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      ChAdOx1 interacts with CAR and PF4 with implications for thrombosis with thrombocytopenia syndrome

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          Abstract

          Abstract

          We observe previously unknown interactions between clinically important adenovirus vector capsids, platelet factor 4, and CAR.

          Abstract

          Vaccines derived from chimpanzee adenovirus Y25 (ChAdOx1), human adenovirus type 26 (HAdV-D26), and human adenovirus type 5 (HAdV-C5) are critical in combatting the severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic. As part of the largest vaccination campaign in history, ultrarare side effects not seen in phase 3 trials, including thrombosis with thrombocytopenia syndrome (TTS), a rare condition resembling heparin-induced thrombocytopenia (HIT), have been observed. This study demonstrates that all three adenoviruses deployed as vaccination vectors versus SARS-CoV-2 bind to platelet factor 4 (PF4), a protein implicated in the pathogenesis of HIT. We have determined the structure of the ChAdOx1 viral vector and used it in state-of-the-art computational simulations to demonstrate an electrostatic interaction mechanism with PF4, which was confirmed experimentally by surface plasmon resonance. These data confirm that PF4 is capable of forming stable complexes with clinically relevant adenoviruses, an important step in unraveling the mechanisms underlying TTS.

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          VMD: Visual molecular dynamics

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            SWISS-MODEL: homology modelling of protein structures and complexes

            Abstract Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated workflows and servers simplify and streamline the homology modelling process, also allowing users without a specific computational expertise to generate reliable protein models and have easy access to modelling results, their visualization and interpretation. Here, we present an update to the SWISS-MODEL server, which pioneered the field of automated modelling 25 years ago and been continuously further developed. Recently, its functionality has been extended to the modelling of homo- and heteromeric complexes. Starting from the amino acid sequences of the interacting proteins, both the stoichiometry and the overall structure of the complex are inferred by homology modelling. Other major improvements include the implementation of a new modelling engine, ProMod3 and the introduction a new local model quality estimation method, QMEANDisCo. SWISS-MODEL is freely available at https://swissmodel.expasy.org.
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              Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK

              Background A safe and efficacious vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), if deployed with high coverage, could contribute to the control of the COVID-19 pandemic. We evaluated the safety and efficacy of the ChAdOx1 nCoV-19 vaccine in a pooled interim analysis of four trials. Methods This analysis includes data from four ongoing blinded, randomised, controlled trials done across the UK, Brazil, and South Africa. Participants aged 18 years and older were randomly assigned (1:1) to ChAdOx1 nCoV-19 vaccine or control (meningococcal group A, C, W, and Y conjugate vaccine or saline). Participants in the ChAdOx1 nCoV-19 group received two doses containing 5 × 1010 viral particles (standard dose; SD/SD cohort); a subset in the UK trial received a half dose as their first dose (low dose) and a standard dose as their second dose (LD/SD cohort). The primary efficacy analysis included symptomatic COVID-19 in seronegative participants with a nucleic acid amplification test-positive swab more than 14 days after a second dose of vaccine. Participants were analysed according to treatment received, with data cutoff on Nov 4, 2020. Vaccine efficacy was calculated as 1 - relative risk derived from a robust Poisson regression model adjusted for age. Studies are registered at ISRCTN89951424 and ClinicalTrials.gov, NCT04324606, NCT04400838, and NCT04444674. Findings Between April 23 and Nov 4, 2020, 23 848 participants were enrolled and 11 636 participants (7548 in the UK, 4088 in Brazil) were included in the interim primary efficacy analysis. In participants who received two standard doses, vaccine efficacy was 62·1% (95% CI 41·0–75·7; 27 [0·6%] of 4440 in the ChAdOx1 nCoV-19 group vs71 [1·6%] of 4455 in the control group) and in participants who received a low dose followed by a standard dose, efficacy was 90·0% (67·4–97·0; three [0·2%] of 1367 vs 30 [2·2%] of 1374; p interaction =0·010). Overall vaccine efficacy across both groups was 70·4% (95·8% CI 54·8–80·6; 30 [0·5%] of 5807 vs 101 [1·7%] of 5829). From 21 days after the first dose, there were ten cases hospitalised for COVID-19, all in the control arm; two were classified as severe COVID-19, including one death. There were 74 341 person-months of safety follow-up (median 3·4 months, IQR 1·3–4·8): 175 severe adverse events occurred in 168 participants, 84 events in the ChAdOx1 nCoV-19 group and 91 in the control group. Three events were classified as possibly related to a vaccine: one in the ChAdOx1 nCoV-19 group, one in the control group, and one in a participant who remains masked to group allocation. Interpretation ChAdOx1 nCoV-19 has an acceptable safety profile and has been found to be efficacious against symptomatic COVID-19 in this interim analysis of ongoing clinical trials. Funding UK Research and Innovation, National Institutes for Health Research (NIHR), Coalition for Epidemic Preparedness Innovations, Bill & Melinda Gates Foundation, Lemann Foundation, Rede D’Or, Brava and Telles Foundation, NIHR Oxford Biomedical Research Centre, Thames Valley and South Midland's NIHR Clinical Research Network, and AstraZeneca.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: VisualizationRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: ValidationRole: VisualizationRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: Formal analysisRole: Methodology
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: MethodologyRole: ResourcesRole: SoftwareRole: VisualizationRole: Writing - review & editing
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: ValidationRole: VisualizationRole: Writing - review & editing
                Role: Formal analysisRole: Software
                Role: InvestigationRole: MethodologyRole: Project administrationRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: ResourcesRole: SupervisionRole: ValidationRole: Writing - review & editing
                Role: MethodologyRole: ResourcesRole: SoftwareRole: SupervisionRole: Writing - review & editing
                Role: Data curationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: InvestigationRole: ResourcesRole: ValidationRole: Visualization
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: Validation
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: MethodologyRole: ResourcesRole: Writing - review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: SupervisionRole: ValidationRole: Writing - original draftRole: Writing - review & editing
                Role: Formal analysisRole: Methodology
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - review & editing
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Journal
                Sci Adv
                Sci Adv
                sciadv
                advances
                Science Advances
                American Association for the Advancement of Science
                2375-2548
                December 2021
                01 December 2021
                : 7
                : 49
                : eabl8213
                Affiliations
                [1 ]Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ 85054, USA.
                [2 ]Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA.
                [3 ]Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA.
                [4 ]Mayo Clinic Cancer Center, Phoenix, AZ 85054, USA.
                [5 ]Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85281, USA.
                [6 ]Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.
                [7 ]School of Molecular Sciences, Arizona State University, Tempe, AZ 85251, USA.
                [8 ]MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824.
                [9 ]Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824.
                [10 ]Computational Structural Biology and Molecular Biophysics, Beckman institute, University of Illinois, IL 61801, USA.
                [11 ]Institute of Infection Immunity and Inflammation, MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK.
                [12 ]Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK.
                [13 ]Eyring Materials Center, Arizona State University, Tempe, AZ 85281, USA.
                [14 ]Analytical Sciences, Biopharmaceutical Development, AstraZeneca, Gaithersburg, MD 20878, USA.
                [15 ]School of Pharmacy and Pharmaceutical Science, College of Biomedical and Life Sciences, Cardiff University, Cardiff CF10 3NB, UK.
                [16 ]Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 W. Baltimore Street, MD 21201, USA.
                [17 ]Center for Vaccine Development and Global Health, University of Maryland School of Medicine, 685 W. Baltimore Street, MD 21201, USA.
                [18 ]Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.
                [19 ]Microbial Sciences, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA.
                Author notes
                [†]

                These authors contributed equally to this work.

                [‡]

                These authors contributed equally to this work.

                [§]

                Present address: Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.

                Author information
                https://orcid.org/0000-0001-8232-0531
                https://orcid.org/0000-0002-6704-8696
                https://orcid.org/0000-0002-4167-2108
                https://orcid.org/0000-0003-1378-6981
                https://orcid.org/0000-0002-2927-7383
                https://orcid.org/0000-0003-0627-4603
                https://orcid.org/0000-0002-4104-1445
                https://orcid.org/0000-0001-6581-8944
                https://orcid.org/0000-0002-1622-3677
                https://orcid.org/0000-0003-0953-4909
                https://orcid.org/0000-0003-3139-6469
                https://orcid.org/0000-0001-8942-8131
                https://orcid.org/0000-0002-4602-8258
                https://orcid.org/0000-0003-0105-2702
                https://orcid.org/0000-0001-9880-6560
                https://orcid.org/0000-0003-0281-5206
                https://orcid.org/0000-0001-8608-7650
                https://orcid.org/0000-0002-9290-0369
                https://orcid.org/0000-0001-9368-0903
                https://orcid.org/0000-0002-9302-1761
                https://orcid.org/0000-0002-9000-2397
                https://orcid.org/0000-0003-2700-2658
                Article
                abl8213
                10.1126/sciadv.abl8213
                8635433
                34851659
                a2cfe5ab-76f5-419c-8007-6f0eed212078
                Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).

                This is an open-access article distributed under the terms of the Creative Commons Attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 07 August 2021
                : 19 October 2021
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: 1531991
                Funded by: FundRef http://dx.doi.org/10.13039/100000015, U.S. Department of Energy;
                Award ID: DE-FG02-91ER20021
                Funded by: FundRef http://dx.doi.org/10.13039/100000015, U.S. Department of Energy;
                Award ID: DE-FG02-91ER20021
                Funded by: FundRef http://dx.doi.org/10.13039/100000052, NIH Office of the Director;
                Award ID: CA195764
                Funded by: FundRef http://dx.doi.org/10.13039/100000052, NIH Office of the Director;
                Award ID: CA234324
                Funded by: FundRef http://dx.doi.org/10.13039/100000054, National Cancer Institute;
                Award ID: CA090628
                Funded by: FundRef http://dx.doi.org/10.13039/100000871, Mayo Clinic;
                Award ID: Kathryn H. and Roger Penske Career Development award
                Funded by: FundRef http://dx.doi.org/10.13039/100000871, Mayo Clinic;
                Award ID: 2020 Eagles 5th District Cancer Telethon Funds for Cancer Research
                Funded by: FundRef http://dx.doi.org/10.13039/100014535, Center for Individualized Medicine, Mayo Clinic;
                Funded by: FundRef http://dx.doi.org/10.13039/100000054, National Cancer Institute;
                Award ID: 5P30CA015083
                Funded by: FundRef http://dx.doi.org/10.13039/100009828, Cancer Research Wales;
                Award ID: 514472
                Funded by: FundRef http://dx.doi.org/10.13039/501100000866, Cardiff University;
                Award ID: AC1170AP02
                Funded by: FundRef http://dx.doi.org/10.13039/501100000289, Cancer Research UK;
                Award ID: C7838/A25173
                Funded by: Mayo-ASU Foundation;
                Funded by: FundRef http://dx.doi.org/10.13039/100011889, Diamond Light Source;
                Award ID: mx-20147
                Funded by: FundRef http://dx.doi.org/10.13039/100006228, Oak Ridge National Laboratory;
                Award ID: DE-AC05-00OR22725
                Funded by: FundRef http://dx.doi.org/10.13039/100007482, Arizona State University;
                Award ID: Start-up Funds
                Funded by: FundRef http://dx.doi.org/10.13039/100000179, NSF Office of the Director;
                Award ID: MCB-1942763
                Funded by: the Gordon and Betty Moore Foundation;
                Funded by: FundRef http://dx.doi.org/10.13039/100014535, Center for Individualized Medicine, Mayo Clinic;
                Funded by: FundRef http://dx.doi.org/10.13039/100000054, National Cancer Institute;
                Award ID: 5P30CA015083
                Funded by: Biodesign Center for Applied Structural Discovery at Arizona State University;
                Categories
                Research Article
                Biomedicine and Life Sciences
                SciAdv r-articles
                Molecular Biology
                Virology
                Coronavirus
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