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Xue S, Han Y, Wu F, Wang Q. Mutations in the SARS-CoV-2 spike receptor binding domain and their delicate balance between ACE2 affinity and antibody evasion. Protein Cell 2024; 15:403-418. [PMID: 38442025 DOI: 10.1093/procel/pwae007] [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: 03/07/2024] Open
Abstract
Intensive selection pressure constrains the evolutionary trajectory of SARS-CoV-2 genomes and results in various novel variants with distinct mutation profiles. Point mutations, particularly those within the receptor binding domain (RBD) of SARS-CoV-2 spike (S) protein, lead to the functional alteration in both receptor engagement and monoclonal antibody (mAb) recognition. Here, we review the data of the RBD point mutations possessed by major SARS-CoV-2 variants and discuss their individual effects on ACE2 affinity and immune evasion. Many single amino acid substitutions within RBD epitopes crucial for the antibody evasion capacity may conversely weaken ACE2 binding affinity. However, this weakened effect could be largely compensated by specific epistatic mutations, such as N501Y, thus maintaining the overall ACE2 affinity for the spike protein of all major variants. The predominant direction of SARS-CoV-2 evolution lies neither in promoting ACE2 affinity nor evading mAb neutralization but in maintaining a delicate balance between these two dimensions. Together, this review interprets how RBD mutations efficiently resist antibody neutralization and meanwhile how the affinity between ACE2 and spike protein is maintained, emphasizing the significance of comprehensive assessment of spike mutations.
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Affiliation(s)
- Song Xue
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yuru Han
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Fan Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
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2
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Faraji N, Zeinali T, Joukar F, Aleali MS, Eslami N, Shenagari M, Mansour-Ghanaei F. Mutational dynamics of SARS-CoV-2: Impact on future COVID-19 vaccine strategies. Heliyon 2024; 10:e30208. [PMID: 38707429 PMCID: PMC11066641 DOI: 10.1016/j.heliyon.2024.e30208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024] Open
Abstract
The rapid emergence of multiple strains of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has sparked profound concerns regarding the ongoing evolution of the virus and its potential impact on global health. Classified by the World Health Organization (WHO) as variants of concern (VOC), these strains exhibit heightened transmissibility and pathogenicity, posing significant challenges to existing vaccine strategies. Despite widespread vaccination efforts, the continual evolution of SARS-CoV-2 variants presents a formidable obstacle to achieving herd immunity. Of particular concern is the coronavirus spike (S) protein, a pivotal viral surface protein crucial for host cell entry and infectivity. Mutations within the S protein have been shown to enhance transmissibility and confer resistance to antibody-mediated neutralization, undermining the efficacy of traditional vaccine platforms. Moreover, the S protein undergoes rapid molecular evolution under selective immune pressure, leading to the emergence of diverse variants with distinct mutation profiles. This review underscores the urgent need for vigilance and adaptation in vaccine development efforts to combat the evolving landscape of SARS-CoV-2 mutations and ensure the long-term effectiveness of global immunization campaigns.
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Affiliation(s)
- Niloofar Faraji
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Tahereh Zeinali
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Farahnaz Joukar
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Maryam Sadat Aleali
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Narges Eslami
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Mohammad Shenagari
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Fariborz Mansour-Ghanaei
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
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3
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Sheward DJ, Pushparaj P, Das H, Greaney AJ, Kim C, Kim S, Hanke L, Hyllner E, Dyrdak R, Lee J, Dopico XC, Dosenovic P, Peacock TP, McInerney GM, Albert J, Corcoran M, Bloom JD, Murrell B, Karlsson Hedestam GB, Hällberg BM. Structural basis of broad SARS-CoV-2 cross-neutralization by affinity-matured public antibodies. Cell Rep Med 2024:101577. [PMID: 38761799 DOI: 10.1016/j.xcrm.2024.101577] [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: 01/26/2023] [Revised: 12/15/2023] [Accepted: 04/24/2024] [Indexed: 05/20/2024]
Abstract
Descendants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant now account for almost all SARS-CoV-2 infections. The Omicron variant and its sublineages have spike glycoproteins that are highly diverged from the pandemic founder and first-generation vaccine strain, resulting in significant evasion from monoclonal antibody therapeutics and vaccines. Understanding how commonly elicited antibodies can broaden to cross-neutralize escape variants is crucial. We isolate IGHV3-53, using "public" monoclonal antibodies (mAbs) from an individual 7 months post infection with the ancestral virus and identify antibodies that exhibit potent and broad cross-neutralization, extending to the BA.1, BA.2, and BA.4/BA.5 sublineages of Omicron. Deep mutational scanning reveals these mAbs' high resistance to viral escape. Structural analysis via cryoelectron microscopy of a representative broadly neutralizing antibody, CAB-A17, in complex with the Omicron BA.1 spike highlights the structural underpinnings of this broad neutralization. By reintroducing somatic hypermutations into a germline-reverted CAB-A17, we delineate the role of affinity maturation in the development of cross-neutralization by a public class of antibodies.
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Affiliation(s)
- Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Allison J Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sungyong Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Erik Hyllner
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Robert Dyrdak
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jimin Lee
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Pia Dosenovic
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | | | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Centre for Structural Systems Biology (CSSB) and Karolinska Institutet VR-RÅC, Notkestraße 85, 22607 Hamburg, Germany.
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4
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Ketaren NE, Mast FD, Fridy PC, Olivier JP, Sanyal T, Sali A, Chait BT, Rout MP, Aitchison JD. Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus. eLife 2024; 12:RP89423. [PMID: 38712823 PMCID: PMC11076045 DOI: 10.7554/elife.89423] [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: 05/08/2024] Open
Abstract
To date, all major modes of monoclonal antibody therapy targeting SARS-CoV-2 have lost significant efficacy against the latest circulating variants. As SARS-CoV-2 omicron sublineages account for over 90% of COVID-19 infections, evasion of immune responses generated by vaccination or exposure to previous variants poses a significant challenge. A compelling new therapeutic strategy against SARS-CoV-2 is that of single-domain antibodies, termed nanobodies, which address certain limitations of monoclonal antibodies. Here, we demonstrate that our high-affinity nanobody repertoire, generated against wild-type SARS-CoV-2 spike protein (Mast et al., 2021), remains effective against variants of concern, including omicron BA.4/BA.5; a subset is predicted to counter resistance in emerging XBB and BQ.1.1 sublineages. Furthermore, we reveal the synergistic potential of nanobody cocktails in neutralizing emerging variants. Our study highlights the power of nanobody technology as a versatile therapeutic and diagnostic tool to combat rapidly evolving infectious diseases such as SARS-CoV-2.
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Affiliation(s)
- Natalia E Ketaren
- Laboratory of Cellular and Structural Biology, The Rockefeller UniversityNew YorkUnited States
| | - Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research InstituteSeattleUnited States
| | - Peter C Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller UniversityNew YorkUnited States
| | - Jean Paul Olivier
- Center for Global Infectious Disease Research, Seattle Children's Research InstituteSeattleUnited States
| | - Tanmoy Sanyal
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, University of California, San FranciscoSan FranciscoUnited States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, University of California, San FranciscoSan FranciscoUnited States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller UniversityNew YorkUnited States
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller UniversityNew YorkUnited States
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research InstituteSeattleUnited States
- Department of Pediatrics, University of WashingtonSeattleUnited States
- Department of Biochemistry, University of WashingtonSeattleUnited States
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5
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Feng S, Reid GE, Clark NM, Harrington A, Uprichard SL, Baker SC. Evidence of SARS-CoV-2 convergent evolution in immunosuppressed patients treated with antiviral therapies. Virol J 2024; 21:105. [PMID: 38715113 PMCID: PMC11075269 DOI: 10.1186/s12985-024-02378-y] [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: 02/05/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND The factors contributing to the accelerated convergent evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not fully understood. Unraveling the contribution of viral replication in immunocompromised patients is important for the early detection of novel mutations and developing approaches to limit COVID-19. METHODS We deep sequenced SARS-CoV-2 RNA from 192 patients (64% hospitalized, 39% immunosuppressed) and compared the viral genetic diversity within the patient groups of different immunity and hospitalization status. Serial sampling of 14 patients was evaluated for viral evolution in response to antiviral treatments. RESULTS We identified hospitalized and immunosuppressed patients with significantly higher levels of viral genetic diversity and variability. Further evaluation of serial samples revealed accumulated mutations associated with escape from neutralizing antibodies in a subset of the immunosuppressed patients treated with antiviral therapies. Interestingly, the accumulated viral mutations that arose in this early Omicron wave, which were not common in the patient viral lineages, represent convergent mutations that are prevalent in the later Omicron sublineages, including the XBB, BA.2.86.1 and its descendent JN sublineages. CONCLUSIONS Our results illustrate the importance of identifying convergent mutations generated during antiviral therapy in immunosuppressed patients, as they may contribute to the future evolutionary landscape of SARS-CoV-2. Our study also provides evidence of a correlation between SARS-CoV-2 convergent mutations and specific antiviral treatments. Evaluating high-confidence genomes from distinct waves in the pandemic with detailed patient metadata allows for discerning of convergent mutations that contribute to the ongoing evolution of SARS-CoV-2.
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Affiliation(s)
- Shuchen Feng
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Gail E Reid
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Nina M Clark
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Amanda Harrington
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Department of Pathology and Laboratory Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Susan L Uprichard
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Susan C Baker
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
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6
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Rubio AA, Baharani VA, Dadonaite B, Parada M, Abernathy ME, Wang Z, Lee YE, Eso MR, Phung J, Ramos I, Chen T, Nesr GE, Bloom JD, Bieniasz PD, Nussenzweig MC, Barnes CO. Bispecific antibodies with broad neutralization potency against SARS-CoV-2 variants of concern. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592584. [PMID: 38766244 PMCID: PMC11100608 DOI: 10.1101/2024.05.05.592584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The ongoing emergence of SARS-CoV-2 variants of concern (VOCs) that reduce the effectiveness of antibody therapeutics necessitates development of next-generation antibody modalities that are resilient to viral evolution. Here, we characterized N-terminal domain (NTD) and receptor binding domain (RBD)-specific monoclonal antibodies previously isolated from COVID-19 convalescent donors for their activity against emergent SARS-CoV-2 VOCs. Among these, the NTD-specific antibody C1596 displayed the greatest breadth of binding to VOCs, with cryo-EM structural analysis revealing recognition of a distinct NTD epitope outside of the site i antigenic supersite. Given C1596's favorable binding profile, we designed a series of bispecific antibodies (bsAbs) termed CoV2-biRNs, that featured both NTD and RBD specificities. Notably, two of the C1596-inclusive bsAbs, CoV2-biRN5 and CoV2-biRN7, retained potent in vitro neutralization activity against all Omicron variants tested, including XBB.1.5, EG.5.1, and BA.2.86, contrasting the diminished potency of parental antibodies delivered as monotherapies or as a cocktail. Furthermore, prophylactic delivery of CoV2-biRN5 significantly reduced the viral load within the lungs of K18-hACE2 mice following challenge with SARS-CoV-2 XBB.1.5. In conclusion, our NTD-RBD bsAbs offer promising potential for the design of resilient, next-generation antibody therapeutics against SARS-CoV-2 VOCs. One Sentence Summary Bispecific antibodies with a highly cross-reactive NTD antibody demonstrate resilience to SARS-CoV-2 variants of concern.
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7
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Adair A, Tan LL, Feng J, Girkin J, Bryant N, Wang M, Mordant F, Chan LJ, Bartlett NW, Subbarao K, Pymm P, Tham WH. Human coronavirus OC43 nanobody neutralizes virus and protects mice from infection. J Virol 2024:e0053124. [PMID: 38709106 DOI: 10.1128/jvi.00531-24] [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: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 05/07/2024] Open
Abstract
Human coronavirus (hCoV) OC43 is endemic to global populations and usually causes asymptomatic or mild upper respiratory tract illness. Here, we demonstrate the neutralization efficacy of isolated nanobodies from alpacas immunized with the S1B and S1C domain of the hCoV-OC43 spike glycoprotein. A total of 40 nanobodies bound to recombinant OC43 protein with affinities ranging from 1 to 149 nM. Two nanobodies WNb 293 and WNb 294 neutralized virus at 0.21 and 1.79 nM, respectively. Intranasal and intraperitoneal delivery of WNb 293 fused to an Fc domain significantly reduced nasal viral load in a mouse model of hCoV-OC43 infection. Using X-ray crystallography, we observed that WNb 293 bound to an epitope on the OC43 S1B domain, distal from the sialoglycan-binding site involved in host cell entry. This result suggests that neutralization mechanism of this nanobody does not involve disruption of glycan binding. Our work provides characterization of nanobodies against hCoV-OC43 that blocks virus entry and reduces viral loads in vivo and may contribute to future nanobody-based therapies for hCoV-OC43 infections. IMPORTANCE The pandemic potential presented by coronaviruses has been demonstrated by the ongoing COVID-19 pandemic and previous epidemics caused by severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus. Outside of these major pathogenic coronaviruses, there are four endemic coronaviruses that infect humans: hCoV-OC43, hCoV-229E, hCoV-HKU1, and hCoV-NL63. We identified a collection of nanobodies against human coronavirus OC43 (hCoV-OC43) and found that two high-affinity nanobodies potently neutralized hCoV-OC43 at low nanomolar concentrations. Prophylactic administration of one neutralizing nanobody reduced viral loads in mice infected with hCoV-OC43, showing the potential for nanobody-based therapies for hCoV-OC43 infections.
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Affiliation(s)
- Amy Adair
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Li Lynn Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Jackson Feng
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jason Girkin
- 3College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Infection Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Nathan Bryant
- 3College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Infection Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Mingyang Wang
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Francesca Mordant
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Li-Jin Chan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nathan W Bartlett
- 3College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Infection Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Phillip Pymm
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Wai-Hong Tham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
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8
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Trepl J, Pasin C, Schneidawind D, Mueller NJ, Manz MG, Bankova AK, Abela IA. Evaluating tixagevimab/cilgavimab prophylaxis in allogeneic haematopoietic cell transplantation recipients for COVID-19 prevention. Br J Haematol 2024; 204:1908-1912. [PMID: 38327109 DOI: 10.1111/bjh.19321] [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: 12/08/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/09/2024]
Abstract
Allogeneic haematopoietic cell transplantation (allo-HCT) recipients exhibit an increased risk of COVID-19, particularly in the early post-transplant phase, due to insufficient vaccine responses. This retrospective study investigated the incidence of SARS-CoV-2 infection in allo-HCT recipients who received tixagevimab/cilgavimab pre-exposure prophylaxis (T/C PrEP) compared to those who did not. Logistic regression, adjusted for sex, age, SARS-CoV-2 vaccination status and immunosuppressive treatment, revealed a significant reduction in the likelihood of SARS-CoV-2 infection risk with T/C PrEP (adjusted odds ratio aOR = 0.26 [0.07, 0.91]). These findings suggest the potential efficacy of monoclonal antibody PrEP in protecting this vulnerable patient population from COVID-19.
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Affiliation(s)
- Julia Trepl
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Chloé Pasin
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Dominik Schneidawind
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Nicolas J Mueller
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Andriyana K Bankova
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
- National Specialized Hospital for Hematological Diseases, Sofia, Bulgaria
| | - Irene A Abela
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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9
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Allerton CMN, Arcari JT, Aschenbrenner LM, Avery M, Bechle BM, Behzadi MA, Boras B, Buzon LM, Cardin RD, Catlin NR, Carlo AA, Coffman KJ, Dantonio A, Di L, Eng H, Farley KA, Ferre RA, Gernhardt SS, Gibson SA, Greasley SE, Greenfield SR, Hurst BL, Kalgutkar AS, Kimoto E, Lanyon LF, Lovett GH, Lian Y, Liu W, Martínez Alsina LA, Noell S, Obach RS, Owen DR, Patel NC, Rai DK, Reese MR, Rothan HA, Sakata S, Sammons MF, Sathish JG, Sharma R, Steppan CM, Tuttle JB, Verhoest PR, Wei L, Yang Q, Yurgelonis I, Zhu Y. A Second-Generation Oral SARS-CoV-2 Main Protease Inhibitor Clinical Candidate for the Treatment of COVID-19. J Med Chem 2024. [PMID: 38687966 DOI: 10.1021/acs.jmedchem.3c02469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Despite the record-breaking discovery, development and approval of vaccines and antiviral therapeutics such as Paxlovid, coronavirus disease 2019 (COVID-19) remained the fourth leading cause of death in the world and third highest in the United States in 2022. Here, we report the discovery and characterization of PF-07817883, a second-generation, orally bioavailable, SARS-CoV-2 main protease inhibitor with improved metabolic stability versus nirmatrelvir, the antiviral component of the ritonavir-boosted therapy Paxlovid. We demonstrate the in vitro pan-human coronavirus antiviral activity and off-target selectivity profile of PF-07817883. PF-07817883 also demonstrated oral efficacy in a mouse-adapted SARS-CoV-2 model at plasma concentrations equivalent to nirmatrelvir. The preclinical in vivo pharmacokinetics and metabolism studies in human matrices are suggestive of improved oral pharmacokinetics for PF-07817883 in humans, relative to nirmatrelvir. In vitro inhibition/induction studies against major human drug metabolizing enzymes/transporters suggest a low potential for perpetrator drug-drug interactions upon single-agent use of PF-07817883.
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Affiliation(s)
| | - Joel T Arcari
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | | | - Melissa Avery
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Bruce M Bechle
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | | | - Britton Boras
- Pfizer Research & Development, La Jolla, California 92121, United States
| | - Leanne M Buzon
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Rhonda D Cardin
- Pfizer Research & Development, Pearl River, New York 10965, United States
| | - Natasha R Catlin
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Anthony A Carlo
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Karen J Coffman
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Alyssa Dantonio
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Li Di
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Heather Eng
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Kathleen A Farley
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Rose Ann Ferre
- Pfizer Research & Development, La Jolla, California 92121, United States
| | | | - Scott A Gibson
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, Utah 84322, United States
| | | | | | - Brett L Hurst
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, Utah 84322, United States
| | - Amit S Kalgutkar
- Pfizer Research & Development, Cambridge, Massachusetts 02139, United States
| | - Emi Kimoto
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Lorraine F Lanyon
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Gabrielle H Lovett
- Pfizer Research & Development, Cambridge, Massachusetts 02139, United States
| | - Yajing Lian
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Wei Liu
- Pfizer Research & Development, La Jolla, California 92121, United States
| | | | - Stephen Noell
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - R Scott Obach
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Dafydd R Owen
- Pfizer Research & Development, Cambridge, Massachusetts 02139, United States
| | - Nandini C Patel
- Pfizer Research & Development, Cambridge, Massachusetts 02139, United States
| | - Devendra K Rai
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Matthew R Reese
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Hussin A Rothan
- Pfizer Research & Development, Pearl River, New York 10965, United States
| | - Sylvie Sakata
- Pfizer Research & Development, La Jolla, California 92121, United States
| | - Matthew F Sammons
- Pfizer Research & Development, Cambridge, Massachusetts 02139, United States
| | - Jean G Sathish
- Pfizer Research & Development, Pearl River, New York 10965, United States
| | - Raman Sharma
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Claire M Steppan
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Jamison B Tuttle
- Pfizer Research & Development, Cambridge, Massachusetts 02139, United States
| | - Patrick R Verhoest
- Pfizer Research & Development, Cambridge, Massachusetts 02139, United States
| | - Liuqing Wei
- Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Qingyi Yang
- Pfizer Research & Development, Cambridge, Massachusetts 02139, United States
| | - Irina Yurgelonis
- Pfizer Research & Development, Pearl River, New York 10965, United States
| | - Yuao Zhu
- Pfizer Research & Development, Pearl River, New York 10965, United States
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10
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Carrascosa-Sàez M, Marqués MC, Geller R, Elena SF, Rahmeh A, Dufloo J, Sanjuán R. Cell type-specific adaptation of the SARS-CoV-2 spike. Virus Evol 2024; 10:veae032. [PMID: 38779130 PMCID: PMC11110937 DOI: 10.1093/ve/veae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/10/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) can infect various human tissues and cell types, principally via interaction with its cognate receptor angiotensin-converting enzyme-2 (ACE2). However, how the virus evolves in different cellular environments is poorly understood. Here, we used experimental evolution to study the adaptation of the SARS-CoV-2 spike to four human cell lines expressing different levels of key entry factors. After twenty passages of a spike-expressing recombinant vesicular stomatitis virus (VSV), cell-type-specific phenotypic changes were observed and sequencing allowed the identification of sixteen adaptive spike mutations. We used VSV pseudotyping to measure the entry efficiency, ACE2 affinity, spike processing, TMPRSS2 usage, and entry pathway usage of all the mutants, alone or in combination. The fusogenicity of the mutant spikes was assessed with a cell-cell fusion assay. Finally, mutant recombinant VSVs were used to measure the fitness advantage associated with selected mutations. We found that the effects of these mutations varied across cell types, both in terms of viral entry and replicative fitness. Interestingly, two spike mutations (L48S and A372T) that emerged in cells expressing low ACE2 levels increased receptor affinity, syncytia induction, and entry efficiency under low-ACE2 conditions. Our results demonstrate specific adaptation of the SARS-CoV-2 spike to different cell types and have implications for understanding SARS-CoV-2 tissue tropism and evolution.
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Affiliation(s)
- Marc Carrascosa-Sàez
- Institute for Integrative Systems Biology (I2SysBio). University of Valencia—CSIC, Paterna, 46980, Spain
| | - María-Carmen Marqués
- Institute for Integrative Systems Biology (I2SysBio). University of Valencia—CSIC, Paterna, 46980, Spain
| | - Ron Geller
- Institute for Integrative Systems Biology (I2SysBio). University of Valencia—CSIC, Paterna, 46980, Spain
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia 46010, Spain
| | - Santiago F Elena
- Institute for Integrative Systems Biology (I2SysBio). University of Valencia—CSIC, Paterna, 46980, Spain
- The Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Amal Rahmeh
- Departament de Medicina i Ciències de La Vida (MELIS), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Jérémy Dufloo
- Institute for Integrative Systems Biology (I2SysBio). University of Valencia—CSIC, Paterna, 46980, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio). University of Valencia—CSIC, Paterna, 46980, Spain
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11
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Inoue T, Yamamoto Y, Sato K, Okemoto-Nakamura Y, Shimizu Y, Ogawa M, Onodera T, Takahashi Y, Wakita T, Kaneko MK, Fukasawa M, Kato Y, Noguchi K. Overcoming antibody-resistant SARS-CoV-2 variants with bispecific antibodies constructed using non-neutralizing antibodies. iScience 2024; 27:109363. [PMID: 38500835 PMCID: PMC10946335 DOI: 10.1016/j.isci.2024.109363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/22/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024] Open
Abstract
A current challenge is the emergence of SARS-CoV-2 variants, such as BQ.1.1 and XBB.1.5, that can evade immune defenses, thereby limiting antibody drug effectiveness. Emergency-use antibody drugs, including the widely effective bebtelovimab, are losing their benefits. One potential approach to address this issue are bispecific antibodies which combine the targeting abilities of two antibodies with distinct epitopes. We engineered neutralizing bispecific antibodies in the IgG-scFv format from two initially non-neutralizing antibodies, CvMab-6 (which binds to the receptor-binding domain [RBD]) and CvMab-62 (targeting a spike protein S2 subunit epitope adjacent to the known anti-S2 antibody epitope). Furthermore, we created a bispecific antibody by incorporating the scFv of bebtelovimab with our anti-S2 antibody, demonstrating significant restoration of effectiveness against bebtelovimab-resistant BQ.1.1 variants. This study highlights the potential of neutralizing bispecific antibodies, which combine existing less effective anti-RBD antibodies with anti-S2 antibodies, to revive the effectiveness of antibody therapeutics compromised by immune-evading variants.
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Affiliation(s)
- Tetsuya Inoue
- Laboratory of Molecular Targeted Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamazaki 2641, Noda, Chiba 278-8510, Japan
| | - Yuichiro Yamamoto
- Laboratory of Molecular Targeted Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamazaki 2641, Noda, Chiba 278-8510, Japan
| | - Kaoru Sato
- Laboratory of Molecular Targeted Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamazaki 2641, Noda, Chiba 278-8510, Japan
| | - Yuko Okemoto-Nakamura
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yoshimi Shimizu
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
- Department of Pharmaceutical Sciences, Teikyo Heisei University, 4-21-2 Nakano, Nakano-ku 164-8530, Japan
| | - Motohiko Ogawa
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Taishi Onodera
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Takaji Wakita
- National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Mika K. Kaneko
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Sendai, Miyagi 980-8575, Japan
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Sendai, Miyagi 980-8575, Japan
| | - Masayoshi Fukasawa
- Laboratory of Molecular Targeted Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamazaki 2641, Noda, Chiba 278-8510, Japan
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yukinari Kato
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Sendai, Miyagi 980-8575, Japan
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Sendai, Miyagi 980-8575, Japan
| | - Kohji Noguchi
- Laboratory of Molecular Targeted Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamazaki 2641, Noda, Chiba 278-8510, Japan
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
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12
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Ray A, Minh Tran TT, Santos Natividade RD, Moreira RA, Simpson JD, Mohammed D, Koehler M, L Petitjean SJ, Zhang Q, Bureau F, Gillet L, Poma AB, Alsteens D. Single-Molecule Investigation of the Binding Interface Stability of SARS-CoV-2 Variants with ACE2. ACS NANOSCIENCE AU 2024; 4:136-145. [PMID: 38644967 PMCID: PMC11027127 DOI: 10.1021/acsnanoscienceau.3c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 04/23/2024]
Abstract
The SARS-CoV-2 pandemic spurred numerous research endeavors to comprehend the virus and mitigate its global severity. Understanding the binding interface between the virus and human receptors is pivotal to these efforts and paramount to curbing infection and transmission. Here we employ atomic force microscopy and steered molecular dynamics simulation to explore SARS-CoV-2 receptor binding domain (RBD) variants and angiotensin-converting enzyme 2 (ACE2), examining the impact of mutations at key residues upon binding affinity. Our results show that the Omicron and Delta variants possess strengthened binding affinity in comparison to the Mu variant. Further, using sera from individuals either vaccinated or with acquired immunity following Delta strain infection, we assess the impact of immunity upon variant RBD/ACE2 complex formation. Single-molecule force spectroscopy analysis suggests that vaccination before infection may provide stronger protection across variants. These results underscore the need to monitor antigenic changes in order to continue developing innovative and effective SARS-CoV-2 abrogation strategies.
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Affiliation(s)
- Ankita Ray
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Thu Thi Minh Tran
- Faculty
of Materials Science and Technology, University
of Science—VNU HCM, 227 Nguyen Van Cu Street, District 5, 700000 Ho Chi Minh City, Vietnam
- Vietnam
National University, 700000 Ho Chi Minh City, Vietnam
| | - Rita dos Santos Natividade
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Rodrigo A. Moreira
- Basque
Center for Applied Mathematics, Mazarredo 14, 48009 Bilbao, Spain
| | - Joshua D. Simpson
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Danahe Mohammed
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Melanie Koehler
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Simon J. L Petitjean
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Qingrong Zhang
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Fabrice Bureau
- Laboratory
of Cellular and Molecular Immunology, GIGA Institute, Liège University, 4000 Liège, Belgium
| | - Laurent Gillet
- Immunology-Vaccinology
Lab of the Faculty of Veterinary Medicine, Liège University, 4000 Liège, Belgium
| | - Adolfo B. Poma
- Institute
of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
| | - David Alsteens
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
- WELBIO
department, WEL Research Institute, 1300 Wavre, Belgium
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13
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Chen L, Sun M, Zhang H, Zhang X, Yao Y, Li M, Li K, Fan P, Zhang H, Qin Y, Zhang Z, Li E, Chen Z, Guan W, Li S, Yu C, Zhang K, Gong R, Chiu S. Potent human neutralizing antibodies against Nipah virus derived from two ancestral antibody heavy chains. Nat Commun 2024; 15:2987. [PMID: 38582870 PMCID: PMC10998907 DOI: 10.1038/s41467-024-47213-8] [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: 08/14/2023] [Accepted: 03/18/2024] [Indexed: 04/08/2024] Open
Abstract
Nipah virus (NiV) is a World Health Organization priority pathogen and there are currently no approved drugs for clinical immunotherapy. Through the use of a naïve human phage-displayed Fab library, two neutralizing antibodies (NiV41 and NiV42) targeting the NiV receptor binding protein (RBP) were identified. Following affinity maturation, antibodies derived from NiV41 display cross-reactivity against both NiV and Hendra virus (HeV), whereas the antibody based on NiV42 is only specific to NiV. Results of immunogenetic analysis reveal a correlation between the maturation of antibodies and their antiviral activity. In vivo testing of NiV41 and its mature form (41-6) show protective efficacy against a lethal NiV challenge in hamsters. Furthermore, a 2.88 Å Cryo-EM structure of the tetrameric RBP and antibody complex demonstrates that 41-6 blocks the receptor binding interface. These findings can be beneficial for the development of antiviral drugs and the design of vaccines with broad spectrum against henipaviruses.
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Affiliation(s)
- Li Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mengmeng Sun
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Huajun Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xinghai Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yanfeng Yao
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Ming Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Kangyin Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pengfei Fan
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, China
| | - Haiwei Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Ye Qin
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhe Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Entao Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, China
| | - Zhen Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Wuxiang Guan
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Shanshan Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Changming Yu
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, China.
| | - Kaiming Zhang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- Department of Urology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Rui Gong
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Hubei Jiangxia Laboratory, Wuhan, Hubei, China.
| | - Sandra Chiu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, China.
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14
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Chen X, Huang X, Ma Q, Kuzmič P, Zhou B, Zhang S, Chen J, Xu J, Liu B, Jiang H, Zhang W, Yang C, Wu S, Huang J, Li H, Long C, Zhao X, Xu H, Sheng Y, Guo Y, Niu C, Xue L, Xu Y, Liu J, Zhang T, Spencer J, Zhu Z, Deng W, Chen X, Chen SH, Zhong N, Xiong X, Yang Z. Preclinical evaluation of the SARS-CoV-2 M pro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir. Nat Microbiol 2024; 9:1075-1088. [PMID: 38553607 PMCID: PMC10994847 DOI: 10.1038/s41564-024-01618-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 01/22/2024] [Indexed: 04/06/2024]
Abstract
Although vaccines are available for SARS-CoV-2, antiviral drugs such as nirmatrelvir are still needed, particularly for individuals in whom vaccines are less effective, such as the immunocompromised, to prevent severe COVID-19. Here we report an α-ketoamide-based peptidomimetic inhibitor of the SARS-CoV-2 main protease (Mpro), designated RAY1216. Enzyme inhibition kinetic analysis shows that RAY1216 has an inhibition constant of 8.4 nM and suggests that it dissociates about 12 times slower from Mpro compared with nirmatrelvir. The crystal structure of the SARS-CoV-2 Mpro:RAY1216 complex shows that RAY1216 covalently binds to the catalytic Cys145 through the α-ketoamide group. In vitro and using human ACE2 transgenic mouse models, RAY1216 shows antiviral activities against SARS-CoV-2 variants comparable to those of nirmatrelvir. It also shows improved pharmacokinetics in mice and rats, suggesting that RAY1216 could be used without ritonavir, which is co-administered with nirmatrelvir. RAY1216 has been approved as a single-component drug named 'leritrelvir' for COVID-19 treatment in China.
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Affiliation(s)
- Xiaoxin Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
- Guangdong Raynovent Biotech Co., Ltd, Guangzhou, China
| | - Xiaodong Huang
- 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, China
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qinhai Ma
- 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, China
| | | | - Biao Zhou
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangzhou National Laboratory, Guangzhou, China
| | - Sai Zhang
- Guangzhou National Laboratory, Guangzhou, China
| | | | - Jinxin Xu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 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, China
| | - Haiming Jiang
- 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, China
| | - Wenjie Zhang
- 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, China
| | - Chunguang Yang
- 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, China
| | - Shiguan Wu
- 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, China
| | | | - Haijun Li
- Guangdong Raynovent Biotech Co., Ltd, Guangzhou, China
| | - Chaofeng Long
- Guangdong Raynovent Biotech Co., Ltd, Guangzhou, China
| | - Xin Zhao
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center Guangzhou), Guangzhou, China
| | - Hongrui Xu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yanan Sheng
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yaoting Guo
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Chuanying Niu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Lu Xue
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yong Xu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | | | - Wenbin Deng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Xinwen Chen
- Guangzhou National Laboratory, Guangzhou, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | | | - Nanshan Zhong
- 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, China.
- Guangzhou National Laboratory, Guangzhou, China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China.
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Zifeng Yang
- 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, China.
- Guangzhou National Laboratory, Guangzhou, China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China.
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15
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Zhang L, Parvin R, Lin S, Chen M, Zheng R, Fan Q, Ye F. Peptide Nucleic Acid Clamp-Assisted Photothermal Multiplexed Digital PCR for Identifying SARS-CoV-2 Variants of Concern. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306088. [PMID: 38243642 PMCID: PMC10987151 DOI: 10.1002/advs.202306088] [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: 08/26/2023] [Revised: 12/16/2023] [Indexed: 01/21/2024]
Abstract
The unprecedented demand for variants diagnosis in response to the COVID-19 epidemic has brought the spotlight onto rapid and accurate detection assays for single nucleotide polymorphisms (SNPs) at multiple locations. However, it is still challenging to ensure simplicity, affordability, and compatibility with multiplexing. Here, a novel technique is presented that combines peptide nucleic acid (PNA) clamps and near-infrared (NIR)-driven digital polymerase chain reaction (dPCR) to identify the Omicron and Delta variants. This is achieved by simultaneously identifying highly conserved mutated signatures at codons 19, 614, and 655 of the spike protein gene. By microfluidically introducing graphene-oxide-nanocomposite into the assembled gelatin microcarriers, they achieved a rapid temperature ramping-up rate and switchable gel-to-sol phase transformation synchronized with PCR activation under NIR irradiation. Two sets of duplex PCR reactions, each classifying respective PNA probes, are emulsified in parallel and illuminated together using a homemade vacuum-based droplet generation device and a programmable NIR control module. This allowed for selective amplification of mutant sequences due to single-base-pair mismatch with PNA blockers. Sequence-recognized bioreactions and fluorescent-color scoring enabled quick identification of variants. This technique achieved a detection limit of 5,100 copies and a 5-fold quantitative resolution, which is promising to unfold minor differences and dynamic changes.
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Affiliation(s)
- Lexiang Zhang
- Joint Centre of Translational Medicinethe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325035China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health); Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhou325000China
- Key Laboratory of Structural Malformations in Children of Zhejiang Provincethe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhouZhejiang325027China
| | - Rokshana Parvin
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health); Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhou325000China
| | - Siyue Lin
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
| | - Mingshuo Chen
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health); Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhou325000China
| | - Ruixuan Zheng
- Joint Centre of Translational Medicinethe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325035China
| | - Qihui Fan
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijingChina100190
| | - Fangfu Ye
- Joint Centre of Translational Medicinethe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325035China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health); Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhou325000China
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijingChina100190
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16
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Zhang Q, Pavlinov I, Ye Y, Zheng W. Therapeutic development targeting host heparan sulfate proteoglycan in SARS-CoV-2 infection. Front Med (Lausanne) 2024; 11:1364657. [PMID: 38618194 PMCID: PMC11014733 DOI: 10.3389/fmed.2024.1364657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024] Open
Abstract
The global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an urgent need for effective therapeutic options. SARS-CoV-2 is a novel coronavirus responsible for the COVID-19 pandemic that has resulted in significant morbidity and mortality worldwide. The virus is known to enter host cells by binding to the angiotensin-converting enzyme 2 (ACE2) receptor, and emerging evidence suggests that heparan sulfate proteoglycans (HSPGs) play a crucial role in facilitating this process. HSPGs are abundant cell surface proteoglycan present in many tissues, including the lung, and have been shown to interact directly with the spike protein of SARS-CoV-2. This review aims to summarize the current understanding of the role of HSPGs in SARS-CoV-2 infection and the potential of developing new therapies targeting HSPGs.
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Affiliation(s)
- Qi Zhang
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Ivan Pavlinov
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Wei Zheng
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
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17
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Amani B, Khodavirdilou L, Rajabkhah K, Kardan Moghaddam V, Akbarzadeh A, Amani B. Efficacy and safety of bamlanivimab in patients with COVID-19: A systematic review and meta-analysis. World J Virol 2024; 13:88660. [PMID: 38616851 PMCID: PMC11008398 DOI: 10.5501/wjv.v13.i1.88660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/09/2023] [Accepted: 12/29/2023] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Monoclonal antibodies (mAbs) have shown clinical benefits against coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Several studies have reported the use of bamlanivimab as a promising treatment option for COVID-19. AIM To synthesize the latest evidence for the efficacy and safety of bamlanivimab alone in the treatment of adult patients with COVID-19. METHODS A literature search was conducted in PubMed, Cochrane Library, Web of Science, medRxiv, and Google Scholar using "SARS-CoV-2", "COVID-19", "LY-CoV555", and "Bamlanivimab" keywords up to January 25, 2023. The quality of included studies was assessed using the Cochrane bias tools. The Comprehensive Meta-Analysis software version 3.0 was used to analyze the data. RESULTS A total of 30 studies involving 47368 patients were included. A significant difference was observed between the bamlanivimab and standard of care/placebo groups in terms of mortality rate [risk ratio (RR) = 50, 95% confidence interval (CI): 0.36-0.70], hospitalization rate (RR = 0.51; 95%CI: 0.39-0.68), and emergency department (ED) visits (RR = 0.69; 95%CI: 0.47-0.99); while the two groups exhibited no significant difference in terms of intensive care unit (ICU) admission (P > 0.05). Compared to other mAbs, bamlanivimab was associated with a higher rate of hospitalization (RR = 1.44; 95%CI: 1.07-1.94). However, no significant difference was detected between the bamlanivimab and other mAbs groups in terms of mortality rate, ICU admission, and ED (P > 0.05). The incidence of any adverse events was similar between the bamlanivimab and control groups (P > 0.05). CONCLUSION Although the results suggest the efficacy and safety of bamlanivimab in COVID-19 patients, further research is required to confirm the efficacy of this drug for the current circulating SARS-CoV-2 variants.
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Affiliation(s)
- Behnam Amani
- Department of Health Management and Economics, School of Public Health, Tehran University of Medical Sciences, Tehran 1416634793, Iran
| | - Lida Khodavirdilou
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX 79106, United States
| | - Kourosh Rajabkhah
- Deputy of Research and Technology, Tehran University of Medical Sciences, Tehran 1416634793, Iran
| | - Vida Kardan Moghaddam
- School of Medicine and Dentistry, Griffith University, Queensland, Brisbane 4222, Australia
| | - Arash Akbarzadeh
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran 1416634793, Iran
| | - Bahman Amani
- Department of Health Management and Economics, School of Public Health, Tehran University of Medical Sciences, Tehran 1416634793, Iran
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18
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Arevalo-Romero JA, Chingaté-López SM, Camacho BA, Alméciga-Díaz CJ, Ramirez-Segura CA. Next-generation treatments: Immunotherapy and advanced therapies for COVID-19. Heliyon 2024; 10:e26423. [PMID: 38434363 PMCID: PMC10907543 DOI: 10.1016/j.heliyon.2024.e26423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in 2019 following prior outbreaks of coronaviruses like SARS and MERS in recent decades, underscoring their high potential of infectivity in humans. Insights from previous outbreaks of SARS and MERS have played a significant role in developing effective strategies to mitigate the global impact of SARS-CoV-2. As of January 7, 2024, there have been 774,075,242 confirmed cases of COVID-19 worldwide. To date, 13.59 billion vaccine doses have been administered, and there have been 7,012,986 documented fatalities (https://www.who.int/) Despite significant progress in addressing the COVID-19 pandemic, the rapid evolution of SARS-CoV-2 challenges human defenses, presenting ongoing global challenges. The emergence of new SARS-CoV-2 lineages, shaped by mutation and recombination processes, has led to successive waves of infections. This scenario reveals the need for next-generation vaccines as a crucial requirement for ensuring ongoing protection against SARS-CoV-2. This demand calls for formulations that trigger a robust adaptive immune response without leading the acute inflammation linked with the infection. Key mutations detected in the Spike protein, a critical target for neutralizing antibodies and vaccine design -specifically within the Receptor Binding Domain region of Omicron variant lineages (B.1.1.529), currently dominant worldwide, have intensified concerns due to their association with immunity evasion from prior vaccinations and infections. As the world deals with this evolving threat, the narrative extends to the realm of emerging variants, each displaying new mutations with implications that remain largely misunderstood. Notably, the JN.1 Omicron lineage is gaining global prevalence, and early findings suggest it stands among the immune-evading variants, a characteristic attributed to its mutation L455S. Moreover, the detrimental consequences of the novel emergence of SARS-CoV-2 lineages bear a particularly critical impact on immunocompromised individuals and older adults. Immunocompromised individuals face challenges such as suboptimal responses to COVID-19 vaccines, rendering them more susceptible to severe disease. Similarly, older adults have an increased risk of severe disease and the presence of comorbid conditions, find themselves at a heightened vulnerability to develop COVID-19 disease. Thus, recognizing these intricate factors is crucial for effectively tailoring public health strategies to protect these vulnerable populations. In this context, this review aims to describe, analyze, and discuss the current progress of the next-generation treatments encompassing immunotherapeutic approaches and advanced therapies emerging as complements that will offer solutions to counter the disadvantages of the existing options. Preliminary outcomes show that these strategies target the virus and address the immunomodulatory responses associated with COVID-19. Furthermore, the capacity to promote tissue repair has been demonstrated, which can be particularly noteworthy for immunocompromised individuals who stand as vulnerable actors in the global landscape of coronavirus infections. The emerging next-generation treatments possess broader potential, offering protection against a wide range of variants and enhancing the ability to counter the impact of the constant evolution of the virus. Furthermore, advanced therapies are projected as potential treatment alternatives for managing Chronic Post-COVID-19 syndromeand addressing its associated long-term complications.
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Affiliation(s)
- Jenny Andrea Arevalo-Romero
- Laboratorio de Investigación en Ingeniería Celular y Molecular, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, IDCBIS, 111611, Bogotá, DC, Colombia
- Instituto de Errores Innatos del Metabolismo, Facultad de Ciencias, Pontificia Universidad Javeriana, 110231, Bogotá, D.C., Colombia
| | - Sandra M. Chingaté-López
- Laboratorio de Investigación en Ingeniería Celular y Molecular, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, IDCBIS, 111611, Bogotá, DC, Colombia
| | - Bernardo Armando Camacho
- Laboratorio de Investigación en Ingeniería Celular y Molecular, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, IDCBIS, 111611, Bogotá, DC, Colombia
| | - Carlos Javier Alméciga-Díaz
- Instituto de Errores Innatos del Metabolismo, Facultad de Ciencias, Pontificia Universidad Javeriana, 110231, Bogotá, D.C., Colombia
| | - Cesar A. Ramirez-Segura
- Laboratorio de Investigación en Ingeniería Celular y Molecular, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, IDCBIS, 111611, Bogotá, DC, Colombia
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19
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Kumar S, Dasgupta S, Sajadi MM, Snyder GA, DeVico AL, Ray K. Discordant Antigenic Properties of Soluble and Virion SARS-CoV-2 Spike Proteins. Viruses 2024; 16:407. [PMID: 38543772 PMCID: PMC10974403 DOI: 10.3390/v16030407] [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: 01/19/2024] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 04/01/2024] Open
Abstract
Efforts to develop vaccine and immunotherapeutic countermeasures against the COVID-19 pandemic focus on targeting the trimeric spike (S) proteins of SARS-CoV-2. Vaccines and therapeutic design strategies must impart the characteristics of virion S from historical and emerging variants onto practical constructs such as soluble, stabilized trimers. The virus spike is a heterotrimer of two subunits: S1, which includes the receptor binding domain (RBD) that binds the cell surface receptor ACE2, and S2, which mediates membrane fusion. Previous studies suggest that the antigenic, structural, and functional characteristics of virion S may differ from current soluble surrogates. For example, it was reported that certain anti-glycan, HIV-1 neutralizing monoclonal antibodies bind soluble SARS-CoV-2 S but do not neutralize SARS-CoV-2 virions. In this study, we used single-molecule fluorescence correlation spectroscopy (FCS) under physiologically relevant conditions to examine the reactivity of broadly neutralizing and non-neutralizing anti-S human monoclonal antibodies (mAbs) isolated in 2020. Binding efficiency was assessed by FCS with soluble S trimers, pseudoviruses and inactivated wild-type virions representing variants emerging from 2020 to date. Anti-glycan mAbs were tested and compared. We find that both anti-S specific and anti-glycan mAbs exhibit variable but efficient binding to a range of stabilized, soluble trimers. Across mAbs, the efficiencies of soluble S binding were positively correlated with reactivity against inactivated virions but not pseudoviruses. Binding efficiencies with pseudoviruses were generally lower than with soluble S or inactivated virions. Among neutralizing mAbs, potency did not correlate with binding efficiencies on any target. No neutralizing activity was detected with anti-glycan antibodies. Notably, the virion S released from membranes by detergent treatment gained more efficient reactivity with anti-glycan, HIV-neutralizing antibodies but lost reactivity with all anti-S mAbs. Collectively, the FCS binding data suggest that virion surfaces present appreciable amounts of both functional and nonfunctional trimers, with neutralizing anti-S favoring the former structures and non-neutralizing anti-glycan mAbs binding the latter. S released from solubilized virions represents a nonfunctional structure bound by anti-glycan mAbs, while engineered soluble trimers present a composite structure that is broadly reactive with both mAb types. The detection of disparate antigenicity and immunoreactivity profiles in engineered and virion-associated S highlight the value of single-virus analyses in designing future antiviral strategies against SARS-CoV-2.
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Affiliation(s)
- Sameer Kumar
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Souradip Dasgupta
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Mohammad M. Sajadi
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Division of Clinical Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Greg A. Snyder
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Anthony L. DeVico
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Krishanu Ray
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
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20
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Muneer A, Xie L, Xie X, Zhang F, Wrobel JA, Xiong Y, Yu X, Wang C, Gheorghe C, Wu P, Song J, Ming GL, Jin J, Song H, Shi PY, Chen X. Targeting G9a translational mechanism of SARS-CoV-2 pathogenesis for multifaceted therapeutics of COVID-19 and its sequalae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583415. [PMID: 38496599 PMCID: PMC10942352 DOI: 10.1101/2024.03.04.583415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
By largely unknown mechanism(s), SARS-CoV-2 hijacks the host translation apparatus to promote COVID-19 pathogenesis. We report that the histone methyltransferase G9a noncanonically regulates viral hijacking of the translation machinery to bring about COVID-19 symptoms of hyperinflammation, lymphopenia, and blood coagulation. Chemoproteomic analysis of COVID-19 patient peripheral mononuclear blood cells (PBMC) identified enhanced interactions between SARS-CoV-2-upregulated G9a and distinct translation regulators, particularly the N 6 -methyladenosine (m 6 A) RNA methylase METTL3. These interactions with translation regulators implicated G9a in translational regulation of COVID-19. Inhibition of G9a activity suppressed SARS-CoV-2 replication in human alveolar epithelial cells. Accordingly, multi-omics analysis of the same alveolar cells identified SARS-CoV-2-induced changes at the transcriptional, m 6 A-epitranscriptional, translational, and post-translational (phosphorylation or secretion) levels that were reversed by inhibitor treatment. As suggested by the aforesaid chemoproteomic analysis, these multi-omics-correlated changes revealed a G9a-regulated translational mechanism of COVID-19 pathogenesis in which G9a directs translation of viral and host proteins associated with SARS-CoV-2 replication and with dysregulation of host response. Comparison of proteomic analyses of G9a inhibitor-treated, SARS-CoV-2 infected cells, or ex vivo culture of patient PBMCs, with COVID-19 patient data revealed that G9a inhibition reversed the patient proteomic landscape that correlated with COVID-19 pathology/symptoms. These data also indicated that the G9a-regulated, inhibitor-reversed, translational mechanism outperformed G9a-transcriptional suppression to ultimately determine COVID-19 pathogenesis and to define the inhibitor action, from which biomarkers of serve symptom vulnerability were mechanistically derived. This cell line-to-patient conservation of G9a-translated, COVID-19 proteome suggests that G9a inhibitors can be used to treat patients with COVID-19, particularly patients with long-lasting COVID-19 sequelae.
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21
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Vitiello A, Sabbatucci M, Ponzo A, Salzano A, Zovi A. A Short Update on the Use of Monoclonal Antibodies in COVID-19. AAPS J 2024; 26:30. [PMID: 38443725 DOI: 10.1208/s12248-024-00904-y] [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] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
Monoclonal antibodies in the prophylaxis and treatment of COVID-19 have been crucial in reducing severe infections when vaccines were unavailable. However, as the virus and its variants have changed over time, the effectiveness of monoclonal antibodies has been questioned. This technical note highlights the need to assess the antiviral activity of these antibodies against new variants and adapt treatment strategies accordingly. On the one hand, in vitro studies have suggested reduced susceptibility of the latest variants to monoclonal antibodies, whereas clinical data still show benefits in reducing severe illness and mortality, indicating that laboratory results do not always mirror real-world outcomes. As a result, although resistance to monoclonal antibodies can develop over time, they could still have an important role in COVID-19 treatment, especially when used in combination, and ongoing research aims to identify effective antibodies against new variants.
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Affiliation(s)
- Antonio Vitiello
- Directorate General for Health Prevention, Italian Ministry of Health, Rome, Italy
| | - Michela Sabbatucci
- Department Infectious Diseases, Italian National Institute of Health, Viale Regina Elena 299, 00161, Rome, Italy
| | - Annarita Ponzo
- Biology Department L. Spallanzani, University of Pavia, Pavia, Italy
| | - Antonio Salzano
- Directorate General for Health Prevention, Italian Ministry of Health, Rome, Italy
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22
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Chesdachai S, Rivera CG, Cole KC, Teaford HR, Gonzalez Suarez ML, Larsen JJ, Ganesh R, Tulledge-Scheitel S, Razonable RR. Comparable outcomes of outpatient remdesivir and sotrovimab among high-risk patients with mild to moderate COVID-19 during the omicron BA.1 surge. Sci Rep 2024; 14:5430. [PMID: 38443438 PMCID: PMC10914739 DOI: 10.1038/s41598-024-56195-y] [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: 11/27/2023] [Accepted: 03/04/2024] [Indexed: 03/07/2024] Open
Abstract
Studies conducted prior to SARS-CoV-2 Omicron demonstrated that sotrovimab and remdesivir reduced hospitalization among high-risk outpatients with mild to moderate COVID-19. However, their effectiveness has not been directly compared. This study examined all high-risk outpatients with mild to moderate COVID-19 who received either remdesivir or sotrovimab at Mayo Clinic during the Omicron BA.1 surge from January to March 2022. COVID-19-related hospitalization or death within 28 days were compared between the two treatment groups. Among 3257 patients, 2158 received sotrovimab and 1099 received remdesivir. Patients treated with sotrovimab were younger and had lower comorbidity but were more likely to be immunocompromised than remdesivir-treated patients. The majority (89%) had received at least one dose of COVID-19 vaccine. COVID-19-related hospitalization (1.5% and 1.0% in remdesivir and sotrovimab, respectively, p = .15) and mortality within 28 days (0.4% in both groups, p = .82) were similarly low. A propensity score weighted analysis demonstrated no significant difference in the outcomes between the two groups. We demonstrated favorable outcomes that were not significantly different between patients treated with remdesivir or sotrovimab.
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Affiliation(s)
- Supavit Chesdachai
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA.
| | | | - Kristin C Cole
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Ravindra Ganesh
- Department of General Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Raymund R Razonable
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA.
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23
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Wilson C, Thomson EC. Resilience to emerging infectious diseases and the importance of scientific innovation. Future Healthc J 2024; 11:100023. [PMID: 38646044 PMCID: PMC11025050 DOI: 10.1016/j.fhj.2024.100023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
This opinion piece emphasies the critical role of translational research in enhancing the UK's resilience against future pandemics. The COVID-19 pandemic demonstrated the lifesaving potential of scientific innovation, including genomic tracking of SARS-CoV-2, vaccine development, data linkage, modelling, and new treatments. These advances, achieved through collaborations between academic institutions, industry, government, public health bodies, and the NHS, occurred at an unprecedented pace. However, the UK's pandemic preparedness planning, as reflected in the 2016 Exercise Cygnus report, notably lacked provision for scientific innovation. This oversight highlights the necessity of integrating innovation and research into future preparedness strategies, not as a luxury but as a vital component of the healthcare infrastructure. The COVID-19 pandemic has underlined the importance of surge capacity for diagnostic labs, vaccine development and deployment strategies, real-time research embedded within the NHS, efficient data sharing, clear public communication, and the use of genomic tools for outbreak surveillance and monitoring pathogen response. Despite world-leading aspects of some of the UK's research response, the need to build much of the infrastructure in real-time led to avoidable delays. A proactive approach in incorporating research and innovation into the NHS's operational framework will be needed to ensure swift, evidence-based responses to future pandemics.
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Affiliation(s)
| | - Emma C. Thomson
- NHS Greater Glasgow & Clyde (NHS GG&C), Glasgow, United Kingdom
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- London School of Hygiene and Tropical Medicine (LSHTM), London, United Kingdom
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24
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Kim JW, Lee JH, Kim HJ, Heo K, Lee Y, Jang HJ, Lee HY, Park JW, Cho YB, Shin HG, Yang HR, Lee HE, Song JY, Lee S. Empowering SARS-CoV-2 variant neutralization with a bifunctional antibody engineered with tandem heptad repeat 2 peptides. J Med Virol 2024; 96:e29506. [PMID: 38445718 DOI: 10.1002/jmv.29506] [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: 11/17/2023] [Revised: 01/28/2024] [Accepted: 02/23/2024] [Indexed: 03/07/2024]
Abstract
With the global pandemic and the continuous mutations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the need for effective and broadly neutralizing treatments has become increasingly urgent. This study introduces a novel strategy that targets two aspects simultaneously, using bifunctional antibodies to inhibit both the attachment of SARS-CoV-2 to host cell membranes and viral fusion. We developed pioneering IgG4-(HR2)4 bifunctional antibodies by creating immunoglobulin G4-based and phage display-derived human monoclonal antibodies (mAbs) that specifically bind to the SARS-CoV-2 receptor-binding domain, engineered with four heptad repeat 2 (HR2) peptides. Our in vitro experiments demonstrate the superior neutralization efficacy of these engineered antibodies against various SARS-CoV-2 variants, ranging from original SARS-CoV-2 strain to the recently emerged Omicron variants, as well as SARS-CoV, outperforming the parental mAb. Notably, intravenous monotherapy with the bifunctional antibody neutralizes a SARS-CoV-2 variant in a murine model without causing significant toxicity. In summary, this study unveils the significant potential of HR2 peptide-driven bifunctional antibodies as a potent and versatile strategy for mitigating SARS-CoV-2 infections. This approach offers a promising avenue for rapid development and management in the face of the continuously evolving SARS-CoV-2 variants, holding substantial promise for pandemic control.
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Affiliation(s)
- Ji Woong Kim
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ji Hyun Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Hyun Jung Kim
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Kyun Heo
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
- Department of Chemistry, Kookmin University, Seoul, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul, Republic of Korea
| | - Yoonwoo Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Hui Jeong Jang
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Ho-Young Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Jun Won Park
- Division of Biomedical Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | - Yea Bin Cho
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ha Gyeong Shin
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ha Rim Yang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Hee Eon Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Jin Young Song
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Sukmook Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
- Department of Chemistry, Kookmin University, Seoul, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul, Republic of Korea
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25
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Chiyyeadu A, Asgedom G, Bruhn M, Rocha C, Schlegel TU, Neumann T, Galla M, Vollmer Barbosa P, Hoffmann M, Ehrhardt K, Ha TC, Morgan M, Schoeder CT, Pöhlmann S, Kalinke U, Schambach A. A tetravalent bispecific antibody outperforms the combination of its parental antibodies and neutralizes diverse SARS-CoV-2 variants. Clin Immunol 2024; 260:109902. [PMID: 38218210 DOI: 10.1016/j.clim.2024.109902] [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: 10/11/2023] [Revised: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
The devastating impact of COVID-19 on global health shows the need to increase our pandemic preparedness. Recombinant therapeutic antibodies were successfully used to treat and protect at-risk patients from COVID-19. However, the currently circulating Omicron subvariants of SARS-CoV-2 are largely resistant to therapeutic antibodies, and novel approaches to generate broadly neutralizing antibodies are urgently needed. Here, we describe a tetravalent bispecific antibody, A7A9 TVB, which actively neutralized many SARS-CoV-2 variants of concern, including early Omicron subvariants. Interestingly, A7A9 TVB neutralized more variants at lower concentration as compared to the combination of its parental monoclonal antibodies, A7K and A9L. A7A9 also reduced the viral load of authentic Omicron BA.1 virus in infected pseudostratified primary human nasal epithelial cells. Overall, A7A9 displayed the characteristics of a potent broadly neutralizing antibody, which may be suitable for prophylactic and therapeutic applications in the clinics, thus highlighting the usefulness of an effective antibody-designing approach.
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Affiliation(s)
- Abhishek Chiyyeadu
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Girmay Asgedom
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Matthias Bruhn
- Institute for Experimental Infection Research, TWINCORE, Center for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625 Hannover, Germany
| | - Cheila Rocha
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Tom U Schlegel
- Institute for Drug Discovery, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Thomas Neumann
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Melanie Galla
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Philippe Vollmer Barbosa
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Markus Hoffmann
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Katrin Ehrhardt
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Teng-Cheong Ha
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Clara T Schoeder
- Institute for Drug Discovery, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Stefan Pöhlmann
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Center for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625 Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, United States of America.
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26
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Nguyen TH, Chen LY, Khan NZ, Lindenbauer A, Bui VC, Zipfel PF, Heinrich D. The Binding of the SARS-CoV-2 Spike Protein to Platelet Factor 4: A Proposed Mechanism for the Generation of Pathogenic Antibodies. Biomolecules 2024; 14:245. [PMID: 38540666 PMCID: PMC10967930 DOI: 10.3390/biom14030245] [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: 12/18/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 04/02/2024] Open
Abstract
Pathogenic platelet factor 4 (PF4) antibodies contributed to the abnormal coagulation profiles in COVID-19 and vaccinated patients. However, the mechanism of what triggers the body to produce these antibodies has not yet been clarified. Similar patterns and many comparable features between the COVID-19 virus and heparin-induced thrombocytopenia (HIT) have been reported. Previously, we identified a new mechanism of autoimmunity in HIT in which PF4-antibodies self-clustered PF4 and exposed binding epitopes for other pathogenic PF4/eparin antibodies. Here, we first proved that the SARS-CoV-2 spike protein (SP) also binds to PF4. The binding was evidenced by the increase in mass and optical intensity as observed through quartz crystal microbalance and immunosorbent assay, while the switching of the surface zeta potential caused by protein interactions and binding affinity of PF4-SP were evaluated by dynamic light scattering and isothermal spectral shift analysis. Based on our results, we proposed a mechanism for the generation of PF4 antibodies in COVID-19 patients. We further validated the changes in zeta potential and interaction affinity between PF4 and SP and found that their binding mechanism differs from ACE2-SP binding. Importantly, the PF4/SP complexes facilitate the binding of anti-PF4/Heparin antibodies. Our findings offer a fresh perspective on PF4 engagement with the SARS-CoV-2 SP, illuminating the role of PF4/SP complexes in severe thrombotic events.
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Affiliation(s)
- Thi-Huong Nguyen
- Institute for Bioprocessing and Analytical Measurement Techniques (iba), 37308 Heilbad Heiligenstadt, Germany
- Faculty of Mathematics and Natural Sciences, Technische Universität Ilmenau, 98694 Ilmenau, Germany
| | - Li-Yu Chen
- Institute for Bioprocessing and Analytical Measurement Techniques (iba), 37308 Heilbad Heiligenstadt, Germany
- Institute of Miccrobiology, Friedrich-Schiller-University, 07745 Jena, Germany
| | - Nida Zaman Khan
- Institute for Bioprocessing and Analytical Measurement Techniques (iba), 37308 Heilbad Heiligenstadt, Germany
- Faculty of Mathematics and Natural Sciences, Technische Universität Ilmenau, 98694 Ilmenau, Germany
| | - Annerose Lindenbauer
- Institute for Bioprocessing and Analytical Measurement Techniques (iba), 37308 Heilbad Heiligenstadt, Germany
| | - Van-Chien Bui
- Department of Water Supply and Wastewater Treatment, Eichsfeldwerke GmbH, 37308 Heilbad Heiligenstadt, Germany
| | - Peter F. Zipfel
- Institute of Miccrobiology, Friedrich-Schiller-University, 07745 Jena, Germany
| | - Doris Heinrich
- Institute for Bioprocessing and Analytical Measurement Techniques (iba), 37308 Heilbad Heiligenstadt, Germany
- Faculty of Mathematics and Natural Sciences, Technische Universität Ilmenau, 98694 Ilmenau, Germany
- Fraunhofer Institut für Silicatforschung, Neunerplatz, 97082 Würzburg, Germany
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27
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Yan J, Bangalore CR, Nikouyan N, Appelberg S, Silva DN, Yao H, Pasetto A, Weber F, Weber S, Larsson O, Höglund U, Bogdanovic G, Grabbe M, Aleman S, Szekely L, Szakos A, Tuvesson O, Gidlund EK, Cadossi M, Salati S, Tegel H, Hober S, Frelin L, Mirazimi A, Ahlén G, Sällberg M. Distinct roles of vaccine-induced SARS-CoV-2-specific neutralizing antibodies and T cells in protection and disease. Mol Ther 2024; 32:540-555. [PMID: 38213030 PMCID: PMC10862018 DOI: 10.1016/j.ymthe.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 12/04/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific neutralizing antibodies (NAbs) lack cross-reactivity between SARS-CoV species and variants and fail to mediate long-term protection against infection. The maintained protection against severe disease and death by vaccination suggests a role for cross-reactive T cells. We generated vaccines containing sequences from the spike or receptor binding domain, the membrane and/or nucleoprotein that induced only T cells, or T cells and NAbs, to understand their individual roles. In three models with homologous or heterologous challenge, high levels of vaccine-induced SARS-CoV-2 NAbs protected against neither infection nor mild histological disease but conferred rapid viral control limiting the histological damage. With no or low levels of NAbs, vaccine-primed T cells, in mice mainly CD8+ T cells, partially controlled viral replication and promoted NAb recall responses. T cells failed to protect against histological damage, presumably because of viral spread and subsequent T cell-mediated killing. Neither vaccine- nor infection-induced NAbs seem to provide long-lasting protective immunity against SARS-CoV-2. Thus, a more realistic approach for universal SARS-CoV-2 vaccines should be to aim for broadly cross-reactive NAbs in combination with long-lasting highly cross-reactive T cells. Long-lived cross-reactive T cells are likely key to prevent severe disease and fatalities during current and future pandemics.
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Affiliation(s)
- Jingyi Yan
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Karolinska ATMP Center, Stockholm, Sweden
| | | | - Negin Nikouyan
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Daniela Nacimento Silva
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Karolinska ATMP Center, Stockholm, Sweden
| | - Haidong Yao
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Karolinska ATMP Center, Stockholm, Sweden
| | - Anna Pasetto
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Karolinska ATMP Center, Stockholm, Sweden
| | - Friedemann Weber
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University Giessen, Giessen, Germany
| | | | | | | | - Gordana Bogdanovic
- Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Malin Grabbe
- Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Soo Aleman
- Infectious Disease Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Laszlo Szekely
- Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
| | - Attila Szakos
- Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
| | | | | | | | | | - Hanna Tegel
- Department of Protein Science, KTH - Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Sophia Hober
- Department of Protein Science, KTH - Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Lars Frelin
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Karolinska ATMP Center, Stockholm, Sweden
| | - Ali Mirazimi
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Public Health Agency of Sweden, Stockholm, Sweden
| | - Gustaf Ahlén
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Karolinska ATMP Center, Stockholm, Sweden
| | - Matti Sällberg
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Karolinska ATMP Center, Stockholm, Sweden.
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28
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Ugrani S. Inhibitor design for TMPRSS2: insights from computational analysis of its backbone hydrogen bonds using a simple descriptor. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:27-46. [PMID: 38157015 PMCID: PMC10853362 DOI: 10.1007/s00249-023-01695-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 01/03/2024]
Abstract
Transmembrane protease serine 2 (TMPRSS2) is an important drug target due to its role in the infection mechanism of coronaviruses including SARS-CoV-2. Current understanding regarding the molecular mechanisms of known inhibitors and insights required for inhibitor design are limited. This study investigates the effect of inhibitor binding on the intramolecular backbone hydrogen bonds (BHBs) of TMPRSS2 using the concept of hydrogen bond wrapping, which is the phenomenon of stabilization of a hydrogen bond in a solvent environment as a result of being surrounded by non-polar groups. A molecular descriptor which quantifies the extent of wrapping around BHBs is introduced for this. First, virtual screening for TMPRSS2 inhibitors is performed by molecular docking using the program DOCK 6 with a Generalized Born surface area (GBSA) scoring function. The docking results are then analyzed using this descriptor and its relationship to the solvent-accessible surface area term ΔGsa of the GBSA score is demonstrated with machine learning regression and principal component analysis. The effect of binding of the inhibitors camostat, nafamostat, and 4-guanidinobenzoic acid (GBA) on the wrapping of important BHBs in TMPRSS2 is also studied using molecular dynamics. For BHBs with a large increase in wrapping groups due to these inhibitors, the radial distribution function of water revealed that certain residues involved in these BHBs, like Gln438, Asp440, and Ser441, undergo preferential desolvation. The findings offer valuable insights into the mechanisms of these inhibitors and may prove useful in the design of new inhibitors.
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Affiliation(s)
- Suraj Ugrani
- Purdue University, West Lafayette, IN, 47907, USA.
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29
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Ghafari M, Hall M, Golubchik T, Ayoubkhani D, House T, MacIntyre-Cockett G, Fryer HR, Thomson L, Nurtay A, Kemp SA, Ferretti L, Buck D, Green A, Trebes A, Piazza P, Lonie LJ, Studley R, Rourke E, Smith DL, Bashton M, Nelson A, Crown M, McCann C, Young GR, Santos RAND, Richards Z, Tariq MA, Cahuantzi R, Barrett J, Fraser C, Bonsall D, Walker AS, Lythgoe K. Prevalence of persistent SARS-CoV-2 in a large community surveillance study. Nature 2024; 626:1094-1101. [PMID: 38383783 PMCID: PMC10901734 DOI: 10.1038/s41586-024-07029-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 01/04/2024] [Indexed: 02/23/2024]
Abstract
Persistent SARS-CoV-2 infections may act as viral reservoirs that could seed future outbreaks1-5, give rise to highly divergent lineages6-8 and contribute to cases with post-acute COVID-19 sequelae (long COVID)9,10. However, the population prevalence of persistent infections, their viral load kinetics and evolutionary dynamics over the course of infections remain largely unknown. Here, using viral sequence data collected as part of a national infection survey, we identified 381 individuals with SARS-CoV-2 RNA at high titre persisting for at least 30 days, of which 54 had viral RNA persisting at least 60 days. We refer to these as 'persistent infections' as available evidence suggests that they represent ongoing viral replication, although the persistence of non-replicating RNA cannot be ruled out in all. Individuals with persistent infection had more than 50% higher odds of self-reporting long COVID than individuals with non-persistent infection. We estimate that 0.1-0.5% of infections may become persistent with typically rebounding high viral loads and last for at least 60 days. In some individuals, we identified many viral amino acid substitutions, indicating periods of strong positive selection, whereas others had no consensus change in the sequences for prolonged periods, consistent with weak selection. Substitutions included mutations that are lineage defining for SARS-CoV-2 variants, at target sites for monoclonal antibodies and/or are commonly found in immunocompromised people11-14. This work has profound implications for understanding and characterizing SARS-CoV-2 infection, epidemiology and evolution.
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Affiliation(s)
- Mahan Ghafari
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Pandemic Science Institute, University of Oxford, Oxford, UK.
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Sydney Infectious Diseases Institute (Sydney ID), School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Daniel Ayoubkhani
- Office for National Statistics, Newport, UK
- Leicester Real World Evidence Unit, Diabetes Research Centre, University of Leicester, Leicester, UK
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester, UK
| | - George MacIntyre-Cockett
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Helen R Fryer
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Laura Thomson
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
| | - Anel Nurtay
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Steven A Kemp
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Biology, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
| | - Luca Ferretti
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
| | - David Buck
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Angie Green
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Amy Trebes
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Paolo Piazza
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Lorne J Lonie
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | | | | | - Darren L Smith
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Matthew Bashton
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Andrew Nelson
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Matthew Crown
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Clare McCann
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Gregory R Young
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Rui Andre Nunes Dos Santos
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Zack Richards
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Mohammad Adnan Tariq
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | | | | | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - David Bonsall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, UK
| | - Ann Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- MRC Clinical Trials Unit at UCL, UCL, London, UK
| | - Katrina Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Pandemic Science Institute, University of Oxford, Oxford, UK.
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30
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Sulimov AV, Ilin IS, Tashchilova AS, Kondakova OA, Kutov DC, Sulimov VB. Docking and other computing tools in drug design against SARS-CoV-2. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024; 35:91-136. [PMID: 38353209 DOI: 10.1080/1062936x.2024.2306336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
The use of computer simulation methods has become an indispensable component in identifying drugs against the SARS-CoV-2 coronavirus. There is a huge body of literature on application of molecular modelling to predict inhibitors against target proteins of SARS-CoV-2. To keep our review clear and readable, we limited ourselves primarily to works that use computational methods to find inhibitors and test the predicted compounds experimentally either in target protein assays or in cell culture with live SARS-CoV-2. Some works containing results of experimental discovery of corresponding inhibitors without using computer modelling are included as examples of a success. Also, some computational works without experimental confirmations are also included if they attract our attention either by simulation methods or by databases used. This review collects studies that use various molecular modelling methods: docking, molecular dynamics, quantum mechanics, machine learning, and others. Most of these studies are based on docking, and other methods are used mainly for post-processing to select the best compounds among those found through docking. Simulation methods are presented concisely, information is also provided on databases of organic compounds that can be useful for virtual screening, and the review itself is structured in accordance with coronavirus target proteins.
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Affiliation(s)
- A V Sulimov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - I S Ilin
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - A S Tashchilova
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - O A Kondakova
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - D C Kutov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - V B Sulimov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
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31
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Shafat T, Grupel D, Porges T, Abuhasira R, Belkin A, Deri O, Oster Y, Zahran S, Horwitz E, Horowitz NA, Khatib H, Batista MV, Cortez AC, Brosh‐Nissimov T, Segman Y, Ishay L, Cohen R, Atamna A, Spallone A, Chemaly RF, Ramos‐Ramos JC, Chowers M, Rogozin E, Oren NC, Keske Ş, Barchad OW, Nesher L. An international multicenter study comparing COVID-19 omicron outcomes in patients with hematological malignancies treated with obinutuzumab versus rituximab. Cancer Med 2024; 13:e6997. [PMID: 38400683 PMCID: PMC10891459 DOI: 10.1002/cam4.6997] [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: 10/18/2023] [Revised: 01/23/2024] [Accepted: 01/28/2024] [Indexed: 02/25/2024] Open
Abstract
OBJECTIVES Hematological malignancy (HM) patients treated with anti-CD20 monoclonal antibodies are at higher risk for severe COVID-19. A previous single-center study showed worse outcomes in patients treated with obinutuzumab compared to rituximab. We examined this hypothesis in a large international multicenter cohort. METHODS We included HM patients from 15 centers, from five countries treated with anti-CD20, comparing those treated with obinutuzumab (O-G) to rituximab (R-G) between December 2021 and June 2022, when Omicron lineage was dominant. RESULTS We collected data on 1048 patients. Within the R-G (n = 762, 73%), 191 (25%) contracted COVID-19 compared to 103 (36%) in the O-G. COVID-19 patients in the O-G were younger (61 ± 11.7 vs. 64 ± 14.5, p = 0.039), had more indolent HM diagnosis (aggressive lymphoma: 3.9% vs. 67.0%, p < 0.001), and most were on maintenance therapy at COVID-19 diagnosis (63.0% vs. 16.8%, p < 0.001). Severe-critical COVID-19 occurred in 31.1% of patients in the O-G and 22.5% in the R-G. In multivariable analysis, O-G had a 2.08-fold increased risk for severe-critical COVID-19 compared to R-G (95% CI 1.13-3.84), adjusted for Charlson comorbidity index, sex, and tixagevimab/cilgavimab (T-C) prophylaxis. Further analysis comparing O-G to R-G demonstrated increased hospitalizations (51.5% vs. 35.6% p = 0.008), ICU admissions (12.6% vs. 5.8%, p = 0.042), but the nonsignificant difference in COVID-19-related mortality (n = 10, 9.7% vs. n = 12, 6.3%, p = 0.293). CONCLUSIONS Despite younger age and a more indolent HM diagnosis, patients receiving obinutuzumab had more severe COVID-19 outcomes than those receiving rituximab. Our findings underscore the need to evaluate the risk-benefit balance when considering obinutuzumab therapy for HM patients during respiratory viral outbreaks.
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Affiliation(s)
- Tali Shafat
- Infectious Diseases Institute, Soroka University Medical Center, and the Faculty of Health SciencesBen‐Gurion University of the NegevBeer‐ShevaIsrael
- Clinical Research Center, Soroka University Medical Center, and the Faculty of Health SciencesBen‐Gurion University of the NegevBeer‐ShevaIsrael
- Department of Infectious Diseases, Infection Control and Employee HealthThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses (ESGREV)BaselSwitzerland
| | - Daniel Grupel
- Department of Clinical Microbiology and Infectious DiseasesHadassah Medical CenterJerusalemIsrael
- Faculty of MedicineHebrew UniversityJerusalemIsrael
| | - Tzvika Porges
- Hematology Department, Soroka University Medical Center, and the Faculty of Health SciencesBen‐Gurion University of the NegevBeer‐ShevaIsrael
| | - Ran Abuhasira
- Clinical Research Center, Soroka University Medical Center, and the Faculty of Health SciencesBen‐Gurion University of the NegevBeer‐ShevaIsrael
| | - Ana Belkin
- Internal Medicine D and Infectious Diseases UnitSheba Medical CenterRamat‐GanIsrael
- Sackler Faculty of MedicineTel Aviv UniversityRamat‐AvivIsrael
| | - Ofir Deri
- Internal Medicine TSheba Medical CenterRamat‐GanIsrael
| | - Yonatan Oster
- Department of Clinical Microbiology and Infectious DiseasesHadassah Medical CenterJerusalemIsrael
- Faculty of MedicineHebrew UniversityJerusalemIsrael
| | - Shadi Zahran
- Department of Clinical Microbiology and Infectious DiseasesHadassah Medical CenterJerusalemIsrael
- Faculty of MedicineHebrew UniversityJerusalemIsrael
| | - Ehud Horwitz
- Department of Clinical Microbiology and Infectious DiseasesHadassah Medical CenterJerusalemIsrael
- Faculty of MedicineHebrew UniversityJerusalemIsrael
| | - Netanel A. Horowitz
- Department of Hematology and Bone Marrow TransplantationRambam Health Care CampusHaifaIsrael
| | - Hazim Khatib
- Department of Hematology and Bone Marrow TransplantationRambam Health Care CampusHaifaIsrael
| | - Marjorie Vieira Batista
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses (ESGREV)BaselSwitzerland
- Department of Infectious DiseasesAC Camargo Cancer CenterSão PauloSão PauloBrazil
| | - Anita Cassoli Cortez
- Department of Hematology and Cell TherapyAC Camargo Cancer CenterSão PauloSão PauloBrazil
| | - Tal Brosh‐Nissimov
- Infectious Diseases UnitSamson Assuta Ashdod University HospitalAshdodIsrael
- The Faculty of Health SciencesBen‐Gurion University of the NegevBeer‐ShevaIsrael
| | - Yafit Segman
- The Faculty of Health SciencesBen‐Gurion University of the NegevBeer‐ShevaIsrael
- Hematology InstituteSamson Assuta Ashdod University HospitalAshdodIsrael
| | - Linor Ishay
- Rappaport Faculty of MedicineTechnionHaifaIsrael
- Hillel Yaffe Medical CenterHaderaIsrael
| | - Regev Cohen
- Rappaport Faculty of MedicineTechnionHaifaIsrael
- Hillel Yaffe Medical CenterHaderaIsrael
| | - Alaa Atamna
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses (ESGREV)BaselSwitzerland
- Infectious Diseases Unit, Rabin Medical CenterBeilinson HospitalPetah TikvaIsrael
| | - Amy Spallone
- Department of Infectious Diseases, Infection Control and Employee HealthThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses (ESGREV)BaselSwitzerland
| | - Roy F. Chemaly
- Department of Infectious Diseases, Infection Control and Employee HealthThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses (ESGREV)BaselSwitzerland
| | - Juan Carlos Ramos‐Ramos
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses (ESGREV)BaselSwitzerland
- Infectious Disease UnitInternal Medicine Service. CIBERINFEC. Hospital Universitario La PazMadridSpain
| | - Michal Chowers
- Meir Medical CentreKfar SabaIsrael
- Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Evgeny Rogozin
- Infectious Diseases unitShamir (Assaf Harofeh) Medical CenterBe'er Ya'akovIsrael
| | - Noga Carmi Oren
- Infectious Diseases unitShamir (Assaf Harofeh) Medical CenterBe'er Ya'akovIsrael
| | - Şiran Keske
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses (ESGREV)BaselSwitzerland
- Department of Infectious DiseasesVKV American HospitalIstanbulTurkey
| | | | - Lior Nesher
- Infectious Diseases Institute, Soroka University Medical Center, and the Faculty of Health SciencesBen‐Gurion University of the NegevBeer‐ShevaIsrael
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses (ESGREV)BaselSwitzerland
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Ketaren NE, Mast FD, Fridy PC, Olivier JP, Sanyal T, Sali A, Chait BT, Rout MP, Aitchison JD. Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.14.549041. [PMID: 37503298 PMCID: PMC10369967 DOI: 10.1101/2023.07.14.549041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
To date, all major modes of monoclonal antibody therapy targeting SARS-CoV-2 have lost significant efficacy against the latest circulating variants. As SARS-CoV-2 omicron sublineages account for over 90% of COVID-19 infections, evasion of immune responses generated by vaccination or exposure to previous variants poses a significant challenge. A compelling new therapeutic strategy against SARS-CoV-2 is that of single domain antibodies, termed nanobodies, which address certain limitations of monoclonal antibodies. Here we demonstrate that our high-affinity nanobody repertoire, generated against wild-type SARS-CoV-2 spike protein (Mast, Fridy et al. 2021), remains effective against variants of concern, including omicron BA.4/BA.5; a subset is predicted to counter resistance in emerging XBB and BQ.1.1 sublineages. Furthermore, we reveal the synergistic potential of nanobody cocktails in neutralizing emerging variants. Our study highlights the power of nanobody technology as a versatile therapeutic and diagnostic tool to combat rapidly evolving infectious diseases such as SARS-CoV-2.
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Affiliation(s)
- Natalia E. Ketaren
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Fred D. Mast
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, USA
| | - Peter C. Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Jean Paul Olivier
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, USA
| | - Tanmoy Sanyal
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94143, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94143, USA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - John D. Aitchison
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, USA
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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Liu W, Huang Z, Xiao J, Wu Y, Xia N, Yuan Q. Evolution of the SARS-CoV-2 Omicron Variants: Genetic Impact on Viral Fitness. Viruses 2024; 16:184. [PMID: 38399960 PMCID: PMC10893260 DOI: 10.3390/v16020184] [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: 12/25/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Over the last three years, the pandemic of COVID-19 has had a significant impact on people's lives and the global economy. The incessant emergence of variant strains has compounded the challenges associated with the management of COVID-19. As the predominant variant from late 2021 to the present, Omicron and its sublineages, through continuous evolution, have demonstrated iterative viral fitness. The comprehensive elucidation of the biological implications that catalyzed this evolution remains incomplete. In accordance with extant research evidence, we provide a comprehensive review of subvariants of Omicron, delineating alterations in immune evasion, cellular infectivity, and the cross-species transmission potential. This review seeks to clarify the underpinnings of biology within the evolution of SARS-CoV-2, thereby providing a foundation for strategic considerations in the post-pandemic era of COVID-19.
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Affiliation(s)
- Wenhao Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Zehong Huang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Jin Xiao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Yangtao Wu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Quan Yuan
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
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Avila-Herrera A, Kimbrel JA, Manuel Martí J, Thissen J, Saada EA, Weisenberger T, Arrildt KT, Segelke BW, Allen JE, Zemla A, Borucki MK. Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies. PLoS One 2024; 19:e0289198. [PMID: 38271318 PMCID: PMC10810540 DOI: 10.1371/journal.pone.0289198] [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: 07/12/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Viral populations in natural infections can have a high degree of sequence diversity, which can directly impact immune escape. However, antibody potency is often tested in vitro with a relatively clonal viral populations, such as laboratory virus or pseudotyped virus stocks, which may not accurately represent the genetic diversity of circulating viral genotypes. This can affect the validity of viral phenotype assays, such as antibody neutralization assays. To address this issue, we tested whether recombinant virus carrying SARS-CoV-2 spike (VSV-SARS-CoV-2-S) stocks could be made more genetically diverse by passage, and if a stock passaged under selective pressure was more capable of escaping monoclonal antibody (mAb) neutralization than unpassaged stock or than viral stock passaged without selective pressures. We passaged VSV-SARS-CoV-2-S four times concurrently in three cell lines and then six times with or without polyclonal antiserum selection pressure. All three of the monoclonal antibodies tested neutralized the viral population present in the unpassaged stock. The viral inoculum derived from serial passage without antiserum selection pressure was neutralized by two of the three mAbs. However, the viral inoculum derived from serial passage under antiserum selection pressure escaped neutralization by all three mAbs. Deep sequencing revealed the rapid acquisition of multiple mutations associated with antibody escape in the VSV-SARS-CoV-2-S that had been passaged in the presence of antiserum, including key mutations present in currently circulating Omicron subvariants. These data indicate that viral stock that was generated under polyclonal antiserum selection pressure better reflects the natural environment of the circulating virus and may yield more biologically relevant outcomes in phenotypic assays. Thus, mAb assessment assays that utilize a more genetically diverse, biologically relevant, virus stock may yield data that are relevant for prediction of mAb efficacy and for enhancing biosurveillance.
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Affiliation(s)
- Aram Avila-Herrera
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Jeffrey A. Kimbrel
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Jose Manuel Martí
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - James Thissen
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Edwin A. Saada
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Tracy Weisenberger
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Kathryn T. Arrildt
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Brent W. Segelke
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Jonathan E. Allen
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Adam Zemla
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Monica K. Borucki
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
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Lima Neto JX, Bezerra KS, Barbosa ED, Araujo RL, Galvão DS, Lyra ML, Oliveira JIN, Akash S, Jardan YAB, Nafidi HA, Bourhia M, Fulco UL. Investigation of protein-protein interactions and hotspot region on the NSP7-NSP8 binding site in NSP12 of SARS-CoV-2. Front Mol Biosci 2024; 10:1325588. [PMID: 38304231 PMCID: PMC10830813 DOI: 10.3389/fmolb.2023.1325588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024] Open
Abstract
Background: The RNA-dependent RNA polymerase (RdRp) complex, essential in viral transcription and replication, is a key target for antiviral therapeutics. The core unit of RdRp comprises the nonstructural protein NSP12, with NSP7 and two copies of NSP8 (NSP81 and NSP82) binding to NSP12 to enhance its affinity for viral RNA and polymerase activity. Notably, the interfaces between these subunits are highly conserved, simplifying the design of molecules that can disrupt their interaction. Methods: We conducted a detailed quantum biochemical analysis to characterize the interactions within the NSP12-NSP7, NSP12-NSP81, and NSP12-NSP82 dimers. Our objective was to ascertain the contribution of individual amino acids to these protein-protein interactions, pinpointing hotspot regions crucial for complex stability. Results: The analysis revealed that the NSP12-NSP81 complex possessed the highest total interaction energy (TIE), with 14 pairs of residues demonstrating significant energetic contributions. In contrast, the NSP12-NSP7 complex exhibited substantial interactions in 8 residue pairs, while the NSP12-NSP82 complex had only one pair showing notable interaction. The study highlighted the importance of hydrogen bonds and π-alkyl interactions in maintaining these complexes. Intriguingly, introducing the RNA sequence with Remdesivir into the complex resulted in negligible alterations in both interaction energy and geometric configuration. Conclusion: Our comprehensive analysis of the RdRp complex at the protein-protein interface provides invaluable insights into interaction dynamics and energetics. These findings can guide the design of small molecules or peptide/peptidomimetic ligands to disrupt these critical interactions, offering a strategic pathway for developing effective antiviral drugs.
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Affiliation(s)
- José Xavier Lima Neto
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Katyanna Sales Bezerra
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Emmanuel Duarte Barbosa
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Roniel Lima Araujo
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | | | | | - Jonas Ivan Nobre Oliveira
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Shopnil Akash
- Department of Pharmacy, Daffodil International University, Dhaka, Bangladesh
| | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec City, QC, Canada
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
| | - Umberto Laino Fulco
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
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36
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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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37
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Mellors J, Carroll M. Direct enhancement of viral neutralising antibody potency by the complement system: a largely forgotten phenomenon. Cell Mol Life Sci 2024; 81:22. [PMID: 38200235 PMCID: PMC10781860 DOI: 10.1007/s00018-023-05074-2] [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: 09/28/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 01/12/2024]
Abstract
Neutralisation assays are commonly used to assess vaccine-induced and naturally acquired immune responses; identify correlates of protection; and inform important decisions on the screening, development, and use of therapeutic antibodies. Neutralisation assays are useful tools that provide the gold standard for measuring the potency of neutralising antibodies, but they are not without limitations. Common methods such as the heat-inactivation of plasma samples prior to neutralisation assays, or the use of anticoagulants such as EDTA for blood collection, can inactivate the complement system. Even in non-heat-inactivated samples, the levels of complement activity can vary between samples. This can significantly impact the conclusions regarding neutralising antibody potency. Restoration of the complement system in these samples can be achieved using an exogenous source of plasma with preserved complement activity or with purified complement proteins. This can significantly enhance the neutralisation titres for some antibodies depending on characteristics such as antibody isotype and the epitope they bind, enable neutralisation with otherwise non-neutralising antibodies, and demonstrate a better relationship between in vitro and in vivo findings. In this review, we discuss the evidence for complement-mediated enhancement of antibody neutralisation against a range of viruses, explore the potential mechanisms which underpin this enhancement, highlight current gaps in the literature, and provide a brief summary of considerations for adopting this approach in future research applications.
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Affiliation(s)
- Jack Mellors
- Centre for Human Genetics and the Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Miles Carroll
- Centre for Human Genetics and the Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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38
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D’Acunto E, Muzi A, Marchese S, Donnici L, Chiarini V, Bucci F, Pavoni E, Ferrara FF, Cappelletti M, Arriga R, Serrao SM, Peluzzi V, Principato E, Compagnone M, Pinto E, Luberto L, Stoppoloni D, Lahm A, Groß R, Seidel A, Wettstein L, Münch J, Goodhead A, Parisot J, De Francesco R, Ciliberto G, Marra E, Aurisicchio L, Roscilli G. Isolation and Characterization of Neutralizing Monoclonal Antibodies from a Large Panel of Murine Antibodies against RBD of the SARS-CoV-2 Spike Protein. Antibodies (Basel) 2024; 13:5. [PMID: 38247569 PMCID: PMC10801580 DOI: 10.3390/antib13010005] [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: 11/15/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
The COVID-19 pandemic, once a global crisis, is now largely under control, a testament to the extraordinary global efforts involving vaccination and public health measures. However, the relentless evolution of SARS-CoV-2, leading to the emergence of new variants, continues to underscore the importance of remaining vigilant and adaptable. Monoclonal antibodies (mAbs) have stood out as a powerful and immediate therapeutic response to COVID-19. Despite the success of mAbs, the evolution of SARS-CoV-2 continues to pose challenges and the available antibodies are no longer effective. New variants require the ongoing development of effective antibodies. In the present study, we describe the generation and characterization of neutralizing mAbs against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein by combining plasmid DNA and recombinant protein vaccination. By integrating genetic immunization for rapid antibody production and the potent immune stimulation enabled by protein vaccination, we produced a rich pool of antibodies, each with unique binding and neutralizing specificities, tested with the ELISA, BLI and FACS assays and the pseudovirus assay, respectively. Here, we present a panel of mAbs effective against the SARS-CoV-2 variants up to Omicron BA.1 and BA.5, with the flexibility to target emerging variants. This approach ensures the preparedness principle is in place to address SARS-CoV-2 actual and future infections.
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Affiliation(s)
- Emanuela D’Acunto
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Alessia Muzi
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Silvia Marchese
- INGM-Istituto Nazionale di Genetica Molecolare “Romeo ed Erica Invernizzi”, 20122 Milan, Italy; (S.M.); (L.D.); (R.D.F.)
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | - Lorena Donnici
- INGM-Istituto Nazionale di Genetica Molecolare “Romeo ed Erica Invernizzi”, 20122 Milan, Italy; (S.M.); (L.D.); (R.D.F.)
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | | | - Federica Bucci
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Emiliano Pavoni
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Fabiana Fosca Ferrara
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Manuela Cappelletti
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Roberto Arriga
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Silvia Maria Serrao
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Valentina Peluzzi
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
- Department of Engineering, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Eugenia Principato
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
- Department of Experimental and Clinical Medicine, University Magna Graecia, 88100 Catanzaro, Italy
| | | | - Eleonora Pinto
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Laura Luberto
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Daniela Stoppoloni
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Armin Lahm
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.G.); (A.S.); (J.M.)
| | - Alina Seidel
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.G.); (A.S.); (J.M.)
| | - Lukas Wettstein
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.G.); (A.S.); (J.M.)
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.G.); (A.S.); (J.M.)
| | - Andrew Goodhead
- Carterra, 825 N. 300 W., Suite C309, Salt Lake City, UT 84103, USA; (A.G.); (J.P.)
| | - Judicael Parisot
- Carterra, 825 N. 300 W., Suite C309, Salt Lake City, UT 84103, USA; (A.G.); (J.P.)
| | - Raffaele De Francesco
- INGM-Istituto Nazionale di Genetica Molecolare “Romeo ed Erica Invernizzi”, 20122 Milan, Italy; (S.M.); (L.D.); (R.D.F.)
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | - Gennaro Ciliberto
- Tumor Immunology and Immunotherapy Unit, IRCSS Regina Elena National Cancer Institute, 00144 Rome, Italy;
| | - Emanuele Marra
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Luigi Aurisicchio
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
| | - Giuseppe Roscilli
- Takis Biotech, 00128 Rome, Italy; (A.M.); (F.B.); (E.P.); (F.F.F.); (M.C.); (R.A.); (S.M.S.); (V.P.); (E.P.); (E.P.); (L.L.); (D.S.); (A.L.); (E.M.); (L.A.)
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39
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Gallucci L, Bazire J, Davidson AD, Shytaj IL. Broad-spectrum antiviral activity of two structurally analogous CYP3A inhibitors against pathogenic human coronaviruses in vitro. Antiviral Res 2024; 221:105766. [PMID: 38042417 DOI: 10.1016/j.antiviral.2023.105766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 12/04/2023]
Abstract
Coronaviruses pose a permanent risk of outbreaks, with three highly pathogenic species and strains (SARS-CoV, MERS-CoV, SARS-CoV-2) having emerged in the last twenty years. Limited antiviral therapies are currently available and their efficacy in randomized clinical trials enrolling SARS-CoV-2 patients has not been consistent, highlighting the need for more potent treatments. We previously showed that cobicistat, a clinically approved inhibitor of Cytochrome P450-3A (CYP3A), has direct antiviral activity against early circulating SARS-CoV-2 strains in vitro and in Syrian hamsters. Cobicistat is a derivative of ritonavir, which is co-administered as pharmacoenhancer with the SARS-CoV-2 protease inhibitor nirmatrelvir, to inhibit its metabolization by CPY3A and preserve its antiviral efficacy. Here, we used automated image analysis for a screening and parallel comparison of the anti-coronavirus effects of cobicistat and ritonavir. Our data show that both drugs display antiviral activity at low micromolar concentrations against multiple SARS-CoV-2 variants in vitro, including epidemiologically relevant Omicron subvariants. Despite their close structural similarity, we found that cobicistat is more potent than ritonavir, as shown by significantly lower EC50 values in monotherapy and higher levels of viral suppression when used in combination with nirmatrelvir. Finally, we show that the antiviral activity of both cobicistat and ritonavir is maintained against other human coronaviruses, including HCoV-229E and the highly pathogenic MERS-CoV. Overall, our results demonstrate that cobicistat has more potent anti-coronavirus activity than ritonavir and suggest that dose adjustments could pave the way to the use of both drugs as broad-spectrum antivirals against highly pathogenic human coronaviruses.
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Affiliation(s)
- Lara Gallucci
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - James Bazire
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
| | - Iart Luca Shytaj
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
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40
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Infante MS, Nemirovsky D, Devlin S, DeWolf S, Tamari R, Dahi PB, Lee YJ, Chung DJ, Politikos I, Barker J, Giralt SA, Babady NE, Ramanathan L, Papanicolaou GA, Seo S, Kamboj M, Perales MA, Shah GL. Outcomes and Management of the SARS-CoV2 Omicron Variant in Recipients of Hematopoietic Cell Transplantation and Chimeric Antigen Receptor T Cell Therapy. Transplant Cell Ther 2024; 30:116.e1-116.e12. [PMID: 37806446 DOI: 10.1016/j.jtct.2023.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/10/2023]
Abstract
Hematopoietic cell transplantation (HCT) and chimeric antigen receptor T cell therapy (CAR-T) recipients who develop Coronavirus disease 2019 (COVID-19) can have decreased overall survival (OS), likely due to disease-inherent and therapy-related immunodeficiency. The availability of COVID-19-directed therapies and vaccines have improved COVID-19-related outcomes, but immunocompromised individuals remain vulnerable. Specifically, the effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant infections, including Omicron and its sublineages, particularly in HCT recipients, remain to be defined. The aim of this study was to compare the impact of SARS-CoV-2 Omicron infections in HCT/CAR-T recipients with outcomes previously reported for ancestral SARS-CoV-2 infections early in the pandemic (March to June 2020). This was a retrospective analysis of adult HCT/CAR-T recipients diagnosed with COVID-19 at Memorial Sloan Kettering Cancer Center between July 2021 and July 2022. We identified 353 patients (172 autologous HCT recipients [49%], 152 allogeneic HCT recipients [43%], and 29 CAR-T recipients [8%]), with a median time from HCT/CAR-T to SARS-CoV-2 infection of 1010 days (interquartile range, 300 to 2046 days). Forty-one patients (12%) were diagnosed with COVID-19 during the delta wave, and 312 patients (88%) were diagnosed during the Omicron wave. Risk factors associated with increased odds of COVID-19-related hospitalization were the presence of 2 or more comorbidities (odds ratio [OR], 4.9; 95% confidence interval [CI], 2.4 to 10.7; P < .001), CAR-T therapy compared to allogeneic HCT (OR, 7.7; 95% CI, 3.0 to 20.0; P < .001), hypogammaglobulinemia (OR, 2.71; 95% CI, 1.06 to 6.40; P = .027), and age at COVID-19 diagnosis (OR, 1.03; 95% CI, 1.0 to 1.05; P = .04). In contrast, infection during the Omicron variant BA5/BA4-dominant period compared to variant BA1 (OR, .21; 95% CI, .03 to .73; P = .037) and more than 3 years from HCT/CAR-T therapy to COVID-19 diagnosis compared to early infection at <100 days (OR, .31; 95% CI, .12 to .79; P = .011) were associated with a decreased odds for hospitalization. The OS at 12 months from COVID-19 diagnosis was 89% (95% CI, 84% to 94%), with 6 of 26 deaths attributable to COVID-19. Patients with the ancestral strain of SAR-CoV-2 had a lower OS at 12 months, with 73% (95% CI, 62% to 84%) versus 89% (95% CI, 84% to 94%; P < .001) in the Omicron cohort. Specific COVID-19 treatment was administered in 62% of patients, and 84% were vaccinated with mRNA COVID-19 vaccines. Vaccinated patients had significantly better OS than unvaccinated patients (90% [95% CI, 86% to 95%] versus 82% [95% CI, 72% to 94%] at 12 months; P = .003). No significant difference in OS was observed in patients infected with the Omicron and those infected with the Delta variant (P = .4) or treated with specific COVID-19 treatments compared with those not treated (P = .2). We observed higher OS in HCT and CAR-T recipients infected with the Omicron variants compared to those infected with the ancestral strain of SARS-CoV2. The use of COVID-19 antivirals, mAbs, and vaccines might have contributed to the improved outcomes.
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Affiliation(s)
- Maria-Stefania Infante
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; University Hospital Infanta Leonor, Madrid, Spain.
| | - David Nemirovsky
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sean Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan DeWolf
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Roni Tamari
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Parastoo B Dahi
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Yeon Joo Lee
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - David J Chung
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Ioannis Politikos
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Juliet Barker
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Sergio A Giralt
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - N Esther Babady
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial SLoan Kettering Cancer Center, New York, New York
| | - Lakshmi Ramanathan
- Clinical Chemistry Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Genovefa A Papanicolaou
- Department of Medicine, Weill Cornell Medical College, New York, New York; Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan Seo
- Department of Medicine, Weill Cornell Medical College, New York, New York; Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mini Kamboj
- Department of Medicine, Weill Cornell Medical College, New York, New York; Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Miguel-Angel Perales
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Gunjan L Shah
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
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41
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Yisimayi A, Song W, Wang J, Jian F, Yu Y, Chen X, Xu Y, Yang S, Niu X, Xiao T, Wang J, Zhao L, Sun H, An R, Zhang N, Wang Y, Wang P, Yu L, Lv Z, Gu Q, Shao F, Jin R, Shen Z, Xie XS, Wang Y, Cao Y. Repeated Omicron exposures override ancestral SARS-CoV-2 immune imprinting. Nature 2024; 625:148-156. [PMID: 37993710 PMCID: PMC10764275 DOI: 10.1038/s41586-023-06753-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/17/2023] [Indexed: 11/24/2023]
Abstract
The continuing emergence of SARS-CoV-2 variants highlights the need to update COVID-19 vaccine compositions. However, immune imprinting induced by vaccination based on the ancestral (hereafter referred to as WT) strain would compromise the antibody response to Omicron-based boosters1-5. Vaccination strategies to counter immune imprinting are critically needed. Here we investigated the degree and dynamics of immune imprinting in mouse models and human cohorts, especially focusing on the role of repeated Omicron stimulation. In mice, the efficacy of single Omicron boosting is heavily limited when using variants that are antigenically distinct from WT-such as the XBB variant-and this concerning situation could be mitigated by a second Omicron booster. Similarly, in humans, repeated Omicron infections could alleviate WT vaccination-induced immune imprinting and generate broad neutralization responses in both plasma and nasal mucosa. Notably, deep mutational scanning-based epitope characterization of 781 receptor-binding domain (RBD)-targeting monoclonal antibodies isolated from repeated Omicron infection revealed that double Omicron exposure could induce a large proportion of matured Omicron-specific antibodies that have distinct RBD epitopes to WT-induced antibodies. Consequently, immune imprinting was largely mitigated, and the bias towards non-neutralizing epitopes observed in single Omicron exposures was restored. On the basis of the deep mutational scanning profiles, we identified evolution hotspots of XBB.1.5 RBD and demonstrated that these mutations could further boost the immune-evasion capability of XBB.1.5 while maintaining high ACE2-binding affinity. Our findings suggest that the WT component should be abandoned when updating COVID-19 vaccines, and individuals without prior Omicron exposure should receive two updated vaccine boosters.
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Affiliation(s)
- Ayijiang Yisimayi
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Weiliang Song
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Jing Wang
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Fanchong Jian
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | | | - Xiaosu Chen
- Institute for Immunology, College of Life Sciences, Nankai University, Tianjin, P. R. China
| | - Yanli Xu
- Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
| | - Sijie Yang
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, P. R. China
| | - Xiao Niu
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Tianhe Xiao
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Joint Graduate Program of Peking-Tsinghua-NIBS, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P. R. China
| | - Jing Wang
- Changping Laboratory, Beijing, P. R. China
| | | | - Haiyan Sun
- Changping Laboratory, Beijing, P. R. China
| | - Ran An
- Changping Laboratory, Beijing, P. R. China
| | - Na Zhang
- Changping Laboratory, Beijing, P. R. China
| | - Yao Wang
- Changping Laboratory, Beijing, P. R. China
| | - Peng Wang
- Changping Laboratory, Beijing, P. R. China
| | | | - Zhe Lv
- Sinovac Biotech, Beijing, P. R. China
| | | | - Fei Shao
- Changping Laboratory, Beijing, P. R. China
| | - Ronghua Jin
- Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
| | - Zhongyang Shen
- Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, P. R. China
| | - Xiaoliang Sunney Xie
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Youchun Wang
- Changping Laboratory, Beijing, P. R. China
- Institute of Medical Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, P. R. China
| | - Yunlong Cao
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China.
- Changping Laboratory, Beijing, P. R. China.
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42
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Wang Y, Cao B. The insights from SARS-CoV-2 antibody treatment for future emerging infectious diseases. THE LANCET. INFECTIOUS DISEASES 2024; 24:2-3. [PMID: 37619583 DOI: 10.1016/s1473-3099(23)00454-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 08/26/2023]
Affiliation(s)
- Yeming Wang
- National Center for Respiratory Medicine, Beijing, China; State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China; National Clinical Research Center for Respiratory Diseases, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Bin Cao
- National Center for Respiratory Medicine, Beijing, China; State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China; National Clinical Research Center for Respiratory Diseases, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing 100029, China.
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43
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Aksu M, Kumar P, Güttler T, Taxer W, Gregor K, Mußil B, Rymarenko O, Stegmann KM, Dickmanns A, Gerber S, Reineking W, Schulz C, Henneck T, Mohamed A, Pohlmann G, Ramazanoglu M, Mese K, Groß U, Ben-Yedidia T, Ovadia O, Fischer DW, Kamensky M, Reichman A, Baumgärtner W, von Köckritz-Blickwede M, Dobbelstein M, Görlich D. Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters. Antiviral Res 2024; 221:105778. [PMID: 38065245 DOI: 10.1016/j.antiviral.2023.105778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/23/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
The ongoing threat of COVID-19 has highlighted the need for effective prophylaxis and convenient therapies, especially for outpatient settings. We have previously developed highly potent single-domain (VHH) antibodies, also known as nanobodies, that target the Receptor Binding Domain (RBD) of the SARS-CoV-2 Spike protein and neutralize the Wuhan strain of the virus. In this study, we present a new generation of anti-RBD nanobodies with superior properties. The primary representative of this group, Re32D03, neutralizes Alpha to Delta as well as Omicron BA.2.75; other members neutralize, in addition, Omicron BA.1, BA.2, BA.4/5, and XBB.1. Crystal structures of RBD-nanobody complexes reveal how ACE2-binding is blocked and also explain the nanobodies' tolerance to immune escape mutations. Through the cryo-EM structure of the Ma16B06-BA.1 Spike complex, we demonstrated how a single nanobody molecule can neutralize a trimeric spike. We also describe a method for large-scale production of these nanobodies in Pichia pastoris, and for formulating them into aerosols. Exposing hamsters to these aerosols, before or even 24 h after infection with SARS-CoV-2, significantly reduced virus load, weight loss and pathogenicity. These results show the potential of aerosolized nanobodies for prophylaxis and therapy of coronavirus infections.
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Affiliation(s)
- Metin Aksu
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Priya Kumar
- University Medical Center Göttingen, Dept. of Molecular Oncology, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Thomas Güttler
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany; Octapharma Biopharmaceuticals GmbH, Im Neuenheimer Feld 590, 69120 Heidelberg, Germany
| | - Waltraud Taxer
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kathrin Gregor
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Bianka Mußil
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Oleh Rymarenko
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kim M Stegmann
- University Medical Center Göttingen, Dept. of Molecular Oncology, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Antje Dickmanns
- University Medical Center Göttingen, Dept. of Molecular Oncology, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Sabrina Gerber
- University Medical Center Göttingen, Dept. of Molecular Oncology, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Wencke Reineking
- Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Claudia Schulz
- Research Center for Emerging Infections and Zoonosis (RIZ), University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Timo Henneck
- Research Center for Emerging Infections and Zoonosis (RIZ), University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany; Department of Biochemistry, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Ahmed Mohamed
- Research Center for Emerging Infections and Zoonosis (RIZ), University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany; Department of Biochemistry, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Gerhard Pohlmann
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Nikolai-Fuchs Str. 1, 30625 Hannover, Germany
| | - Mehmet Ramazanoglu
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Nikolai-Fuchs Str. 1, 30625 Hannover, Germany
| | - Kemal Mese
- University Medical Center Göttingen, Dept. of Medical Microbiology and Virology, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Uwe Groß
- University Medical Center Göttingen, Dept. of Medical Microbiology and Virology, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Tamar Ben-Yedidia
- Scinai Immunotherapeutics Ltd., Jerusalem BioPark, Hadassah Ein Kerem, Jerusalem, 9112001, Israel
| | - Oded Ovadia
- Scinai Immunotherapeutics Ltd., Jerusalem BioPark, Hadassah Ein Kerem, Jerusalem, 9112001, Israel
| | - Dalit Weinstein Fischer
- Scinai Immunotherapeutics Ltd., Jerusalem BioPark, Hadassah Ein Kerem, Jerusalem, 9112001, Israel
| | - Merav Kamensky
- Scinai Immunotherapeutics Ltd., Jerusalem BioPark, Hadassah Ein Kerem, Jerusalem, 9112001, Israel
| | - Amir Reichman
- Scinai Immunotherapeutics Ltd., Jerusalem BioPark, Hadassah Ein Kerem, Jerusalem, 9112001, Israel
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Maren von Köckritz-Blickwede
- Research Center for Emerging Infections and Zoonosis (RIZ), University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany; Department of Biochemistry, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Matthias Dobbelstein
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany; University Medical Center Göttingen, Dept. of Molecular Oncology, Justus von Liebig Weg 11, 37077 Göttingen, Germany.
| | - Dirk Görlich
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany.
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Pradhan S, Swanson CJ, Leff C, Tengganu I, Bergeman MH, Wisna GBM, Hogue IB, Hariadi RF. Viral Attachment Blocking Chimera Composed of DNA Origami and Nanobody Inhibits Pseudorabies Virus Infection In Vitro. ACS NANO 2023; 17:23317-23330. [PMID: 37982733 PMCID: PMC10787579 DOI: 10.1021/acsnano.3c01408] [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] [Indexed: 11/21/2023]
Abstract
Antivirals are indispensable tools that can be targeted at viral domains directly or at cellular domains indirectly to obstruct viral infections and reduce pathogenicity. Despite their transformative use in healthcare, antivirals have been clinically approved to treat only 10 of the more than 200 known pathogenic human viruses. Additionally, many virus functions are intimately coupled with host cellular processes, which presents challenges in antiviral development due to the limited number of clear targets per virus, necessitating extensive insight into these molecular processes. Compounding this challenge, many viral pathogens have evolved to evade effective antivirals. We hypothesize that a viral attachment blocking chimera (VirABloC) composed of a viral binder and a bulky scaffold that sterically blocks interactions between a viral particle and a host cell may be suitable for the development of antivirals that are agnostic to the extravirion epitope that is being bound. We test this hypothesis by modifying a nanobody that specifically recognizes a nonessential epitope presented on the extravirion surface of pseudorabies virus strain 486 with a 3-dimensional wireframe DNA origami structure ∼100 nm in diameter. The nanobody switches from having no inhibitory properties to 4.2 ± 0.9 nM IC50 when conjugated with the DNA origami scaffold. Mechanistic studies support that inhibition is mediated by the noncovalent attachment of the DNA origami scaffold to the virus particle, which obstructs the attachment of the viruses onto host cells. These results support the potential of VirABloC as a generalizable approach to developing antivirals.
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Affiliation(s)
- Swechchha Pradhan
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85281, United States
| | - Carter J Swanson
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85281, United States
| | - Chloe Leff
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85281, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
| | - Isadonna Tengganu
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85281, United States
| | - Melissa H Bergeman
- School of Life Science, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, Arizona 85281, United States
| | - Gde B M Wisna
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85281, United States
- Department of Physics, Arizona State University, Tempe, Arizona 85281, United States
| | - Ian B Hogue
- School of Life Science, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, Arizona 85281, United States
| | - Rizal F Hariadi
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85281, United States
- Department of Physics, Arizona State University, Tempe, Arizona 85281, United States
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Niwa R, Sakai K, Lung MSY, Matsumoto T, Mikawa R, Maehana S, Suzuki M, Yamamoto Y, Maurissen TL, Hirabayashi A, Noda T, Kubo M, Gotoh S, Woltjen K. ACE2 knockout hinders SARS-CoV-2 propagation in iPS cell-derived airway and alveolar epithelial cells. Front Cell Dev Biol 2023; 11:1290876. [PMID: 38149046 PMCID: PMC10750251 DOI: 10.3389/fcell.2023.1290876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/26/2023] [Indexed: 12/28/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, continues to spread around the world with serious cases and deaths. It has also been suggested that different genetic variants in the human genome affect both the susceptibility to infection and severity of disease in COVID-19 patients. Angiotensin-converting enzyme 2 (ACE2) has been identified as a cell surface receptor for SARS-CoV and SARS-CoV-2 entry into cells. The construction of an experimental model system using human iPS cells would enable further studies of the association between viral characteristics and genetic variants. Airway and alveolar epithelial cells are cell types of the lung that express high levels of ACE2 and are suitable for in vitro infection experiments. Here, we show that human iPS cell-derived airway and alveolar epithelial cells are highly susceptible to viral infection of SARS-CoV-2. Using gene knockout with CRISPR-Cas9 in human iPS cells we demonstrate that ACE2 plays an essential role in the airway and alveolar epithelial cell entry of SARS-CoV-2 in vitro. Replication of SARS-CoV-2 was strongly suppressed in ACE2 knockout (KO) lung cells. Our model system based on human iPS cell-derived lung cells may be applied to understand the molecular biology regulating viral respiratory infection leading to potential therapeutic developments for COVID-19 and the prevention of future pandemics.
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Affiliation(s)
- Ryo Niwa
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kouji Sakai
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mandy Siu Yu Lung
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Tomoko Matsumoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ryuta Mikawa
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shotaro Maehana
- Department of Microbiology, Kitasato University School of Allied Health Sciences, Kanagawa, Japan
- Regenerative Medicine and Cell Design Research Facility, Kitasato University School of Allied Health Sciences, Kanagawa, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuki Yamamoto
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Thomas L. Maurissen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ai Hirabayashi
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Makoto Kubo
- Department of Microbiology, Kitasato University School of Allied Health Sciences, Kanagawa, Japan
- Regenerative Medicine and Cell Design Research Facility, Kitasato University School of Allied Health Sciences, Kanagawa, Japan
| | - Shimpei Gotoh
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
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46
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Guo H, Cho B, Hinton PR, He S, Yu Y, Ramesh AK, Sivaccumar JP, Ku Z, Campo K, Holland S, Sachdeva S, Mensch C, Dawod M, Whitaker A, Eisenhauer P, Falcone A, Honce R, Botten JW, Carroll SF, Keyt BA, Womack AW, Strohl WR, Xu K, Zhang N, An Z, Ha S, Shiver JW, Fu TM. An ACE2 decamer viral trap as a durable intervention solution for current and future SARS-CoV. Emerg Microbes Infect 2023; 12:2275598. [PMID: 38078382 PMCID: PMC10768737 DOI: 10.1080/22221751.2023.2275598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/19/2023] [Indexed: 12/18/2023]
Abstract
The capacity of SARS-CoV-2 to evolve poses challenges to conventional prevention and treatment options such as vaccination and monoclonal antibodies, as they rely on viral receptor binding domain (RBD) sequences from previous strains. Additionally, animal CoVs, especially those of the SARS family, are now appreciated as a constant pandemic threat. We present here a new antiviral approach featuring inhalation delivery of a recombinant viral trap composed of ten copies of angiotensin-converting enzyme 2 (ACE2) fused to the IgM Fc. This ACE2 decamer viral trap is designed to inhibit SARS-CoV-2 entry function, regardless of viral RBD sequence variations as shown by its high neutralization potency against all known SARS-CoV-2 variants, including Omicron BQ.1, BQ.1.1, XBB.1 and XBB.1.5. In addition, it demonstrates potency against SARS-CoV-1, human NL63, as well as bat and pangolin CoVs. The multivalent trap is effective in both prophylactic and therapeutic settings since a single intranasal dosing confers protection in human ACE2 transgenic mice against viral challenges. Lastly, this molecule is stable at ambient temperature for more than twelve weeks and can sustain physical stress from aerosolization. These results demonstrate the potential of a decameric ACE2 viral trap as an inhalation solution for ACE2-dependent coronaviruses of current and future pandemic concerns.
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Affiliation(s)
| | | | | | - Sijia He
- IGM Biosciences, Mountain View, CA, USA
| | | | - Ashwin Kumar Ramesh
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jwala Priyadarsini Sivaccumar
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | | | | | | | | | - Annalis Whitaker
- Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT, USA
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
| | - Philip Eisenhauer
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
| | - Allison Falcone
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
| | - Rebekah Honce
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
| | - Jason W. Botten
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | | | | | | | | | - Kai Xu
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sha Ha
- IGM Biosciences, Mountain View, CA, USA
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de Souza AS, de Souza RF, Guzzo CR. Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1). J Comput Aided Mol Des 2023; 37:585-606. [PMID: 37792106 DOI: 10.1007/s10822-023-00534-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023]
Abstract
Herein, we conducted simulations of trimeric Spike from several SARS-CoV-2 variants of concern (Delta and Omicron sub-variants BA.2, BA.5, and BQ.1) and investigated the mechanisms by which specific mutations confer resistance to neutralizing antibodies. We observed that the mutations primarily affect the cooperation between protein domains within and between protomers. The substitutions K417N and L452R expand hydrogen bonding interactions, reducing their interaction with neutralizing antibodies. By interacting with nearby residues, the K444T and N460K mutations in the SpikeBQ.1 variant potentially reduces solvent exposure, thereby promoting resistance to antibodies. We also examined the impact of D614G, P681R, and P681H substitutions on Spike protein structure that may be related to infectivity. The D614G substitution influences communication between a glycine residue and neighboring domains, affecting the transition between up- and -down RBD states. The P681R mutation, found in the Delta variant, enhances correlations between protein subunits, while the P681H mutation in Omicron sub-variants weakens long-range interactions that may be associated with reduced fusogenicity. Using a multiple linear regression model, we established a connection between inter-protomer communication and loss of sensitivity to neutralizing antibodies. Our findings underscore the importance of structural communication between protein domains and provide insights into potential mechanisms of immune evasion by SARS-CoV-2. Overall, this study deepens our understanding of how specific mutations impact SARS-CoV-2 infectivity and shed light on how the virus evades the immune system.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil.
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil.
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Funk MA, Leitner J, Gerner MC, Hammerler JM, Salzer B, Lehner M, Battin C, Gumpelmair S, Stiasny K, Grabmeier-Pfistershammer K, Steinberger P. Interrogating ligand-receptor interactions using highly sensitive cellular biosensors. Nat Commun 2023; 14:7804. [PMID: 38016944 PMCID: PMC10684770 DOI: 10.1038/s41467-023-43589-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
Interactions of membrane-resident proteins are important targets for therapeutic interventions but most methods to study them are either costly, laborious or fail to reflect the physiologic interaction of membrane resident proteins in trans. Here we describe highly sensitive cellular biosensors as a tool to study receptor-ligand pairs. They consist of fluorescent reporter cells that express chimeric receptors harboring ectodomains of cell surface molecules and intracellular signaling domains. We show that a broad range of molecules can be integrated into this platform and we demonstrate its applicability to highly relevant research areas, including the characterization of immune checkpoints and the probing of cells for the presence of receptors or ligands. The platform is suitable to evaluate the interactions of viral proteins with host receptors and to test for neutralization capability of drugs or biological samples. Our results indicate that cellular biosensors have broad utility as a tool to study protein-interactions.
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Affiliation(s)
- Maximilian A Funk
- Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Division for Immune Receptors and T cell activation, Medical University of Vienna, Vienna, Austria
| | - Judith Leitner
- Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Division for Immune Receptors and T cell activation, Medical University of Vienna, Vienna, Austria.
| | - Marlene C Gerner
- Division of Biomedical Science, University of Applied Sciences FH Campus Wien, Vienna, Austria
| | - Jasmin M Hammerler
- Division of Biomedical Science, University of Applied Sciences FH Campus Wien, Vienna, Austria
| | - Benjamin Salzer
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- Christian Doppler Laboratory for Next Generation CAR T Cells, Vienna, Austria
| | - Manfred Lehner
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- Christian Doppler Laboratory for Next Generation CAR T Cells, Vienna, Austria
| | - Claire Battin
- Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Division for Immune Receptors and T cell activation, Medical University of Vienna, Vienna, Austria
| | - Simon Gumpelmair
- Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Division for Immune Receptors and T cell activation, Medical University of Vienna, Vienna, Austria
| | - Karin Stiasny
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | | | - Peter Steinberger
- Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Division for Immune Receptors and T cell activation, Medical University of Vienna, Vienna, Austria.
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Chaves-Blanco L, de Salazar A, Fuentes A, Viñuela L, Perez-Florido J, Dopazo J, García F. Evaluation of a combined detection of SARS-CoV-2 and its variants using real-time allele-specific PCR strategy: an advantage for clinical practice. Epidemiol Infect 2023; 151:e201. [PMID: 37997654 PMCID: PMC10753446 DOI: 10.1017/s095026882300184x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/08/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023] Open
Abstract
This study aimed to assess the ability of a real-time reverse transcription polymerase chain reaction (RT-PCR) with multiple targets to detect SARS-CoV-2 and its variants in a single test. Nasopharyngeal specimens were collected from patients in Granada, Spain, between January 2021 and December 2022. Five allele-specific RT-PCR kits were used sequentially, with each kit designed to detect a predominant variant at the time. When the Alpha variant was dominant, the kit included the HV69/70 deletion, E and N genes. When Delta replaced Alpha, the kit incorporated the L452R mutation in addition to E and N genes. When Omicron became dominant, L452R was replaced with the N679K mutation. Before incorporating each variant kit, a comparative analysis was carried out with SARS-CoV-2 whole genome sequencing (WGS). The results demonstrated that RT-PCR with multiple targets can provide rapid and effective detection of SARS-CoV-2 and its variants in a single test. A very high degree of agreement (96.2%) was obtained between the comparison of RT-PCR and WGS. Allele-specific RT-PCR assays make it easier to implement epidemiological surveillance systems for effective public health decision making.
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Affiliation(s)
- Lucía Chaves-Blanco
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
| | - Adolfo de Salazar
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Ana Fuentes
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Laura Viñuela
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Javier Perez-Florido
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Sevilla, Sevilla, Spain
| | - Joaquín Dopazo
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Sevilla, Sevilla, Spain
- FPS/ELIXIR-ES, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, Sevilla, Spain
| | - Federico García
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
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50
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Lorenzo-Redondo R, de Sant’Anna Carvalho AM, Hultquist JF, Ozer EA. SARS-CoV-2 genomics and impact on clinical care for COVID-19. J Antimicrob Chemother 2023; 78:ii25-ii36. [PMID: 37995357 PMCID: PMC10667012 DOI: 10.1093/jac/dkad309] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/02/2023] [Indexed: 11/25/2023] Open
Abstract
The emergence and worldwide spread of SARS-CoV-2 during the COVID-19 pandemic necessitated the adaptation and rapid deployment of viral WGS and analysis techniques that had been previously applied on a more limited basis to other viral pathogens, such as HIV and influenza viruses. The need for WGS was driven in part by the low mutation rate of SARS-CoV-2, which necessitated measuring variation along the entire genome sequence to effectively differentiate lineages and characterize viral evolution. Several WGS approaches designed to maximize throughput and accuracy were quickly adopted by surveillance labs around the world. These broad-based SARS-CoV-2 genomic sequencing efforts revealed ongoing evolution of the virus, highlighted by the successive emergence of new viral variants throughout the course of the pandemic. These genomic insights were instrumental in characterizing the effects of viral mutations on transmissibility, immune escape and viral tropism, which in turn helped guide public health policy, the use of monoclonal antibody therapeutics and vaccine development strategies. As the use of direct-acting antivirals for the treatment of COVID-19 became more widespread, the potential for emergence of antiviral resistance has driven ongoing efforts to delineate resistance mutations and to monitor global sequence databases for their emergence. Given the critical role of viral genomics in the international effort to combat the COVID-19 pandemic, coordinated efforts should be made to expand global genomic surveillance capacity and infrastructure towards the anticipation and prevention of future pandemics.
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Affiliation(s)
- Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Alexandre Machado de Sant’Anna Carvalho
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
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