledge of immunity to SARS-CoV-2 and help inform vaccine design. Here we describe a detailed protocol for an in vitro assay based on the enzyme-linked immunosorbent assay (ELISA) to assess mucosal antibody response to SARS-CoV-2 spike protein in human saliva. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: ELISA measurement of mucosal antibodies to SARS-CoV-2 spike protein in human saliva.
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Affiliation(s)
- Disha Bhavsar
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kaori Sano
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, Tokyo, Japan
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna, Vienna, Austria
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16
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Puccinelli RR, Sama SS, Worthington CM, Puschnik AS, Pak JE, Gómez-Sjöberg R. Open-source milligram-scale, four channel, automated protein purification system. PLoS One 2024; 19:e0297879. [PMID: 38394072 PMCID: PMC10889886 DOI: 10.1371/journal.pone.0297879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/10/2024] [Indexed: 02/25/2024] Open
Abstract
Liquid chromatography purification of multiple recombinant proteins, in parallel, could catalyze research and discovery if the processes are fast and approach the robustness of traditional, "one-protein-at-a-time" purification. Here, we report an automated, four channel chromatography platform that we have designed and validated for parallelized protein purification at milligram scales. The device can purify up to four proteins (each with its own single column), has inputs for up to eight buffers or solvents that can be directed to any of the four columns via a network of software-driven valves, and includes an automated fraction collector with ten positions for 1.5 or 5.0 mL collection tubes and four positions for 50 mL collection tubes for each column output. The control software can be accessed either via Python scripting, giving users full access to all steps of the purification process, or via a simple-to-navigate touch screen graphical user interface that does not require knowledge of the command line or any programming language. Using our instrument, we report milligram-scale, parallelized, single-column purification of a panel of mammalian cell expressed coronavirus (SARS-CoV-2, HCoV-229E, HCoV-OC43, HCoV-229E) trimeric Spike and monomeric Receptor Binding Domain (RBD) antigens, and monoclonal antibodies targeting SARS-CoV-2 Spike (S) and Influenza Hemagglutinin (HA). We include a detailed hardware build guide, and have made the controlling software open source, to allow others to build and customize their own protein purifier systems.
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Affiliation(s)
- Robert R. Puccinelli
- Chan Zuckerberg Biohub - San Francisco, San Francisco, California, United States of America
| | - Samia S. Sama
- Chan Zuckerberg Biohub - San Francisco, San Francisco, California, United States of America
| | | | - Andreas S. Puschnik
- Chan Zuckerberg Biohub - San Francisco, San Francisco, California, United States of America
| | - John E. Pak
- Chan Zuckerberg Biohub - San Francisco, San Francisco, California, United States of America
| | - Rafael Gómez-Sjöberg
- Chan Zuckerberg Biohub - San Francisco, San Francisco, California, United States of America
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17
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Halfmann PJ, Loeffler K, Duffy A, Kuroda M, Yang JE, Wright ER, Kawaoka Y, Kane RS. Broad protection against clade 1 sarbecoviruses after a single immunization with cocktail spike-protein-nanoparticle vaccine. Nat Commun 2024; 15:1284. [PMID: 38346966 PMCID: PMC10861510 DOI: 10.1038/s41467-024-45495-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/25/2024] [Indexed: 02/15/2024] Open
Abstract
The 2002 SARS outbreak, the 2019 emergence of COVID-19, and the continuing evolution of immune-evading SARS-CoV-2 variants together highlight the need for a broadly protective vaccine against ACE2-utilizing sarbecoviruses. While updated variant-matched formulations are a step in the right direction, protection needs to extend beyond SARS-CoV-2 and its variants to include SARS-like viruses. Here, we introduce bivalent and trivalent vaccine formulations using our spike protein nanoparticle platform that completely protect female hamsters against BA.5 and XBB.1 challenges with no detectable virus in the lungs. The trivalent cocktails elicit highly neutralizing responses against all tested Omicron variants and the bat sarbecoviruses SHC014 and WIV1. Finally, our 614D/SHC014/XBB trivalent spike formulation completely protects human ACE2-transgenic female hamsters against challenges with WIV1 and SHC014 with no detectable virus in the lungs. Collectively, these results illustrate that our trivalent protein-nanoparticle cocktail can provide broad protection against SARS-CoV-2-like and SARS-CoV-1-like sarbecoviruses.
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Affiliation(s)
- Peter J Halfmann
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Kathryn Loeffler
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Augustine Duffy
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Makoto Kuroda
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, Cryo-EM Research Center, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, Midwest Center for Cryo-Electron Tomography, University of Wisconsin, Madison, WI, 53706, USA
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, Cryo-EM Research Center, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, Midwest Center for Cryo-Electron Tomography, University of Wisconsin, Madison, WI, 53706, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA.
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan.
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, 162-8655, Japan.
| | - Ravi S Kane
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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18
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Sankhala RS, Dussupt V, Chen WH, Bai H, Martinez EJ, Jensen JL, Rees PA, Hajduczki A, Chang WC, Choe M, Yan L, Sterling SL, Swafford I, Kuklis C, Soman S, King J, Corbitt C, Zemil M, Peterson CE, Mendez-Rivera L, Townsley SM, Donofrio GC, Lal KG, Tran U, Green EC, Smith C, de Val N, Laing ED, Broder CC, Currier JR, Gromowski GD, Wieczorek L, Rolland M, Paquin-Proulx D, van Dyk D, Britton Z, Rajan S, Loo YM, McTamney PM, Esser MT, Polonis VR, Michael NL, Krebs SJ, Modjarrad K, Joyce MG. Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain. Structure 2024; 32:131-147.e7. [PMID: 38157856 PMCID: PMC11145656 DOI: 10.1016/j.str.2023.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/14/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024]
Abstract
Given the continuous emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VoCs), immunotherapeutics that target conserved epitopes on the spike (S) glycoprotein have therapeutic advantages. Here, we report the crystal structure of the SARS-CoV-2 S receptor-binding domain (RBD) at 1.95 Å and describe flexibility and distinct conformations of the angiotensin-converting enzyme 2 (ACE2)-binding site. We identify a set of SARS-CoV-2-reactive monoclonal antibodies (mAbs) with broad RBD cross-reactivity including SARS-CoV-2 Omicron subvariants, SARS-CoV-1, and other sarbecoviruses and determine the crystal structures of mAb-RBD complexes with Ab246 and CR3022 mAbs targeting the class IV site, WRAIR-2134, which binds the recently designated class V epitope, and WRAIR-2123, the class I ACE2-binding site. The broad reactivity of class IV and V mAbs to conserved regions of SARS-CoV-2 VoCs and other sarbecovirus provides a framework for long-term immunotherapeutic development strategies.
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Affiliation(s)
- Rajeshwer S Sankhala
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Vincent Dussupt
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Wei-Hung Chen
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Hongjun Bai
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Elizabeth J Martinez
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Jaime L Jensen
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Phyllis A Rees
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Agnes Hajduczki
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - William C Chang
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Misook Choe
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Lianying Yan
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Spencer L Sterling
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Isabella Swafford
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Caitlin Kuklis
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sandrine Soman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jocelyn King
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Courtney Corbitt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Michelle Zemil
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Caroline E Peterson
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Letzibeth Mendez-Rivera
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Samantha M Townsley
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Gina C Donofrio
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Kerri G Lal
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Ursula Tran
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Ethan C Green
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Clayton Smith
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA
| | - Eric D Laing
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Jeffrey R Currier
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Gregory D Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Lindsay Wieczorek
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Morgane Rolland
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Dominic Paquin-Proulx
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Dewald van Dyk
- Antibody Discovery and Protein Engineering (ADPE), BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Zachary Britton
- Antibody Discovery and Protein Engineering (ADPE), BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Saravanan Rajan
- Antibody Discovery and Protein Engineering (ADPE), BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Yueh Ming Loo
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Patrick M McTamney
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Mark T Esser
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Victoria R Polonis
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Nelson L Michael
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Shelly J Krebs
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - M Gordon Joyce
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
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19
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Voss WN, Mallory MA, Byrne PO, Marchioni JM, Knudson SA, Powers JM, Leist SR, Dadonaite B, Townsend DR, Kain J, Huang Y, Satterwhite E, Castillo IN, Mattocks M, Paresi C, Munt JE, Scobey T, Seeger A, Premkumar L, Bloom JD, Georgiou G, McLellan JS, Baric RS, Lavinder JJ, Ippolito GC. Hybrid immunity to SARS-CoV-2 arises from serological recall of IgG antibodies distinctly imprinted by infection or vaccination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576742. [PMID: 38545622 PMCID: PMC10970720 DOI: 10.1101/2024.01.22.576742] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
We used plasma IgG proteomics to study the molecular composition and temporal durability of polyclonal IgG antibodies triggered by ancestral SARS-CoV-2 infection, vaccination, or their combination ("hybrid immunity"). Infection, whether primary or post-vaccination, mainly triggered an anti-spike antibody response to the S2 domain, while vaccination predominantly induced anti-RBD antibodies. Immunological imprinting persisted after a secondary (hybrid) exposure, with >60% of the ensuing serological response originating from the initial antibodies generated during the first exposure. We highlight one instance where hybrid immunity arising from breakthrough infection resulted in a marked increase in the breadth and affinity of a highly abundant vaccination-elicited plasma IgG antibody, SC27. With an intrinsic binding affinity surpassing a theoretical maximum (K D < 5 pM), SC27 demonstrated potent neutralization of various SARS-CoV-2 variants and SARS-like zoonotic viruses (IC 50 ∼0.1-1.75 nM) and provided robust protection in vivo . Cryo-EM structural analysis unveiled that SC27 binds to the RBD class 1/4 epitope, with both VH and VL significantly contributing to the binding interface. These findings suggest that exceptionally broad and potent antibodies can be prevalent in plasma and can largely dictate the nature of serological neutralization. HIGHLIGHTS ▪ Infection and vaccination elicit unique IgG antibody profiles at the molecular level▪ Immunological imprinting varies between infection (S2/NTD) and vaccination (RBD)▪ Hybrid immunity maintains the imprint of first infection or first vaccination▪ Hybrid immune IgG plasma mAbs have superior neutralization potency and breadth.
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20
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Johnson NV, Wall SC, Kramer KJ, Holt CM, Periasamy S, Richardson S, Suryadevara N, Andreano E, Paciello I, Pierleoni G, Piccini G, Huang Y, Ge P, Allen JD, Uno N, Shiakolas AR, Pilewski KA, Nargi RS, Sutton RE, Abu-Shmais AA, Parks R, Haynes BF, Carnahan RH, Crowe JE, Montomoli E, Rappuoli R, Bukreyev A, Ross TM, Sautto GA, McLellan JS, Georgiev IS. Discovery and Characterization of a Pan-betacoronavirus S2-binding antibody. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575741. [PMID: 38293237 PMCID: PMC10827111 DOI: 10.1101/2024.01.15.575741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Three coronaviruses have spilled over from animal reservoirs into the human population and caused deadly epidemics or pandemics. The continued emergence of coronaviruses highlights the need for pan-coronavirus interventions for effective pandemic preparedness. Here, using LIBRA-seq, we report a panel of 50 coronavirus antibodies isolated from human B cells. Of these antibodies, 54043-5 was shown to bind the S2 subunit of spike proteins from alpha-, beta-, and deltacoronaviruses. A cryo-EM structure of 54043-5 bound to the pre-fusion S2 subunit of the SARS-CoV-2 spike defined an epitope at the apex of S2 that is highly conserved among betacoronaviruses. Although non-neutralizing, 54043-5 induced Fc-dependent antiviral responses, including ADCC and ADCP. In murine SARS-CoV-2 challenge studies, protection against disease was observed after introduction of Leu234Ala, Leu235Ala, and Pro329Gly (LALA-PG) substitutions in the Fc region of 54043-5. Together, these data provide new insights into the protective mechanisms of non-neutralizing antibodies and define a broadly conserved epitope within the S2 subunit.
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Affiliation(s)
- Nicole V. Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Steven C. Wall
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Kevin J. Kramer
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Clinton M. Holt
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Program in Chemical and Physical Biology, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Sivakumar Periasamy
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Simone Richardson
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | | | - Emanuele Andreano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena 53100, Italy
| | - Ida Paciello
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena 53100, Italy
| | - Giulio Pierleoni
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena 53100, Italy
| | | | - Ying Huang
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Pan Ge
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
| | - James D. Allen
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
| | - Naoko Uno
- Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44196, USA
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
| | - Andrea R. Shiakolas
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Kelsey A. Pilewski
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Rachel S. Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Rachel E. Sutton
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Alexandria A. Abu-Shmais
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
- Departments of Medicine and Immunology, Duke University, Durham, NC 27710, USA
| | - Robert H. Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
- Department of Pediatrics, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Emanuele Montomoli
- VisMederi Research S.r.l., Siena 53100, Italy
- VisMederi S.r.l, Siena 53100, Italy
- Department of Molecular and Developmental Medicine, University of Siena, Siena 53100, Italy
| | - Rino Rappuoli
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena 53100, Italy
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena 53100, Italy
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Ted M. Ross
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
- Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44196, USA
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Giuseppe A. Sautto
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ivelin S. Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Computer Science, Vanderbilt University; Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University; Nashville, TN 37232, USA
- Program in Computational Microbiology and Immunology, Vanderbilt University Medical Center; Nashville, TN 37232, USA
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21
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Adams LJ, VanBlargan LA, Liu Z, Gilchuk P, Zhao H, Chen RE, Raju S, Chong Z, Whitener BM, Shrihari S, Jethva PN, Gross ML, Crowe JE, Whelan SPJ, Diamond MS, Fremont DH. A broadly reactive antibody targeting the N-terminal domain of SARS-CoV-2 spike confers Fc-mediated protection. Cell Rep Med 2023; 4:101305. [PMID: 38039973 PMCID: PMC10772349 DOI: 10.1016/j.xcrm.2023.101305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 08/21/2023] [Accepted: 11/06/2023] [Indexed: 12/03/2023]
Abstract
Most neutralizing anti-SARS-CoV-2 monoclonal antibodies (mAbs) target the receptor binding domain (RBD) of the spike (S) protein. Here, we characterize a panel of mAbs targeting the N-terminal domain (NTD) or other non-RBD epitopes of S. A subset of NTD mAbs inhibits SARS-CoV-2 entry at a post-attachment step and avidly binds the surface of infected cells. One neutralizing NTD mAb, SARS2-57, protects K18-hACE2 mice against SARS-CoV-2 infection in an Fc-dependent manner. Structural analysis demonstrates that SARS2-57 engages an antigenic supersite that is remodeled by deletions common to emerging variants. In neutralization escape studies with SARS2-57, this NTD site accumulates mutations, including a similar deletion, but the addition of an anti-RBD mAb prevents such escape. Thus, our study highlights a common strategy of immune evasion by SARS-CoV-2 variants and how targeting spatially distinct epitopes, including those in the NTD, may limit such escape.
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Affiliation(s)
- Lucas J Adams
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Haiyan Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rita E Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Saravanan Raju
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zhenlu Chong
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bradley M Whitener
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Swathi Shrihari
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Prashant N Jethva
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
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22
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Jiang M, Fang C, Ma Y. Deciphering the rule of antigen-antibody amino acid interaction. Front Immunol 2023; 14:1269916. [PMID: 38111576 PMCID: PMC10725943 DOI: 10.3389/fimmu.2023.1269916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/13/2023] [Indexed: 12/20/2023] Open
Abstract
Purpose Antigenic drift is the biggest challenge for mutagenic RNA virus vaccine development. The primary purpose is to determine the IEMM (immune escape mutation map) of 20 amino acids' replacement to reveal the rule of the viral immune escape. Methods To determine the relationship between epitope mutation and immune escape, we use universal protein tags as a linear epitope model. To describe and draw amino acid linkage diagrams, mutations of protein tags are classified into four categories: IEM (immune escape mutation), ADERM (antibody-dependent enhancement risk mutation), EQM (equivalent mutation), and IVM (invalid mutation). To overcome the data limitation, a general antigen-antibody (Ag-Ab) interaction map was constructed by analyzing the published three-dimensional (3D) Ag-Ab interaction patterns. Results (i) One residue interacts with multiple amino acids in antigen-antibody interaction. (ii) Most amino acid replacements are IVM and EQM. (iii) Once aromatic amino acids replace non-aromatic amino acids, the mutation is often IEM. (iv) Substituting residues with the same physical and chemical properties easily leads to IVM. Therefore, this study has important theoretical significance for future research on antigenic drift, antibody rescue, and vaccine renewal design. Conclusion The antigenic epitope mutations were typed into IEM, ADERM, EQM, and IVM types to describe and quantify the results of antigenic mutations. The antigen-antibody interaction rule was summarized as a one-to-many interaction rule. To sum up, the epitope mutation rules were defined as IVM and EQM predomination rules and the aryl mutation escape rule.
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Affiliation(s)
| | | | - Yongping Ma
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, Basical Medical Collage, Chongqing Medical University, Chongqing, China
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23
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Wang R, Han Y, Zhang R, Zhu J, Nan X, Liu Y, Yang Z, Zhou B, Yu J, Lin Z, Li J, Chen P, Wang Y, Li Y, Liu D, Shi X, Wang X, Zhang Q, Yang YR, Li T, Zhang L. Dissecting the intricacies of human antibody responses to SARS-CoV-1 and SARS-CoV-2 infection. Immunity 2023; 56:2635-2649.e6. [PMID: 37924813 DOI: 10.1016/j.immuni.2023.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/25/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023]
Abstract
The 2003 severe acute respiratory syndrome coronavirus (SARS-CoV-1) causes more severe disease than SARS-CoV-2, which is responsible for COVID-19. However, our understanding of antibody response to SARS-CoV-1 infection remains incomplete. Herein, we studied the antibody responses in 25 SARS-CoV-1 convalescent patients. Plasma neutralization was higher and lasted longer in SARS-CoV-1 patients than in severe SARS-CoV-2 patients. Among 77 monoclonal antibodies (mAbs) isolated, 60 targeted the receptor-binding domain (RBD) and formed 7 groups (RBD-1 to RBD-7) based on their distinct binding and structural profiles. Notably, RBD-7 antibodies bound to a unique RBD region interfaced with the N-terminal domain of the neighboring protomer (NTD proximal) and were more prevalent in SARS-CoV-1 patients. Broadly neutralizing antibodies for SARS-CoV-1, SARS-CoV-2, and bat and pangolin coronaviruses were also identified. These results provide further insights into the antibody response to SARS-CoV-1 and inform the design of more effective strategies against diverse human and animal coronaviruses.
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Affiliation(s)
- Ruoke Wang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
| | - Yang Han
- Department of Infectious Diseases, Peking Union Medical College Hospital, Beijing 100730, China; State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing 100005, China
| | - Rui Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jiayi Zhu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Xuanyu Nan
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Yaping Liu
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ziqing Yang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Bini Zhou
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jinfang Yu
- 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
| | - Zichun Lin
- 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
| | - Jinqian Li
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Peng Chen
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yangjunqi Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Yujie Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Dongsheng Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xuanling Shi
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - 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
| | - Qi Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yuhe R Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Taisheng Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Beijing 100730, China; State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing 100005, China.
| | - Linqi Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, 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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24
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Clark T, Subramanian V, Jayaraman A, Fitzpatrick E, Gopal R, Pentakota N, Rurak T, Anand S, Viglione A, Raman R, Tharakaraman K, Sasisekharan R. Enhancing antibody affinity through experimental sampling of non-deleterious CDR mutations predicted by machine learning. Commun Chem 2023; 6:244. [PMID: 37945793 PMCID: PMC10636138 DOI: 10.1038/s42004-023-01037-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
The application of machine learning (ML) models to optimize antibody affinity to an antigen is gaining prominence. Unfortunately, the small and biased nature of the publicly available antibody-antigen interaction datasets makes it challenging to build an ML model that can accurately predict binding affinity changes due to mutations (ΔΔG). Recognizing these inherent limitations, we reformulated the problem to ask whether an ML model capable of classifying deleterious vs non-deleterious mutations can guide antibody affinity maturation in a practical setting. To test this hypothesis, we developed a Random Forest classifier (Antibody Random Forest Classifier or AbRFC) with expert-guided features and integrated it into a computational-experimental workflow. AbRFC effectively predicted non-deleterious mutations on an in-house validation dataset that is free of biases seen in the publicly available training datasets. Furthermore, experimental screening of a limited number of predictions from the model (<10^2 designs) identified affinity-enhancing mutations in two unrelated SARS-CoV-2 antibodies, resulting in constructs with up to 1000-fold increased binding to the SARS-COV-2 RBD. Our findings indicate that accurate prediction and screening of non-deleterious mutations using machine learning offers a powerful approach to improving antibody affinity.
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Affiliation(s)
- Thomas Clark
- Altus Enterprises, 900 Middlesex Turnpike, Billerica, MA, USA
| | | | - Akila Jayaraman
- Altus Enterprises, 900 Middlesex Turnpike, Billerica, MA, USA
| | | | - Ranjani Gopal
- Altus Enterprises, 900 Middlesex Turnpike, Billerica, MA, USA
| | | | - Troy Rurak
- Altus Enterprises, 900 Middlesex Turnpike, Billerica, MA, USA
| | - Shweta Anand
- Altus Enterprises, 900 Middlesex Turnpike, Billerica, MA, USA
| | | | - Rahul Raman
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
| | | | - Ram Sasisekharan
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
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25
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Onyango TB, Zhou F, Bredholt G, Brokstad KA, Lartey S, Mohn KGI, Özgümüs T, Kittang BR, Linchausen DW, Shafiani S, Elyanow R, Blomberg B, Langeland N, Cox RJ. SARS-CoV-2 specific immune responses in overweight and obese COVID-19 patients. Front Immunol 2023; 14:1287388. [PMID: 38022529 PMCID: PMC10653322 DOI: 10.3389/fimmu.2023.1287388] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
Obesity is a known risk factor for severe respiratory tract infections. In this prospective study, we assessed the impact of being obese or overweight on longitudinal SARS-CoV-2 humoral and cellular responses up to 18 months after infection. 274 patients provided blood samples at regular time intervals up to 18 months including obese (BMI ≥30, n=32), overweight (BMI 25-29.9, n=103) and normal body weight (BMI 18.5-24.9, n=134) SARS-CoV-2 patients. We determined SARS-CoV-2 spike-specific IgG, IgA, IgM levels by ELISA and neutralising antibody titres by neutralisation assay. RBD- and spike-specific memory B cells were investigated by ELISpot, spike- and non-spike-specific IFN-γ, IL-2 and IFN-γ/IL-2 secreting T cells by FluoroSpot and T cell receptor (TCR) sequencing was performed. Higher BMI correlated with increased COVID-19 severity. Humoral and cellular responses were stronger in overweight and obese patients than normal weight patients and associated with higher spike-specific IgG binding titres relative to neutralising antibody titres. Linear regression models demonstrated that BMI, age and COVID-19 severity correlated independently with higher SARS-CoV-2 immune responses. We found an increased proportion of unique SARS-CoV-2 specific T cell clonotypes after infection in overweight and obese patients. COVID-19 vaccination boosted humoral and cellular responses irrespective of BMI, although stronger immune boosting was observed in normal weight patients. Overall, our results highlight more severe disease and an over-reactivity of the immune system in overweight and obese patients after SARS-CoV-2 infection, underscoring the importance of recognizing overweight/obese individuals as a risk group for prioritisation for COVID-19 vaccination.
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Affiliation(s)
| | - Fan Zhou
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Geir Bredholt
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Karl A. Brokstad
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Sarah Lartey
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kristin G.-I. Mohn
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Türküler Özgümüs
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | | | | | | | | | - Bjørn Blomberg
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
- National Advisory Unit for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
- National Advisory Unit for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Rebecca Jane Cox
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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26
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Jassoy C, Biemann R, Hönemann M. Low BAU/ml values with 4 of 5 SARS CoV-2 spike-specific monoclonal antibodies in the Roche Elecsys antibody assay. J Virol Methods 2023; 321:114786. [PMID: 37516369 DOI: 10.1016/j.jviromet.2023.114786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
BACKGROUND The Abbott SARS-CoV-2 IgG Quant II assay and the Roche Elecsys double antigen sandwich (DAgS) immunoassay measure SARS-CoV-2 receptor binding domain (RBD)-specific antibodies in serum samples in different ways. The IgG Quant II assay uses an antigen in combination with a secondary antibody and the DAgS assay uses two antigens. The aim of the study was to investigate whether the assays give comparable results with monoclonal antibodies. MATERIAL AND METHODS The immunoassays were tested with the RBD-specific human monoclonal antibodies (mAbs) casirivimab. imdevimab, CR3022, etesevimab and sotrovimab. The mAbs were tested at various concentrations in µg/ml, alone or in combination and the relative light units (RLU) and binding antibody units (BAU)/ml were determined. RESULTS With 1 µg/ml of casirivimab, imdevimab, CR3022 and etesevimab the Abbott IgG II Quant assay yielded between 65 and 158 BAU/ml and the Elecsys assay < 0.4 - 7.1 BAU/ml. In the DAgS assay, the addition of a second and a third mAb increased the BAU/ml values synergistically. With increasing concentrations of the mAb combinations in µg/ml the Abbott IgG Quant II assay showed proportionate and the Elecsys DAgS assay disproportionate increases in BAU/ml. With 1 µg/ml sotrovimab the Abbott assay gave 39 and the Elecsys assay 136 BAU/ml. The DAgS assay showed a high dose hook effect in the µg/ml range. CONCLUSIONS The secondary antibody-based and the DAgS-based SARS CoV-2 antibody assays gave very different results with 4 of 5 mAbs. This suggests that the two assays measure different binding characteristics. The ability of antibodies to cross-link multiple antigen-antibody complexes may contribute to the measurement signal in the DAgS assay.
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Affiliation(s)
- Christian Jassoy
- Institute for Medical Microbiology and Virology, University Hospital and Medical Faculty, University of Leipzig, Leipzig, Germany.
| | - Ronald Biemann
- Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital and Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Mario Hönemann
- Institute for Medical Microbiology and Virology, University Hospital and Medical Faculty, University of Leipzig, Leipzig, Germany
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27
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Tulsian NK, Palur RV, Qian X, Gu Y, D/O Shunmuganathan B, Samsudin F, Wong YH, Lin J, Purushotorman K, Kozma MM, Wang B, Lescar J, Wang CI, Gupta RK, Bond PJ, MacAry PA. Defining neutralization and allostery by antibodies against COVID-19 variants. Nat Commun 2023; 14:6967. [PMID: 37907459 PMCID: PMC10618280 DOI: 10.1038/s41467-023-42408-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 10/10/2023] [Indexed: 11/02/2023] Open
Abstract
The changing landscape of SARS-CoV-2 Spike protein is linked to the emergence of variants, immune-escape and reduced efficacy of the existing repertoire of anti-viral antibodies. The functional activity of neutralizing antibodies is linked to their quaternary changes occurring as a result of antibody-Spike trimer interactions. Here, we reveal the conformational dynamics and allosteric perturbations linked to binding of novel human antibodies and the viral Spike protein. We identified epitope hotspots, and associated changes in Spike dynamics that distinguish weak, moderate and strong neutralizing antibodies. We show the impact of mutations in Wuhan-Hu-1, Delta, and Omicron variants on differences in the antibody-induced conformational changes in Spike and illustrate how these render certain antibodies ineffective. Antibodies with similar binding affinities may induce destabilizing or stabilizing allosteric effects on Spike, with implications for neutralization efficacy. Our results provide mechanistic insights into the functional modes and synergistic behavior of human antibodies against COVID-19 and may assist in designing effective antiviral strategies.
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Affiliation(s)
- Nikhil Kumar Tulsian
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
- Department of Biochemistry, National University of Singapore, Singapore, 117546, Singapore.
| | - Raghuvamsi Venkata Palur
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138761, Singapore
| | - Xinlei Qian
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
| | - Yue Gu
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore
| | - Bhuvaneshwari D/O Shunmuganathan
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore
| | - Firdaus Samsudin
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138761, Singapore
| | - Yee Hwa Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Experimental Medicine Building, Singapore, 636921, Singapore
| | - Jianqing Lin
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Experimental Medicine Building, Singapore, 636921, Singapore
| | - Kiren Purushotorman
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore
| | - Mary McQueen Kozma
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
| | - Bei Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Experimental Medicine Building, Singapore, 636921, Singapore
| | - Cheng-I Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
| | - Ravindra Kumar Gupta
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Peter John Bond
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138761, Singapore.
| | - Paul Anthony MacAry
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore.
- Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore.
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28
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Hueting D, Schriever K, Sun R, Vlachiotis S, Zuo F, Du L, Persson H, Hofström C, Ohlin M, Walldén K, Buggert M, Hammarström L, Marcotte H, Pan-Hammarström Q, Andréll J, Syrén PO. Design, structure and plasma binding of ancestral β-CoV scaffold antigens. Nat Commun 2023; 14:6527. [PMID: 37845250 PMCID: PMC10579346 DOI: 10.1038/s41467-023-42200-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/03/2023] [Indexed: 10/18/2023] Open
Abstract
We report the application of ancestral sequence reconstruction on coronavirus spike protein, resulting in stable and highly soluble ancestral scaffold antigens (AnSAs). The AnSAs interact with plasma of patients recovered from COVID-19 but do not bind to the human angiotensin-converting enzyme 2 (ACE2) receptor. Cryo-EM analysis of the AnSAs yield high resolution structures (2.6-2.8 Å) indicating a closed pre-fusion conformation in which all three receptor-binding domains (RBDs) are facing downwards. The structures reveal an intricate hydrogen-bonding network mediated by well-resolved loops, both within and across monomers, tethering the N-terminal domain and RBD together. We show that AnSA-5 can induce and boost a broad-spectrum immune response against the wild-type RBD as well as circulating variants of concern in an immune organoid model derived from tonsils. Finally, we highlight how AnSAs are potent scaffolds by replacing the ancestral RBD with the wild-type sequence, which restores ACE2 binding and increases the interaction with convalescent plasma.
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Affiliation(s)
- David Hueting
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Karen Schriever
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rui Sun
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Stelios Vlachiotis
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fanglei Zuo
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Likun Du
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Helena Persson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Drug Discovery and Development Platform, Science for Life Laboratory, Solna, Sweden
| | - Camilla Hofström
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Drug Discovery and Development Platform, Science for Life Laboratory, Solna, Sweden
| | - Mats Ohlin
- Drug Discovery and Development Platform, Science for Life Laboratory, Solna, Sweden
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Karin Walldén
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Marcus Buggert
- Center for Infectious Disease, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Lennart Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Harold Marcotte
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Qiang Pan-Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Juni Andréll
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Per-Olof Syrén
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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29
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Cioffi VB, de Castro-Amarante MF, Lulla A, Andreata-Santos R, Cruz MC, Moreno ACR, de Oliveira Silva M, de Miranda Peres B, de Freitas Junior LHG, Moraes CB, Durigon EL, Gordon NC, Hyvönen M, de Souza Ferreira LC, Balan A. SARS-CoV-2 Spike protein peptides displayed in the Pyrococcus furiosus RAD system preserve epitopes antigenicity, immunogenicity, and virus-neutralizing activity of antibodies. Sci Rep 2023; 13:16821. [PMID: 37798298 PMCID: PMC10556064 DOI: 10.1038/s41598-023-43720-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023] Open
Abstract
Amongst the potential contribution of protein or peptide-display systems to study epitopes with relevant immunological features, the RAD display system stands out as a highly stable scaffold protein that allows the presentation of constrained target peptides. Here, we employed the RAD display system to present peptides derived from the SARS-CoV-2 Spike (S) protein as a tool to detect specific serum antibodies and to generate polyclonal antibodies capable of inhibiting SARS-CoV-2 infectivity in vitro. 44 linear S-derived peptides were genetically fused with the RAD scaffold (RAD-SCoV-epitopes) and screened for antigenicity with sera collected from COVID-19-infected patients. In a second step, selected RAD-SCoV-epitopes were used to immunize mice and generate antibodies. Phenotypic screening showed that some of these antibodies were able to recognize replicating viral particles in VERO CCL-81 and most notably seven of the RAD-SCoV-epitopes were able to induce antibodies that inhibited viral infection. Our findings highlight the RAD display system as an useful platform for the immunological characterization of peptides and a potentially valuable strategy for the design of antigens for peptide-based vaccines, for epitope-specific antibody mapping, and for the development of antibodies for diagnostic and therapeutic purposes.
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Affiliation(s)
- Victor Bolsanelli Cioffi
- Laboratory of Applied Structural Biology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Maria Fernanda de Castro-Amarante
- Laboratory of Vaccine Development, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Aleksei Lulla
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Robert Andreata-Santos
- Laboratory of Vaccine Development, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Mario Costa Cruz
- Core Facilities to Support Research (CEFAP), Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, São Paulo, 173005508-000, Brazil
| | - Ana Carolina Ramos Moreno
- Laboratory of Vaccine Development, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
- Vaccine Development Laboratory, Butantan Institute, Av. Vital Brasil, 1500, São Paulo, SP, 05503-900, Brazil
| | - Mariângela de Oliveira Silva
- Phenotypic Screening Platform, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Bianca de Miranda Peres
- Phenotypic Screening Platform, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Lucio Holanda Gondim de Freitas Junior
- Phenotypic Screening Platform, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Carolina Borsoi Moraes
- Phenotypic Screening Platform, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Edison Luiz Durigon
- Laboratory of Clinical and Molecular Virology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
- Institut Pasteur de São Paulo, Av. Prof. Lucio Martins Rodrigues, 370, São Paulo, 05508-020, Brazil
| | - Nicola Coker Gordon
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Luís Carlos de Souza Ferreira
- Laboratory of Vaccine Development, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
- Institut Pasteur de São Paulo, Av. Prof. Lucio Martins Rodrigues, 370, São Paulo, 05508-020, Brazil
| | - Andrea Balan
- Laboratory of Applied Structural Biology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil.
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30
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Connor RI, Sakharkar M, Rappazzo CG, Kaku CI, Curtis NC, Shin S, Wieland-Alter WF, Weiner JA, Ackerman ME, Walker LM, Lee J, Wright PF. Characteristics and functions of infection-enhancing antibodies to the N-terminal domain of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558444. [PMID: 37786672 PMCID: PMC10541592 DOI: 10.1101/2023.09.19.558444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Characterization of functional antibody responses to the N-terminal domain (NTD) of the SARS-CoV-2 spike (S) protein has included identification of both potent neutralizing activity and putative enhancement of infection. Fcγ-receptor (FcγR)-independent enhancement of SARS-CoV-2 infection mediated by NTD-binding monoclonal antibodies (mAbs) has been observed in vitro , but the functional significance of these antibodies in vivo is not clear. Here we studied 1,213 S-binding mAbs derived from longitudinal sampling of B-cells collected from eight COVID-19 convalescent patients and identified 72 (5.9%) mAbs that enhanced infection in a VSV-SARS-CoV-2-S-Wuhan pseudovirus (PV) assay. The majority (68%) of these mAbs recognized the NTD, were identified in patients with mild and severe disease, and persisted for at least five months post-infection. Enhancement of PV infection by NTD-binding mAbs was not observed using intestinal (Caco-2) and respiratory (Calu-3) epithelial cells as infection targets and was diminished or lost against SARS-CoV-2 variants of concern (VOC). Proteomic deconvolution of the serum antibody repertoire from two of the convalescent subjects identified, for the first time, NTD-binding, infection-enhancing mAbs among the circulating immunoglobulins directly isolated from serum ( i.e ., functionally secreted antibody). Functional analysis of these mAbs demonstrated robust activation of FcγRIIIa associated with antibody binding to recombinant S proteins. Taken together, these findings suggest functionally active NTD-specific mAbs arise frequently during natural infection and can last as major serum clonotypes during convalescence. These antibodies display diverse attributes that include FcγR activation, and may be selected against by mutations in NTD associated with SARS-CoV-2 VOC.
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31
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Tauzin A, Beaudoin-Bussières G, Benlarbi M, Nayrac M, Bo Y, Gendron-Lepage G, Medjahed H, Perreault J, Gokool L, Arlotto P, Morrisseau C, Tremblay C, Kaufmann DE, Martel-Laferrière V, Levade I, Côté M, Bazin R, Finzi A. Humoral Responses Elicited after a Fifth Dose of SARS-CoV-2 mRNA Bivalent Vaccine. Viruses 2023; 15:1926. [PMID: 37766332 PMCID: PMC10535273 DOI: 10.3390/v15091926] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
While an important part of the world's population is vaccinated against SARS-CoV-2, new variants continue to emerge. We observe that even after a fifth dose of the mRNA bivalent vaccine, most vaccinated individuals have antibodies that poorly neutralize several Omicron subvariants, including BQ.1.1, XBB, XBB.1.5, FD.1.1, and CH.1.1. However, Fc-effector functions remain strong and stable over time against new variants, which may partially explain why vaccines continue to be effective. We also observe that donors who have been recently infected have stronger antibody functional activities, including neutralization and Fc-effector functions, supporting the observations that hybrid immunity leads to better humoral responses.
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Affiliation(s)
- Alexandra Tauzin
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Mehdi Benlarbi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Manon Nayrac
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, and Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | | | | | - Josée Perreault
- Héma-Québec, Affaires Médicales et Innovation, Quebec, QC G1V 5C3, Canada
| | - Laurie Gokool
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
| | | | | | - Cécile Tremblay
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Daniel E. Kaufmann
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Médecine, Université de Montréal, Montreal, QC H3T 1J4, Canada
- Division of Infectious Diseases, Department of Medicine, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland
| | - Valérie Martel-Laferrière
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Inès Levade
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, and Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Renée Bazin
- Héma-Québec, Affaires Médicales et Innovation, Quebec, QC G1V 5C3, Canada
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
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32
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Bostanghadiri N, Ziaeefar P, Mofrad MG, Yousefzadeh P, Hashemi A, Darban-Sarokhalil D. COVID-19: An Overview of SARS-CoV-2 Variants-The Current Vaccines and Drug Development. BIOMED RESEARCH INTERNATIONAL 2023; 2023:1879554. [PMID: 37674935 PMCID: PMC10480030 DOI: 10.1155/2023/1879554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/07/2023] [Accepted: 08/04/2023] [Indexed: 09/08/2023]
Abstract
The world is presently in crisis facing an outbreak of a health-threatening microorganism known as COVID-19, responsible for causing uncommon viral pneumonia in humans. The virus was first reported in Wuhan, China, in early December 2019, and it quickly became a global concern due to the pandemic. Challenges in this regard have been compounded by the emergence of several variants such as B.1.1.7, B.1.351, P1, and B.1.617, which show an increase in transmission power and resistance to therapies and vaccines. Ongoing researches are focused on developing and manufacturing standard treatment strategies and effective vaccines to control the pandemic. Despite developing several vaccines such as Pfizer/BioNTech and Moderna approved by the U.S. Food and Drug Administration (FDA) and other vaccines in phase 4 clinical trials, preventive measures are mandatory to control the COVID-19 pandemic. In this review, based on the latest findings, we will discuss different types of drugs as therapeutic options and confirmed or developing vaccine candidates against SARS-CoV-2. We also discuss in detail the challenges posed by the variants and their effect on therapeutic and preventive interventions.
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Affiliation(s)
- Narjess Bostanghadiri
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Pardis Ziaeefar
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Morvarid Golrokh Mofrad
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Parsa Yousefzadeh
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Hashemi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Darban-Sarokhalil
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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33
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Zhao F, Yuan M, Keating C, Shaabani N, Limbo O, Joyce C, Woehl J, Barman S, Burns A, Tran Q, Zhu X, Ricciardi M, Peng L, Smith J, Huang D, Briney B, Sok D, Nemazee D, Teijaro JR, Wilson IA, Burton DR, Jardine JG. Broadening a SARS-CoV-1-neutralizing antibody for potent SARS-CoV-2 neutralization through directed evolution. Sci Signal 2023; 16:eabk3516. [PMID: 37582161 DOI: 10.1126/scisignal.abk3516] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 07/27/2023] [Indexed: 08/17/2023]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for strategies to rapidly develop neutralizing monoclonal antibodies that can function as prophylactic and therapeutic agents and to help guide vaccine design. Here, we demonstrate that engineering approaches can be used to refocus an existing antibody that neutralizes one virus but not a related virus. Through a rapid affinity maturation strategy, we engineered CR3022, a SARS-CoV-1-neutralizing antibody, to bind to the receptor binding domain of SARS-CoV-2 with >1000-fold increased affinity. The engineered CR3022 neutralized SARS-CoV-2 and provided prophylactic protection from viral challenge in a small animal model of SARS-CoV-2 infection. Deep sequencing throughout the engineering process paired with crystallographic analysis of engineered CR3022 elucidated the molecular mechanisms by which the antibody can accommodate sequence differences in the epitopes between SARS-CoV-1 and SARS-CoV-2. This workflow provides a blueprint for the rapid broadening of neutralization of an antibody from one virus to closely related but resistant viruses.
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Affiliation(s)
- Fangzhu Zhao
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Celina Keating
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
| | - Namir Shaabani
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oliver Limbo
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - Collin Joyce
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jordan Woehl
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - Shawn Barman
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alison Burns
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
| | - Quoc Tran
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Ricciardi
- Department of Pathology, George Washington University, Washington, DC 20052, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jessica Smith
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - Deli Huang
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
- Center for Viral Systems Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - David Nemazee
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Teijaro
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Joseph G Jardine
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
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34
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Chia WN, Tan CW, Tan AWK, Young B, Starr TN, Lopez E, Fibriansah G, Barr J, Cheng S, Yeoh AYY, Yap WC, Lim BL, Ng TS, Sia WR, Zhu F, Chen S, Zhang J, Kwek MSS, Greaney AJ, Chen M, Au GG, Paradkar PN, Peiris M, Chung AW, Bloom JD, Lye D, Lok S, Wang LF. Potent pan huACE2-dependent sarbecovirus neutralizing monoclonal antibodies isolated from a BNT162b2-vaccinated SARS survivor. SCIENCE ADVANCES 2023; 9:eade3470. [PMID: 37494438 PMCID: PMC10371021 DOI: 10.1126/sciadv.ade3470] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 06/23/2023] [Indexed: 07/28/2023]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern such as Omicron hampered efforts in controlling the ongoing coronavirus disease 2019 pandemic due to their ability to escape neutralizing antibodies induced by vaccination or prior infection, highlighting the need to develop broad-spectrum vaccines and therapeutics. Most human monoclonal antibodies (mAbs) reported to date have not demonstrated true pan-sarbecovirus neutralizing breadth especially against animal sarbecoviruses. Here, we report the isolation and characterization of highly potent mAbs targeting the receptor binding domain (RBD) of huACE2-dependent sarbecovirus from a SARS-CoV survivor vaccinated with BNT162b2. Among the six mAbs identified, one (E7) showed better huACE2-dependent sarbecovirus neutralizing potency and breadth than any other mAbs reported to date. Mutagenesis and cryo-electron microscopy studies indicate that these mAbs have a unique RBD contact footprint and that E7 binds to a quaternary structure-dependent epitope.
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Affiliation(s)
- Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Aaron Wai Kit Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Barnaby Young
- National Center of Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute, Seattle, WA, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Ester Lopez
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Guntur Fibriansah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Jennifer Barr
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Samuel Cheng
- School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Aileen Ying-Yan Yeoh
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Wee Chee Yap
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Beng Lee Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Thiam-Seng Ng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Wan Rong Sia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Shiwei Chen
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Jinyan Zhang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Madeline Sheng Si Kwek
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute, Seattle, WA, USA
| | - Mark Chen
- National Center of Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Gough G. Au
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Prasad N. Paradkar
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong, China
- Centre for Immunology & Infection, New Territories, Hong Kong, China
- HKU-Pasteur Research Pole, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Amy W. Chung
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute, Seattle, WA, USA
| | - David Lye
- National Center of Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sheemei Lok
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore, Singapore
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35
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Albornoz EA, Amarilla AA, Modhiran N, Parker S, Li XX, Wijesundara DK, Aguado J, Zamora AP, McMillan CLD, Liang B, Peng NYG, Sng JDJ, Saima FT, Fung JN, Lee JD, Paramitha D, Parry R, Avumegah MS, Isaacs A, Lo MW, Miranda-Chacon Z, Bradshaw D, Salinas-Rebolledo C, Rajapakse NW, Wolvetang EJ, Munro TP, Rojas-Fernandez A, Young PR, Stacey KJ, Khromykh AA, Chappell KJ, Watterson D, Woodruff TM. SARS-CoV-2 drives NLRP3 inflammasome activation in human microglia through spike protein. Mol Psychiatry 2023; 28:2878-2893. [PMID: 36316366 PMCID: PMC10615762 DOI: 10.1038/s41380-022-01831-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 09/19/2022] [Accepted: 10/07/2022] [Indexed: 01/21/2023]
Abstract
Coronavirus disease-2019 (COVID-19) is primarily a respiratory disease, however, an increasing number of reports indicate that SARS-CoV-2 infection can also cause severe neurological manifestations, including precipitating cases of probable Parkinson's disease. As microglial NLRP3 inflammasome activation is a major driver of neurodegeneration, here we interrogated whether SARS-CoV-2 can promote microglial NLRP3 inflammasome activation. Using SARS-CoV-2 infection of transgenic mice expressing human angiotensin-converting enzyme 2 (hACE2) as a COVID-19 pre-clinical model, we established the presence of virus in the brain together with microglial activation and NLRP3 inflammasome upregulation in comparison to uninfected mice. Next, utilising a model of human monocyte-derived microglia, we identified that SARS-CoV-2 isolates can bind and enter human microglia in the absence of viral replication. This interaction of virus and microglia directly induced robust inflammasome activation, even in the absence of another priming signal. Mechanistically, we demonstrated that purified SARS-CoV-2 spike glycoprotein activated the NLRP3 inflammasome in LPS-primed microglia, in a ACE2-dependent manner. Spike protein also could prime the inflammasome in microglia through NF-κB signalling, allowing for activation through either ATP, nigericin or α-synuclein. Notably, SARS-CoV-2 and spike protein-mediated microglial inflammasome activation was significantly enhanced in the presence of α-synuclein fibrils and was entirely ablated by NLRP3-inhibition. Finally, we demonstrate SARS-CoV-2 infected hACE2 mice treated orally post-infection with the NLRP3 inhibitory drug MCC950, have significantly reduced microglial inflammasome activation, and increased survival in comparison with untreated SARS-CoV-2 infected mice. These results support a possible mechanism of microglial innate immune activation by SARS-CoV-2, which could explain the increased vulnerability to developing neurological symptoms akin to Parkinson's disease in COVID-19 infected individuals, and a potential therapeutic avenue for intervention.
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Affiliation(s)
- Eduardo A Albornoz
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Alberto A Amarilla
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Naphak Modhiran
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Sandra Parker
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Xaria X Li
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Danushka K Wijesundara
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
- Vaxxas Pty. Ltd., Woolloongabba, QLD, 4102, Australia
| | - Julio Aguado
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Adriana Pliego Zamora
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Christopher L D McMillan
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Benjamin Liang
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Nias Y G Peng
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Julian D J Sng
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Fatema Tuj Saima
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Jenny N Fung
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St Lucia, QLD, 4072, Australia
| | - John D Lee
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Devina Paramitha
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Rhys Parry
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Michael S Avumegah
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Ariel Isaacs
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Martin W Lo
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Zaray Miranda-Chacon
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
- Molecular Medicine Laboratory, Medical School, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Daniella Bradshaw
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St Lucia, QLD, 4072, Australia
| | | | - Niwanthi W Rajapakse
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Ernst J Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Trent P Munro
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | | | - Paul R Young
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
- Australian Infectious Disease Research Centre, Global Virus Network Centre of Excellence Brisbane, Brisbane, QLD, 4072 and 4029, Australia
| | - Katryn J Stacey
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Alexander A Khromykh
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
- Australian Infectious Disease Research Centre, Global Virus Network Centre of Excellence Brisbane, Brisbane, QLD, 4072 and 4029, Australia
| | - Keith J Chappell
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
- Australian Infectious Disease Research Centre, Global Virus Network Centre of Excellence Brisbane, Brisbane, QLD, 4072 and 4029, Australia
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Trent M Woodruff
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St Lucia, QLD, 4072, Australia.
- Queensland Brain Institute, University of Queensland, St Lucia, QLD, 4072, Australia.
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36
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Halfmann PJ, Loeffler K, Duffy A, Kuroda M, Kawaoka Y, Kane RS. Broad Protection Against Clade 1 Sarbecoviruses After a Single Immunization with Cocktail Spike-Protein-Nanoparticle Vaccine. RESEARCH SQUARE 2023:rs.3.rs-3088907. [PMID: 37461652 PMCID: PMC10350183 DOI: 10.21203/rs.3.rs-3088907/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The 2002 SARS outbreak, the 2019 emergence of COVID-19, and the continuing evolution of immune-evading SARS-CoV-2 variants together highlight the need for a broadly protective vaccine against ACE2-utilizing sarbecoviruses. While updated variant-matched formulations such as Pfizer-BioNTech's bivalent vaccine are a step in the right direction, protection needs to extend beyond SARS-CoV-2 and its variants to include SARS-like viruses. Here, we introduce bivalent and trivalent vaccine formulations using our spike protein nanoparticle platform that completely protected hamsters against BA.5 and XBB.1 challenges with no detectable virus in the lungs. The trivalent cocktails elicited highly neutralizing responses against all tested Omicron variants and the bat sarbecoviruses SHC014 and WIV1. Finally, our 614D/SHC014/XBB trivalent spike formulation completely protected human ACE2-transgenic hamsters against challenges with WIV1 and SHC014 with no detectable virus in the lungs. Collectively, these results illustrate that our trivalent protein-nanoparticle cocktail can provide broad protection against SARS-CoV-2-like and SARS-CoV-1-like sarbecoviruses.
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Affiliation(s)
- Peter J. Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Kathryn Loeffler
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Augustine Duffy
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Makoto Kuroda
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo 162-8655, Japan
| | - Ravi S. Kane
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
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37
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Guenthoer J, Lilly M, Starr TN, Dadonaite B, Lovendahl KN, Croft JT, Stoddard CI, Chohan V, Ding S, Ruiz F, Kopp MS, Finzi A, Bloom JD, Chu HY, Lee KK, Overbaugh J. Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection. Proc Natl Acad Sci U S A 2023; 120:e2220948120. [PMID: 37253011 PMCID: PMC10265947 DOI: 10.1073/pnas.2220948120] [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: 01/27/2023] [Accepted: 04/28/2023] [Indexed: 06/01/2023] Open
Abstract
The antiviral benefit of antibodies can be compromised by viral escape especially for rapidly evolving viruses. Therefore, durable, effective antibodies must be both broad and potent to counter newly emerging, diverse strains. Discovery of such antibodies is critically important for SARS-CoV-2 as the global emergence of new variants of concern (VOC) has compromised the efficacy of therapeutic antibodies and vaccines. We describe a collection of broad and potent neutralizing monoclonal antibodies (mAbs) isolated from an individual who experienced a breakthrough infection with the Delta VOC. Four mAbs potently neutralize the Wuhan-Hu-1 vaccine strain, the Delta VOC, and also retain potency against the Omicron VOCs through BA.4/BA.5 in both pseudovirus-based and authentic virus assays. Three mAbs also retain potency to recently circulating VOCs XBB.1.5 and BQ.1.1 and one also potently neutralizes SARS-CoV-1. The potency of these mAbs was greater against Omicron VOCs than all but one of the mAbs that had been approved for therapeutic applications. The mAbs target distinct epitopes on the spike glycoprotein, three in the receptor-binding domain (RBD) and one in an invariant region downstream of the RBD in subdomain 1 (SD1). The escape pathways we defined at single amino acid resolution with deep mutational scanning show they target conserved, functionally constrained regions of the glycoprotein, suggesting escape could incur a fitness cost. Overall, these mAbs are unique in their breadth across VOCs, their epitope specificity, and include a highly potent mAb targeting a rare epitope outside of the RBD in SD1.
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Affiliation(s)
- Jamie Guenthoer
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Michelle Lilly
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Tyler N. Starr
- Department of Biochemistry, University of Utah, Salt Lake City, UT84112
| | | | - Klaus N. Lovendahl
- Department of Medicinal Chemistry, University of Washington, Seattle, WA98195
| | - Jacob T. Croft
- Department of Medicinal Chemistry, University of Washington, Seattle, WA98195
| | | | - Vrasha Chohan
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QCH2X 0A9, Canada
| | - Felicitas Ruiz
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Mackenzie S. Kopp
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QCH2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QCH2X 0A9, Canada
| | - Jesse D. Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- HHMI, Seattle, WA98195
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA98195
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA98195
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
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Puente-Massaguer E, Beyer A, Loganathan M, Sapse I, Carreño JM, Bajic G, Sun W, Palese P, Krammer F. Bioprocess development for universal influenza vaccines based on inactivated split chimeric and mosaic hemagglutinin viruses. Front Bioeng Biotechnol 2023; 11:1097349. [PMID: 37342504 PMCID: PMC10277804 DOI: 10.3389/fbioe.2023.1097349] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 05/10/2023] [Indexed: 06/23/2023] Open
Abstract
Seasonal influenza viruses account for 1 billion infections worldwide every year, including 3-5 million cases of severe illness and up to 650,000 deaths. The effectiveness of current influenza virus vaccines is variable and relies on the immunodominant hemagglutinin (HA) and to a lesser extent on the neuraminidase (NA), the viral surface glycoproteins. Efficient vaccines that refocus the immune response to conserved epitopes on the HA are needed to tackle infections by influenza virus variants. Sequential vaccination with chimeric HA (cHA) and mosaic HA (mHA) constructs has proven to induce immune responses to the HA stalk domain and conserved epitopes on the HA head. In this study, we developed a bioprocess to manufacture cHA and mHA inactivated split vaccines and a method to quantify HA with a prefusion stalk based on a sandwich enzyme-linked immunosorbent assay. Virus inactivation with beta-propiolactone (βPL) and splitting with Triton X-100 yielded the highest amount of prefusion HA and enzymatically active NA. In addition, the quantity of residual Triton X-100 and ovalbumin (OVA) was reduced to very low levels in the final vaccine preparations. The bioprocess shown here provides the basis to manufacture inactivated split cHA and mHA vaccines for pre-clinical research and future clinical trials in humans, and can also be applied to produce vaccines based on other influenza viruses.
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Affiliation(s)
- Eduard Puente-Massaguer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Annika Beyer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Madhumathi Loganathan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Iden Sapse
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Weina Sun
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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Struble EB, Rawson JMO, Stantchev T, Scott D, Shapiro MA. Uses and Challenges of Antiviral Polyclonal and Monoclonal Antibody Therapies. Pharmaceutics 2023; 15:pharmaceutics15051538. [PMID: 37242780 DOI: 10.3390/pharmaceutics15051538] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Viral diseases represent a major public health concerns and ever-present risks for developing into future pandemics. Antiviral antibody therapeutics, either alone or in combination with other therapies, emerged as valuable preventative and treatment options, including during global emergencies. Here we will discuss polyclonal and monoclonal antiviral antibody therapies, focusing on the unique biochemical and physiological properties that make them well-suited as therapeutic agents. We will describe the methods of antibody characterization and potency assessment throughout development, highlighting similarities and differences between polyclonal and monoclonal products as appropriate. In addition, we will consider the benefits and challenges of antiviral antibodies when used in combination with other antibodies or other types of antiviral therapeutics. Lastly, we will discuss novel approaches to the characterization and development of antiviral antibodies and identify areas that would benefit from additional research.
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Affiliation(s)
- Evi B Struble
- Division of Plasma Derivatives, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Jonathan M O Rawson
- Division of Antivirals, Office of Infectious Diseases, Office of New Drugs, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Tzanko Stantchev
- Division of Biotechnology Review and Research 1, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Dorothy Scott
- Division of Plasma Derivatives, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Marjorie A Shapiro
- Division of Biotechnology Review and Research 1, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
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40
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Yu K, Liu B, Yu H, Sun C, Wang X, Li G, Dong M, Wang Y, Zhang J, Xu N, Liu W. A neutralizing bispecific single-chain antibody against SARS-CoV-2 Omicron variant produced based on CR3022. Front Cell Infect Microbiol 2023; 13:1155293. [PMID: 37207187 PMCID: PMC10189128 DOI: 10.3389/fcimb.2023.1155293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/21/2023] [Indexed: 05/21/2023] Open
Abstract
Introduction The constantly mutating SARS-CoV-2 has been infected an increasing number of people, hence the safe and efficacious treatment are urgently needed to combat the COVID-19 pandemic. Currently, neutralizing antibodies (Nabs), targeting the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein are potentially effective therapeutics against COVID-19. As a new form of antibody, bispecific single chain antibodies (BscAbs) can be easily expressed in E. coli and exhibits broad-spectrum antiviral activity. Methods In this study, we constructed two BscAbs 16-29, 16-3022 and three single chain variable fragments (scFv) S1-16, S2-29 and S3022 as a comparison to explore their antiviral activity against SARS-CoV-2. The affinity of the five antibodies was characterized by ELISA and SPR and the neutralizing activity of them was analyzed using pseudovirus or authentic virus neutralization assay. Bioinformatics and competitive ELISA methods were used to identify different epitopes on RBD. Results Our results revealed the potent neutralizing activity of two BscAbs 16-29 and 16-3022 against SARS-CoV-2 original strain and Omicron variant infection. In addition, we also found that SARS-CoV RBD-targeted scFv S3022 could play a synergistic role with other SARS-CoV-2 RBD-targeted antibodies to enhance neutralizing activity in the form of a BscAb or in cocktail therapies. Discussion This innovative approach offers a promising avenue for the development of subsequent antibody therapies against SARSCoV-2. Combining the advantages of cocktails and single-molecule strategies, BscAb therapy has the potential to be developed as an effective immunotherapeutic for clinical use to mitigate the ongoing pandemic.
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Affiliation(s)
- Kaikai Yu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Science, Changchun, Jilin, China
| | - Bin Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Haotian Yu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Science, Changchun, Jilin, China
| | - Chengbiao Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Science, Changchun, Jilin, China
| | - Xuefeng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Science, Changchun, Jilin, China
| | - Guorui Li
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
| | - Mingxin Dong
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Science, Changchun, Jilin, China
| | - Yan Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Science, Changchun, Jilin, China
| | - Jianxu Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Science, Changchun, Jilin, China
| | - Na Xu
- Academic Affairs Office, Jilin Medical University, Jilin, Jilin, China
| | - Wensen Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Science, Changchun, Jilin, China
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41
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Chang CC, Algaissi A, Lai CC, Chang CK, Lin JS, Wang YS, Chang BH, Chang YC, Chen WT, Fan YQ, Peng BH, Chao CY, Tzeng SR, Liang PH, Sung WC, Hu AYC, Chang SC, Chang MF. Subunit vaccines with a saponin-based adjuvant boost humoral and cellular immunity to MERS coronavirus. Vaccine 2023; 41:3337-3346. [PMID: 37085450 PMCID: PMC10083212 DOI: 10.1016/j.vaccine.2023.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/15/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) outbreaks have constituted a public health issue with drastic mortality higher than 34%, necessitating the development of an effective vaccine. During MERS-CoV infection, the trimeric spike protein on the viral envelope is primarily responsible for attachment to host cellular receptor, dipeptidyl peptidase 4 (DPP4). With the goal of generating a protein-based prophylactic, we designed a subunit vaccine comprising the recombinant S1 protein with a trimerization motif (S1-Fd) and examined its immunogenicity and protective immune responses in combination with various adjuvants. We found that sera from immunized wild-type and human DPP4 transgenic mice contained S1-specific antibodies that can neutralize MERS-CoV infection in susceptible cells. Vaccination with S1-Fd protein in combination with a saponin-based QS-21 adjuvant provided long-term humoral as well as cellular immunity in mice. Our findings highlight the significance of the trimeric S1 protein in the development of MERS-CoV vaccines and offer a suitable adjuvant, QS-21, to induce robust and prolonged memory T cell response.
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Affiliation(s)
- Chi-Chieh Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Abdullah Algaissi
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555, USA; Center for Biodefense and Emerging Disease, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Chia-Chun Lai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 35053, Taiwan; College of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chun-Kai Chang
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100025, Taiwan
| | - Jr-Shiuan Lin
- Graduate Institute of Immunology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yi-Shiang Wang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Bo-Hau Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yu-Chiuan Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Wei-Ting Chen
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Yong-Qing Fan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Bi-Hung Peng
- Department of Neurosciences, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Chih-Yu Chao
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Shiou-Ru Tzeng
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Pi-Hui Liang
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100025, Taiwan
| | - Wang-Chou Sung
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 35053, Taiwan
| | - Alan Yung-Chih Hu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 35053, Taiwan
| | - Shin C Chang
- Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Ming-Fu Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan.
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42
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Borghi M, Gallinaro A, Pirillo MF, Canitano A, Michelini Z, De Angelis ML, Cecchetti S, Tinari A, Falce C, Mariotti S, Capocefalo A, Chiantore MV, Iacobino A, Di Virgilio A, van Gils MJ, Sanders RW, Lo Presti A, Nisini R, Negri D, Cara A. Different configurations of SARS-CoV-2 spike protein delivered by integrase-defective lentiviral vectors induce persistent functional immune responses, characterized by distinct immunogenicity profiles. Front Immunol 2023; 14:1147953. [PMID: 37090707 PMCID: PMC10113491 DOI: 10.3389/fimmu.2023.1147953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/13/2023] [Indexed: 04/08/2023] Open
Abstract
Several COVID-19 vaccine strategies utilizing new formulations for the induction of neutralizing antibodies (nAbs) and T cell immunity are still under evaluation in preclinical and clinical studies. Here we used Simian Immunodeficiency Virus (SIV)-based integrase defective lentiviral vector (IDLV) delivering different conformations of membrane-tethered Spike protein in the mouse immunogenicity model, with the aim of inducing persistent nAbs against multiple SARS-CoV-2 variants of concern (VoC). Spike modifications included prefusion-stabilizing double proline (2P) substitutions, mutations at the furin cleavage site (FCS), D614G mutation and truncation of the cytoplasmic tail (delta21) of ancestral and Beta (B.1.351) Spike, the latter mutation to markedly improve IDLV membrane-tethering. BALB/c mice were injected once with IDLV delivering the different forms of Spike or the recombinant trimeric Spike protein with 2P substitutions and FCS mutations in association with a squalene-based adjuvant. Anti-receptor binding domain (RBD) binding Abs, nAbs and T cell responses were detected up to six months from a single immunization with escalating doses of vaccines in all mice, but with different levels and kinetics. Results indicated that IDLV delivering the Spike protein with all the combined modifications, outperformed the other candidates in terms of T cell immunity and level of both binding Abs and nAbs soon after the single immunization and persistence over time, showing the best capacity to neutralize all formerly circulating VoC Alpha, Beta, Gamma and Delta. Although present, the lowest response was detected against Omicron variants (BA.1, BA.2 and BA.4/5), suggesting that the magnitude of immune evasion may be related to the higher genetic distance of Omicron as indicated by increased number of amino acid substitutions in Spike acquired during virus evolution.
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Affiliation(s)
- Martina Borghi
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | | | - Andrea Canitano
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Zuleika Michelini
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Laura De Angelis
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Serena Cecchetti
- Confocal Microscopy Unit, Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Antonella Tinari
- Center for Gender Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Chiara Falce
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Sabrina Mariotti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Antonio Capocefalo
- Department of Veterinary Public Health & Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | | | - Angelo Iacobino
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Antonio Di Virgilio
- Center for Animal Research and Welfare, Istituto Superiore di Sanità, Rome, Italy
| | - Marit J. van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | | | - Roberto Nisini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Donatella Negri
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
- *Correspondence: Donatella Negri, ; Andrea Cara,
| | - Andrea Cara
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
- *Correspondence: Donatella Negri, ; Andrea Cara,
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43
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Hasan TN, Naqvi SS, Rehman MU, Ullah R, Ammad M, Arshad N, Ain QU, Perween S, Hussain A. Ginger ring compounds as an inhibitor of spike binding protein of alpha, beta, gamma and delta variants of SARS-CoV-2: An in-silico study. NARRA J 2023; 3:e98. [PMID: 38455706 PMCID: PMC10919719 DOI: 10.52225/narra.v3i1.98] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/01/2023] [Indexed: 03/09/2024]
Abstract
The available drugs against coronavirus disease 2019 (COVOD-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are limited. This study aimed to identify ginger-derived compounds that might neutralize SARS-CoV-2 and prevent its entry into host cells. Ring compounds of ginger were screened against spike (S) protein of alpha, beta, gamma, and delta variants of SARS-CoV-2. The S protein FASTA sequence was retrieved from Global Initiative on Sharing Avian Influenza Data (GISAID) and converted into ".pdb" format using Open Babel tool. A total of 306 compounds were identified from ginger through food and phyto-databases. Out of those, 38 ring compounds were subjected to docking analysis using CB Dock online program which implies AutoDock Vina for docking. The Vina score was recorded, which reflects the affinity between ligands and receptors. Further, the Protein Ligand Interaction Profiler (PLIP) program for detecting the type of interaction between ligand-receptor was used. SwissADME was used to compute druglikeness parameters and pharmacokinetics characteristics. Furthermore, energy minimization was performed by using Swiss PDB Viewer (SPDBV) and energy after minimization was recorded. Molecular dynamic simulation was performed to find the stability of protein-ligand complex and root-mean- square deviation (RMSD) as well as root-mean-square fluctuation (RMSF) were calculated and recorded by using myPresto v5.0. Our study suggested that 17 out of 38 ring compounds of ginger were very likely to bind the S protein of SARS-CoV-2. Seventeen out of 38 ring compounds showed high affinity of binding with S protein of alpha, beta, gamma, and delta variants of SARS-CoV-2. The RMSD showed the stability of the complex was parallel to the S protein monomer. These computer-aided predictions give an insight into the possibility of ginger ring compounds as potential anti-SARS-CoV-2 worthy of in vitro investigations.
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Affiliation(s)
- Tarique N. Hasan
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
- School of Life Sciences, Manipal Academy of Higher Education, Dubai, United Arab Emirates
| | - Syed S. Naqvi
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Mati Ur Rehman
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
- College de Paris, France
| | - Rooh Ullah
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Muhammad Ammad
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Narmeen Arshad
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Qurat Ul Ain
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Shabana Perween
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Arif Hussain
- School of Life Sciences, Manipal Academy of Higher Education, Dubai, United Arab Emirates
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44
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Dickey TH, Ma R, Orr-Gonzalez S, Ouahes T, Patel P, McAleese H, Butler B, Eudy E, Eaton B, Murphy M, Kwan JL, Salinas ND, Holbrook MR, Lambert LE, Tolia NH. Design of a stabilized RBD enables potently neutralizing SARS-CoV-2 single-component nanoparticle vaccines. Cell Rep 2023; 42:112266. [PMID: 36943870 PMCID: PMC9986124 DOI: 10.1016/j.celrep.2023.112266] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/27/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023] Open
Abstract
Waning immunity and emerging variants necessitate continued vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Improvements in vaccine safety, tolerability, and ease of manufacturing would benefit these efforts. Here, we develop a potent and easily manufactured nanoparticle vaccine displaying the spike receptor-binding domain (RBD). Computational design to stabilize the RBD, eliminate glycosylation, and focus the immune response to neutralizing epitopes results in an RBD immunogen that resolves issues hindering the efficient nanoparticle display of the native RBD. This non-glycosylated RBD can be genetically fused to diverse single-component nanoparticle platforms, maximizing manufacturing ease and flexibility. All engineered RBD nanoparticles elicit potently neutralizing antibodies in mice that far exceed monomeric RBDs. A 60-copy particle (noNAG-RBD-E2p) also elicits potently neutralizing antibodies in non-human primates. The neutralizing antibody titers elicited by noNAG-RBD-E2p are comparable to a benchmark stabilized spike antigen and reach levels against Omicron BA.5 that suggest that it would provide protection against emerging variants.
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Affiliation(s)
- Thayne H Dickey
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Rui Ma
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Sachy Orr-Gonzalez
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Tarik Ouahes
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Palak Patel
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Holly McAleese
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Brandi Butler
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Elizabeth Eudy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Brett Eaton
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Michael Murphy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Jennifer L Kwan
- Epidemiology and Population Studies Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Nichole D Salinas
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Michael R Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Lynn E Lambert
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Niraj H Tolia
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
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45
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Yue H, Nowak RP, Overwijn D, Payne NC, Fischinger S, Atyeo C, Lam EC, St. Denis K, Brais LK, Konishi Y, Sklavenitis-Pistofidis R, Baden LR, Nilles EJ, Karlson EW, Yu XG, Li JZ, Woolley AE, Ghobrial IM, Meyerhardt JA, Balazs AB, Alter G, Mazitschek R, Fischer ES. Diagnostic TR-FRET assays for detection of antibodies in patient samples. CELL REPORTS METHODS 2023; 3:100421. [PMID: 37056371 PMCID: PMC10088089 DOI: 10.1016/j.crmeth.2023.100421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/15/2022] [Accepted: 02/14/2023] [Indexed: 02/22/2023]
Abstract
Serological assays are important diagnostic tools for surveying exposure to the pathogen, monitoring immune response post vaccination, and managing spread of the infectious agent among the population. Current serological laboratory assays are often limited because they require the use of specialized laboratory technology and/or work with a limited number of sample types. Here, we evaluate an alternative by developing time-resolved Förster resonance energy transfer (TR-FRET) homogeneous assays that exhibited exceptional versatility, scalability, and sensitivity and outperformed or matched currently used strategies in terms of sensitivity, specificity, and precision. We validated the performance of the assays measuring total immunoglobulin G (IgG) levels; antibodies against severe acute respiratory syndrome coronavirus (SARS-CoV) or Middle Eastern respiratory syndrome (MERS)-CoV spike (S) protein; and SARS-CoV-2 S and nucleocapsid (N) proteins and applied it to several large sample sets and real-world applications. We further established a TR-FRET-based ACE2-S competition assay to assess the neutralization propensity of the antibodies. Overall, these TR-FRET-based serological assays can be rapidly extended to other antigens and are compatible with commonly used plate readers.
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Affiliation(s)
- Hong Yue
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Radosław P. Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Daan Overwijn
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - N. Connor Payne
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Center for Systems Biology, Massachusetts General Hospital (MGH), Boston, MA 02114, USA
| | - Stephanie Fischinger
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Evan C. Lam
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Kerri St. Denis
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Lauren K. Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yoshinobu Konishi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Romanos Sklavenitis-Pistofidis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lindsey R. Baden
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Eric J. Nilles
- Department of Emergency Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | | | - Xu G. Yu
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Jonathan Z. Li
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ann E. Woolley
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Irene M. Ghobrial
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Alejandro B. Balazs
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Galit Alter
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital (MGH), Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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46
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Silva RP, Huang Y, Nguyen AW, Hsieh CL, Olaluwoye OS, Kaoud TS, Wilen RE, Qerqez AN, Park JG, Khalil AM, Azouz LR, Le KC, Bohanon AL, DiVenere AM, Liu Y, Lee AG, Amengor DA, Shoemaker SR, Costello SM, Padlan EA, Marqusee S, Martinez-Sobrido L, Dalby KN, D'Arcy S, McLellan JS, Maynard JA. Identification of a conserved S2 epitope present on spike proteins from all highly pathogenic coronaviruses. eLife 2023; 12:e83710. [PMID: 36942851 PMCID: PMC10030117 DOI: 10.7554/elife.83710] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/04/2023] [Indexed: 03/23/2023] Open
Abstract
To address the ongoing SARS-CoV-2 pandemic and prepare for future coronavirus outbreaks, understanding the protective potential of epitopes conserved across SARS-CoV-2 variants and coronavirus lineages is essential. We describe a highly conserved, conformational S2 domain epitope present only in the prefusion core of β-coronaviruses: SARS-CoV-2 S2 apex residues 980-1006 in the flexible hinge. Antibody RAY53 binds the native hinge in MERS-CoV and SARS-CoV-2 spikes on the surface of mammalian cells and mediates antibody-dependent cellular phagocytosis and cytotoxicity against SARS-CoV-2 spike in vitro. Hinge epitope mutations that ablate antibody binding compromise pseudovirus infectivity, but changes elsewhere that affect spike opening dynamics, including those found in Omicron BA.1, occlude the epitope and may evade pre-existing serum antibodies targeting the S2 core. This work defines a third class of S2 antibody while providing insights into the potency and limitations of S2 core epitope targeting.
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Affiliation(s)
- Rui P Silva
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Yimin Huang
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Annalee W Nguyen
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Oladimeji S Olaluwoye
- Department of Chemistry and Biochemistry, The University of Texas at DallasDallasUnited States
| | - Tamer S Kaoud
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at AustinAustinUnited States
| | - Rebecca E Wilen
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Ahlam N Qerqez
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Jun-Gyu Park
- Texas Biomedical Research InstituteSan AntonioUnited States
- Laboratory of Veterinary Zoonosis, College of Veterinary Medicine, Chonnam National UniversityGwangjuRepublic of Korea
| | - Ahmed M Khalil
- Texas Biomedical Research InstituteSan AntonioUnited States
| | - Laura R Azouz
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Kevin C Le
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Amanda L Bohanon
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Andrea M DiVenere
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Yutong Liu
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Alison G Lee
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Dzifa A Amengor
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Sophie R Shoemaker
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Shawn M Costello
- Biophysics Graduate Program, University of California, BerkeleyBerkeleyUnited States
| | | | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | | | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at AustinAustinUnited States
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, The University of Texas at DallasDallasUnited States
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
- LaMontagne Center for Infectious Diseases, The University of Texas at AustinAustinUnited States
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
- LaMontagne Center for Infectious Diseases, The University of Texas at AustinAustinUnited States
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47
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Horvath D, Temperton N, Mayora-Neto M, Da Costa K, Cantoni D, Horlacher R, Günther A, Brosig A, Morath J, Jakobs B, Groettrup M, Hoschuetzky H, Rohayem J, Ter Meulen J. Novel intranasal vaccine targeting SARS-CoV-2 receptor binding domain to mucosal microfold cells and adjuvanted with TLR3 agonist Riboxxim™ elicits strong antibody and T-cell responses in mice. Sci Rep 2023; 13:4648. [PMID: 36944687 PMCID: PMC10029786 DOI: 10.1038/s41598-023-31198-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/08/2023] [Indexed: 03/23/2023] Open
Abstract
SARS-CoV-2 continues to circulate in the human population necessitating regular booster immunization for its long-term control. Ideally, vaccines should ideally not only protect against symptomatic disease, but also prevent transmission via asymptomatic shedding and cover existing and future variants of the virus. This may ultimately only be possible through induction of potent and long-lasting immune responses in the nasopharyngeal tract, the initial entry site of SARS-CoV-2. To this end, we have designed a vaccine based on recombinantly expressed receptor binding domain (RBD) of SARS-CoV-2, fused to the C-terminus of C. perfringens enterotoxin, which is known to target Claudin-4, a matrix molecule highly expressed on mucosal microfold (M) cells of the nasal and bronchial-associated lymphoid tissues. To further enhance immune responses, the vaccine was adjuvanted with a novel toll-like receptor 3/RIG-I agonist (Riboxxim™), consisting of synthetic short double stranded RNA. Intranasal prime-boost immunization of mice induced robust mucosal and systemic anti-SARS-CoV-2 neutralizing antibody responses against SARS-CoV-2 strains Wuhan-Hu-1, and several variants (B.1.351/beta, B.1.1.7/alpha, B.1.617.2/delta), as well as systemic T-cell responses. A combination vaccine with M-cell targeted recombinant HA1 from an H1N1 G4 influenza strain also induced mucosal and systemic antibodies against influenza. Taken together, the data show that development of an intranasal SARS-CoV-2 vaccine based on recombinant RBD adjuvanted with a TLR3 agonist is feasible, also as a combination vaccine against influenza.
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Affiliation(s)
- Dennis Horvath
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Canterbury, UK
| | - Martin Mayora-Neto
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Canterbury, UK
| | - Kelly Da Costa
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Canterbury, UK
| | - Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Canterbury, UK
| | | | | | | | | | | | - Marcus Groettrup
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Jacques Rohayem
- Riboxx Pharmaceuticals, Radebeul, Dresden, Germany and Institute of Virology, Dresden University of Technology, Dresden, Germany
| | - Jan Ter Meulen
- Institute of Virology, Philipps University Marburg, Marburg, Germany.
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48
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Hariharan VN, Shin M, Chang CW, O’Reilly D, Biscans A, Yamada K, Guo Z, Somasundaran M, Tang Q, Monopoli K, Krishnamurthy PM, Devi G, McHugh N, Cooper DA, Echeverria D, Cruz J, Chan IL, Liu P, Lim SY, McConnell J, Singh SP, Hildebrand S, Sousa J, Davis SM, Kennedy Z, Ferguson C, Godinho BMDC, Thillier Y, Caiazzi J, Ly S, Muhuri M, Kelly K, Humphries F, Cousineau A, Parsi KM, Li Q, Wang Y, Maehr R, Gao G, Korkin D, McDougall WM, Finberg RW, Fitzgerald KA, Wang JP, Watts JK, Khvorova A. Divalent siRNAs are bioavailable in the lung and efficiently block SARS-CoV-2 infection. Proc Natl Acad Sci U S A 2023; 120:e2219523120. [PMID: 36893269 PMCID: PMC10089225 DOI: 10.1073/pnas.2219523120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/05/2023] [Indexed: 03/11/2023] Open
Abstract
The continuous evolution of SARS-CoV-2 variants complicates efforts to combat the ongoing pandemic, underscoring the need for a dynamic platform for the rapid development of pan-viral variant therapeutics. Oligonucleotide therapeutics are enhancing the treatment of numerous diseases with unprecedented potency, duration of effect, and safety. Through the systematic screening of hundreds of oligonucleotide sequences, we identified fully chemically stabilized siRNAs and ASOs that target regions of the SARS-CoV-2 genome conserved in all variants of concern, including delta and omicron. We successively evaluated candidates in cellular reporter assays, followed by viral inhibition in cell culture, with eventual testing of leads for in vivo antiviral activity in the lung. Previous attempts to deliver therapeutic oligonucleotides to the lung have met with only modest success. Here, we report the development of a platform for identifying and generating potent, chemically modified multimeric siRNAs bioavailable in the lung after local intranasal and intratracheal delivery. The optimized divalent siRNAs showed robust antiviral activity in human cells and mouse models of SARS-CoV-2 infection and represent a new paradigm for antiviral therapeutic development for current and future pandemics.
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Affiliation(s)
- Vignesh N. Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Minwook Shin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Ching-Wen Chang
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Daniel O’Reilly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Zhiru Guo
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Mohan Somasundaran
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Kathryn Monopoli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | | | - Gitali Devi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - David A. Cooper
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - John Cruz
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Io Long Chan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Ping Liu
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Sun-Young Lim
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jill McConnell
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Satya Prakash Singh
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Sarah M. Davis
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Zachary Kennedy
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Chantal Ferguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Bruno M. D. C. Godinho
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Yann Thillier
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Socheata Ly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Manish Muhuri
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Fiachra Humphries
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Alyssa Cousineau
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Krishna Mohan Parsi
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Qi Li
- MassBiologics, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Yang Wang
- MassBiologics, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - René Maehr
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Guangping Gao
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA01655
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Dmitry Korkin
- Department of Computer Science, and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA01609
| | - William M. McDougall
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Robert W. Finberg
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Katherine A. Fitzgerald
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jennifer P. Wang
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jonathan K. Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
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49
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Jugler C, Sun H, Nguyen K, Palt R, Felder M, Steinkellner H, Chen Q. A novel plant-made monoclonal antibody enhances the synergetic potency of an antibody cocktail against the SARS-CoV-2 Omicron variant. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:549-559. [PMID: 36403203 PMCID: PMC9946148 DOI: 10.1111/pbi.13970] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/06/2022] [Accepted: 11/12/2022] [Indexed: 06/01/2023]
Abstract
This study describes a novel, neutralizing monoclonal antibody (mAb), 11D7, discovered by mouse immunization and hybridoma generation, against the parental Wuhan-Hu-1 RBD of SARS-CoV-2. We further developed this mAb into a chimeric human IgG and recombinantly expressed it in plants to produce a mAb with human-like, highly homogenous N-linked glycans that has potential to impart greater potency and safety as a therapeutic. The epitope of 11D7 was mapped by competitive binding with well-characterized mAbs, suggesting that it is a Class 4 RBD-binding mAb that binds to the RBD outside the ACE2 binding site. Of note, 11D7 maintains recognition against the B.1.1.529 (Omicron) RBD, as well neutralizing activity. We also provide evidence that this novel mAb may be useful in providing additional synergy to established antibody cocktails, such as Evusheld™ containing the antibodies tixagevimab and cilgavimab, against the Omicron variant. Taken together, 11D7 is a unique mAb that neutralizes SARS-CoV-2 through a mechanism that is not typical among developed therapeutic mAbs and by being produced in ΔXFT Nicotiana benthamiana plants, highlights the potential of plants to be an economic and safety-friendly alternative platform for generating mAbs to address the evolving SARS-CoV-2 crisis.
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Affiliation(s)
- Collin Jugler
- The Biodesign InstituteArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Haiyan Sun
- The Biodesign InstituteArizona State UniversityTempeArizonaUSA
| | - Katherine Nguyen
- School of Molecular SciencesArizona State UniversityTempeArizonaUSA
| | - Roman Palt
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life SciencesViennaAustria
| | | | - Herta Steinkellner
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Qiang Chen
- The Biodesign InstituteArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
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50
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Chonira V, Kwon YD, Gorman J, Case JB, Ku Z, Simeon R, Casner RG, Harris DR, Olia AS, Stephens T, Shapiro L, Bender MF, Boyd H, Teng IT, Tsybovsky Y, Krammer F, Zhang N, Diamond MS, Kwong PD, An Z, Chen Z. A potent and broad neutralization of SARS-CoV-2 variants of concern by DARPins. Nat Chem Biol 2023; 19:284-291. [PMID: 36411391 PMCID: PMC10294592 DOI: 10.1038/s41589-022-01193-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 09/30/2022] [Indexed: 11/22/2022]
Abstract
We report the engineering and selection of two synthetic proteins-FSR16m and FSR22-for the possible treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. FSR16m and FSR22 are trimeric proteins composed of DARPin SR16m or SR22 fused with a T4 foldon. Despite selection by a spike protein from a now historical SARS-CoV-2 strain, FSR16m and FSR22 exhibit broad-spectrum neutralization of SARS-CoV-2 strains, inhibiting authentic B.1.351, B.1.617.2 and BA.1.1 viruses, with respective IC50 values of 3.4, 2.2 and 7.4 ng ml-1 for FSR16m. Cryo-EM structures revealed that these DARPins recognize a region of the receptor-binding domain (residues 456, 475, 486, 487 and 489) overlapping a critical portion of the angiotensin-converting enzyme 2 (ACE2)-binding surface. K18-hACE2 transgenic mice inoculated with B.1.617.2 and receiving intranasally administered FSR16m showed less weight loss and 10-100-fold lower viral burden in upper and lower respiratory tracts. The strong and broad neutralization potency makes FSR16m and FSR22 promising candidates for the prevention and treatment of infection by SARS-CoV-2.
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Affiliation(s)
- Vikas Chonira
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Young D Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Rudo Simeon
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Ryan G Casner
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Darcy R Harris
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tyler Stephens
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Michael F Bender
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hannah Boyd
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai (ISMMS), New York City, NY, USA
- Department of Pathology, Molecular and Cell based Medicine, ISMMS, New York City, NY, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA.
- Department of Pathology and Immunology, Department of Molecular Microbiology, and The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Zhilei Chen
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, USA.
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