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Bosch AM, Guzman HV, Pérez R. Adsorption-Driven Deformation and Footprints of the RBD Proteins in SARS-CoV-2 Variants on Biological and Inanimate Surfaces. J Chem Inf Model 2024; 64:5977-5990. [PMID: 39083670 DOI: 10.1021/acs.jcim.4c00460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Respiratory viruses, carried through airborne microdroplets, frequently adhere to surfaces, including plastics and metals. However, our understanding of the interactions between viruses and materials remains limited, particularly in scenarios involving polarizable surfaces. Here, we investigate the role of the receptor-binding domain (RBD) of the spike protein mutations on the adsorption of SARS-CoV-2 to hydrophobic and hydrophilic surfaces employing molecular simulations. To contextualize our findings, we contrast the interactions on inanimate surfaces with those on native biological interfaces, specifically the angiotensin-converting enzyme 2. Notably, we identify a 2-fold increase in structural deformations for the protein's receptor binding motif (RBM) onto inanimate surfaces, indicative of enhanced shock-absorbing mechanisms. Furthermore, the distribution of adsorbed amino acids (landing footprints) on the inanimate surface reveals a distinct regional asymmetry relative to the biological interface, with roughly half of the adsorbed amino acids arranged in opposite sites. In spite of the H-bonds formed at the hydrophilic substrate, the simulations consistently show a higher number of contacts and interfacial area with the hydrophobic surface, where the wild-type RBD adsorbs more strongly than the Delta or Omicron RBDs. In contrast, the adsorption of Delta and Omicron to hydrophilic surfaces was characterized by a distinctive hopping-pattern. The novel shock-absorbing mechanisms identified in the virus adsorption on inanimate surfaces show the embedded high-deformation capacity of the RBD without losing its secondary structure, which could lead to current experimental strategies in the design of virucidal surfaces.
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Affiliation(s)
- Antonio M Bosch
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Horacio V Guzman
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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2
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Zhang M, Leong MW, Mitch WA, Blish CA, Boehm A. Persistence and free chlorine disinfection of human coronaviruses and their surrogates in water. Appl Environ Microbiol 2024; 90:e0005524. [PMID: 38511945 PMCID: PMC11022552 DOI: 10.1128/aem.00055-24] [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: 01/11/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
The coronavirus disease 2019 pandemic illustrates the importance of understanding the behavior and control of human pathogenic viruses in the environment. Exposure via water (drinking, bathing, and recreation) is a known route of transmission of viruses to humans, but the literature is relatively void of studies on the persistence of many viruses, especially coronaviruses, in water and their susceptibility to chlorine disinfection. To fill that knowledge gap, we evaluated the persistence and free chlorine disinfection of human coronavirus OC43 (HCoV-OC43) and its surrogates, murine hepatitis virus (MHV) and porcine transmissible gastroenteritis virus (TGEV), in drinking water and laboratory buffer using cell culture methods. The decay rate constants of human coronavirus and its surrogates in water varied, depending on virus and water matrix. In drinking water without disinfectant addition, MHV showed the largest decay rate constant (estimate ± standard error, 2.25 ± 0.09 day-1) followed by HCoV-OC43 (0.99 ± 0.12 day-1) and TGEV (0.65 ± 0.06 day-1), while in phosphate buffer without disinfectant addition, HCoV-OC43 (0.51 ± 0.10 day-1) had a larger decay rate constant than MHV (0.28 ± 0.03 day-1) and TGEV (0.24 ± 0.02 day-1). Upon free chlorine disinfection, the inactivation rates of coronaviruses were independent of free chlorine concentration and were not affected by water matrix, though they still varied between viruses. TGEV showed the highest susceptibility to free chlorine disinfection with the inactivation rate constant of 113.50 ± 7.50 mg-1 min-1 L, followed by MHV (81.33 ± 4.90 mg-1 min-1 L) and HCoV-OC43 (59.42 ± 4.41 mg-1 min-1 L). IMPORTANCE This study addresses an important knowledge gap on enveloped virus persistence and disinfection in water. Results have immediate practical applications for shaping evidence-based water policies, particularly in the development of disinfection strategies for pathogenic virus control.
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Affiliation(s)
- Mengyang Zhang
- Department of Civil and Environmental Engineering, School of Engineering and Doerr School of Sustainability, Stanford University, Stanford, California, USA
| | - Michelle Wei Leong
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - William A. Mitch
- Department of Civil and Environmental Engineering, School of Engineering and Doerr School of Sustainability, Stanford University, Stanford, California, USA
| | - Catherine A. Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Alexandria Boehm
- Department of Civil and Environmental Engineering, School of Engineering and Doerr School of Sustainability, Stanford University, Stanford, California, USA
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3
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Comet M, Dijkman PM, Boer Iwema R, Franke T, Masiulis S, Schampers R, Raschdorf O, Grollios F, Pryor EE, Drulyte I. Tomo Live: an on-the-fly reconstruction pipeline to judge data quality for cryo-electron tomography workflows. Acta Crystallogr D Struct Biol 2024; 80:247-258. [PMID: 38512070 PMCID: PMC10994173 DOI: 10.1107/s2059798324001840] [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: 10/31/2023] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
Data acquisition and processing for cryo-electron tomography can be a significant bottleneck for users. To simplify and streamline the cryo-ET workflow, Tomo Live, an on-the-fly solution that automates the alignment and reconstruction of tilt-series data, enabling real-time data-quality assessment, has been developed. Through the integration of Tomo Live into the data-acquisition workflow for cryo-ET, motion correction is performed directly after each of the acquired tilt angles. Immediately after the tilt-series acquisition has completed, an unattended tilt-series alignment and reconstruction into a 3D volume is performed. The results are displayed in real time in a dedicated remote web platform that runs on the microscope hardware. Through this web platform, users can review the acquired data (aligned stack and 3D volume) and several quality metrics that are obtained during the alignment and reconstruction process. These quality metrics can be used for fast feedback for subsequent acquisitions to save time. Parameters such as Alignment Accuracy, Deleted Tilts and Tilt Axis Correction Angle are visualized as graphs and can be used as filters to export only the best tomograms (raw data, reconstruction and intermediate data) for further processing. Here, the Tomo Live algorithms and workflow are described and representative results on several biological samples are presented. The Tomo Live workflow is accessible to both expert and non-expert users, making it a valuable tool for the continued advancement of structural biology, cell biology and histology.
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Affiliation(s)
- Maxime Comet
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Patricia M. Dijkman
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Reint Boer Iwema
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Tilman Franke
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Simonas Masiulis
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Ruud Schampers
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Oliver Raschdorf
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Fanis Grollios
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Edward E. Pryor
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Ieva Drulyte
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
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4
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Ali A, Ganguillet S, Turgay Y, Keys TG, Causa E, Fradique R, Lutz-Bueno V, Chesnov S, Tan-Lin CW, Lentsch V, Kotar J, Cicuta P, Mezzenga R, Slack E, Radiom M. Surface Cross-Linking by Macromolecular Tethers Enhances Virus-like Particles' Resilience to Mucosal Stress Factors. ACS NANO 2024; 18:3382-3396. [PMID: 38237058 PMCID: PMC10832050 DOI: 10.1021/acsnano.3c10339] [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: 10/21/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/31/2024]
Abstract
Virus-like particles (VLPs) are emerging as nanoscaffolds in a variety of biomedical applications including delivery of vaccine antigens and cargo such as mRNA to mucosal surfaces. These soft, colloidal, and proteinaceous structures (capsids) are nevertheless susceptible to mucosal environmental stress factors. We cross-linked multiple capsid surface amino acid residues using homobifunctional polyethylene glycol tethers to improve the persistence and survival of the capsid to model mucosal stressors. Surface cross-linking enhanced the stability of VLPs assembled from Acinetobacter phage AP205 coat proteins in low pH (down to pH 4.0) and high protease concentration conditions (namely, in pig and mouse gastric fluids). Additionally, it increased the stiffness of VLPs under local mechanical indentation applied using an atomic force microscopy cantilever tip. Small angle X-ray scattering revealed an increase in capsid diameter after cross-linking and an increase in capsid shell thickness with the length of the PEG cross-linkers. Moreover, surface cross-linking had no effect on the VLPs' mucus translocation and accumulation on the epithelium of in vitro 3D human nasal epithelial tissues with mucociliary clearance. Finally, it did not compromise VLPs' function as vaccines in mouse subcutaneous vaccination models. Compared to PEGylation without cross-linking, the stiffness of surface cross-linked VLPs were higher for the same length of the PEG molecule, and also the lifetimes of surface cross-linked VLPs were longer in the gastric fluids. Surface cross-linking using macromolecular tethers, but not simple conjugation of these molecules, thus offers a viable means to enhance the resilience and survival of VLPs for mucosal applications.
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Affiliation(s)
- Ahmed Ali
- Department
of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Suwannee Ganguillet
- Department
of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Yagmur Turgay
- Department
of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Timothy G. Keys
- Department
of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Erika Causa
- Biological
and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Ricardo Fradique
- Biological
and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Viviane Lutz-Bueno
- Paul
Scherrer Institute (PSI), Villigen 5232, Switzerland
- Laboratoire
Léon Brillouin, CEA-CNRS (UMR-12), CEA Saclay, Université
Paris-Saclay, Gif-sur-Yvette Cedex 91191, France
| | - Serge Chesnov
- Functional
Genomics Centre Zürich (FGCZ), University of Zürich/ETH
Zürich, Zürich 8057, Switzerland
| | - Chia-Wei Tan-Lin
- Functional
Genomics Centre Zürich (FGCZ), University of Zürich/ETH
Zürich, Zürich 8057, Switzerland
| | - Verena Lentsch
- Department
of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Jurij Kotar
- Biological
and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Pietro Cicuta
- Biological
and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Raffaele Mezzenga
- Department
of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Emma Slack
- Department
of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Milad Radiom
- Department
of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
- Biological
and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K.
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5
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Cantero M, Rodríguez-Espinosa MJ, Strobl K, Ibáñez P, Díez-Martínez A, Martín-González N, Jiménez-Zaragoza M, Ortega-Esteban A, de Pablo PJ. Atomic Force Microscopy of Viruses: Stability, Disassembly, and Genome Release. Methods Mol Biol 2024; 2694:317-338. [PMID: 37824011 DOI: 10.1007/978-1-0716-3377-9_15] [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] [Indexed: 10/13/2023]
Abstract
In atomic force microscopy (AFM), the probe is a nanometric tip located at the end of a microcantilever which palpates the specimen under study as a blind person manages a walking stick. In this way, AFM allows obtaining nanometric resolution images of individual protein shells, such as viruses, in liquid milieu. Beyond imaging, AFM also enables not only the manipulation of single protein cages but also the evaluation of each physicochemical property which is able of inducing any measurable mechanical perturbation to the microcantilever that holds the tip. In this chapter, we start revising some recipes for adsorbing protein shells on surfaces and how the geometrical dilation of tips can affect to the AFM topographies. This work also deals with the abilities of AFM to monitor TGEV coronavirus under changing conditions of the liquid environment. Subsequently, we describe several AFM approaches to study cargo release, aging, and multilayered viruses with single indentation and fatigue assays. Finally, we comment on a combined AFM/fluorescence application to study the influence of crowding on GFP packed within individual P22 bacteriophage capsids.
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Affiliation(s)
- Miguel Cantero
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - María Jesús Rodríguez-Espinosa
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Klara Strobl
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo Ibáñez
- Department of Theoretical Physics of Condensed Matter, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alejandro Díez-Martínez
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Manuel Jiménez-Zaragoza
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alvaro Ortega-Esteban
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pedro José de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain.
- Solid Condensed Matter Institute IFIMAC, Universidad Autónoma de Madrid, Madrid, Spain.
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6
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Hu Z, Tian X, Lai R, Ji C, Li X. Airborne transmission of common swine viruses. Porcine Health Manag 2023; 9:50. [PMID: 37908005 PMCID: PMC10619269 DOI: 10.1186/s40813-023-00346-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/25/2023] [Indexed: 11/02/2023] Open
Abstract
The transmission of viral aerosols poses a vulnerable aspect in the biosecurity measures aimed at preventing and controlling swine virus in pig production. Consequently, comprehending and mitigating the spread of aerosols holds paramount significance for the overall well-being of pig populations. This paper offers a comprehensive review of transmission characteristics, influential factors and preventive strategies of common swine viral aerosols. Firstly, certain viruses such as foot-and-mouth disease virus (FMDV), porcine reproductive and respiratory syndrome virus (PRRSV), influenza A viruses (IAV), porcine epidemic diarrhea virus (PEDV) and pseudorabies virus (PRV) have the potential to be transmitted over long distances (exceeding 150 m) through aerosols, thereby posing a substantial risk primarily to inter-farm transmission. Additionally, other viruses like classical swine fever virus (CSFV) and African swine fever virus (ASFV) can be transmitted over short distances (ranging from 0 to 150 m) through aerosols, posing a threat primarily to intra-farm transmission. Secondly, various significant factors, including aerosol particle sizes, viral strains, the host sensitivity to viruses, weather conditions, geographical conditions, as well as environmental conditions, exert a considerable influence on the transmission of viral aerosols. Researches on these factors serve as a foundation for the development of strategies to combat viral aerosol transmission in pig farms. Finally, we propose several preventive and control strategies that can be implemented in pig farms, primarily encompassing the implementation of early warning models, viral aerosol detection, and air pretreatment. This comprehensive review aims to provide a valuable reference for the formulation of efficient measures targeted at mitigating the transmission of viral aerosols among swine populations.
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Affiliation(s)
- Zhiqiang Hu
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Xiajin Economic Development Zone, Qingwo Venture Park, Dezhou, 253200, Shandong Province, People's Republic of China
- Shandong New Hope Liuhe Co., Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, People's Republic of China
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd (NHLH Academy of Swine Research), 6596 Dongfanghong East Road, Yuanqiao Town, Dezhou, 253000, Shandong, People's Republic of China
- China Agriculture Research System-Yangling Comprehensive Test Station, Intersection of Changqing Road and Park Road 1, Yangling District, Xianyang, People's Republic of China
| | - Xiaogang Tian
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Xiajin Economic Development Zone, Qingwo Venture Park, Dezhou, 253200, Shandong Province, People's Republic of China
- Shandong New Hope Liuhe Co., Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, People's Republic of China
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd (NHLH Academy of Swine Research), 6596 Dongfanghong East Road, Yuanqiao Town, Dezhou, 253000, Shandong, People's Republic of China
| | - Ranran Lai
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Xiajin Economic Development Zone, Qingwo Venture Park, Dezhou, 253200, Shandong Province, People's Republic of China
- Shandong New Hope Liuhe Co., Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, People's Republic of China
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd (NHLH Academy of Swine Research), 6596 Dongfanghong East Road, Yuanqiao Town, Dezhou, 253000, Shandong, People's Republic of China
| | - Chongxing Ji
- Key Laboratory of Feed and Livestock and Poultry Products Quality and Safety Control, Ministry of Agriculture and Rural Affairs, New Hope Liuhe Co., Ltd, 316 Jinshi Road, Chengdu, 610100, Sichuan, People's Republic of China
- Shandong New Hope Liuhe Co., Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, People's Republic of China
| | - Xiaowen Li
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Xiajin Economic Development Zone, Qingwo Venture Park, Dezhou, 253200, Shandong Province, People's Republic of China.
- Key Laboratory of Feed and Livestock and Poultry Products Quality and Safety Control, Ministry of Agriculture and Rural Affairs, New Hope Liuhe Co., Ltd, 316 Jinshi Road, Chengdu, 610100, Sichuan, People's Republic of China.
- Shandong New Hope Liuhe Co., Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, People's Republic of China.
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd (NHLH Academy of Swine Research), 6596 Dongfanghong East Road, Yuanqiao Town, Dezhou, 253000, Shandong, People's Republic of China.
- China Agriculture Research System-Yangling Comprehensive Test Station, Intersection of Changqing Road and Park Road 1, Yangling District, Xianyang, People's Republic of China.
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7
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Cantero M, Cvirkaite-Krupovic V, Krupovic M, de Pablo PJ. Mechanical tomography of an archaeal lemon-shaped virus reveals membrane-like fluidity of the capsid and liquid nucleoprotein cargo. Proc Natl Acad Sci U S A 2023; 120:e2307717120. [PMID: 37824526 PMCID: PMC10589707 DOI: 10.1073/pnas.2307717120] [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: 05/08/2023] [Accepted: 09/08/2023] [Indexed: 10/14/2023] Open
Abstract
Archaeal lemon-shaped viruses have unique helical capsids composed of highly hydrophobic protein strands which can slide past each other resulting in remarkable morphological reorganization. Here, using atomic force microscopy, we explore the biomechanical properties of the lemon-shaped virions of Sulfolobus monocaudavirus 1 (SMV1), a double-stranded DNA virus which infects hyperthermophilic (~80 °C) and acidophilic (pH ~ 2) archaea. Our results reveal that SMV1 virions are extremely soft and withstand repeated extensive deformations, reaching remarkable strains of 80% during multiple cycles of consecutive mechanical assaults, yet showing scarce traces of disruption. SMV1 virions can reversibly collapse wall-to-wall, reducing their volume by ~90%. Beyond revealing the exceptional malleability of the SMV1 protein shell, our data also suggest a fluid-like nucleoprotein cargo which can flow inside the capsid, resisting and accommodating mechanical deformations without further alteration. Our experiments suggest a packing fraction of the virus core to be as low as 11%, with the amount of the accessory proteins almost four times exceeding that of the viral genome. Our findings indicate that SMV1 protein capsid displays biomechanical properties of lipid membranes, which is not found among protein capsids of other viruses. The remarkable malleability and fluidity of the SMV1 virions are likely necessary for the structural transformations during the infection and adaptation to extreme environmental conditions.
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Affiliation(s)
- Miguel Cantero
- Departamento de Física de la Materia Condensada C03, Universidad Autónoma de Madrid, Madrid28049, Spain
| | | | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris75015, France
| | - Pedro J. de Pablo
- Departamento de Física de la Materia Condensada C03, Universidad Autónoma de Madrid, Madrid28049, Spain
- Instituto de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid28049, Spain
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8
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Jiang Y, Fu Y, Xu X, Guo X, Wang F, Xu X, Huang YW, Shi J, Shen C. Production of singlet oxygen from photosensitizer erythrosine for facile inactivation of coronavirus on mask. ENVIRONMENT INTERNATIONAL 2023; 177:107994. [PMID: 37267731 DOI: 10.1016/j.envint.2023.107994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/28/2023] [Accepted: 05/23/2023] [Indexed: 06/04/2023]
Abstract
The global health crisis caused by the COVID-19 pandemic has led to a surge in demand and use of personal protective equipment (PPE) such as masks, putting great pressure on social production and the environment.It is urgent to find an efficient and non-destructive disinfection method for the safe reuse of PPE. This study proposes a PPE disinfection method that uses erythrosine, a U.S. Food and Drug Administration-approved food dye, as photosensitizer to produce singlet oxygen for virus inactivation, and indicates the completion of disinfection by its photobleaching color change.After spraying 100 μL of 10 μM erythrosine on the surface of the mask for 3 times and light exposure for 25 min, the titer of coronavirus decreased by more than 99.999%, and the color of erythrosine on the mask surface disappeared. In addition, the structure of the mask was intact and the filtration efficiency was maintained at > 95% after 10 cycles of erythrosine treatment.Therefore, this disinfection method can provide at least 10 cycles of reuse with the advantages of high safety and convenient, and the completion of disinfection can be indicated by its photobleaching, which is suitable for hospitals and daily life to reduce the consumption of PPE.
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Affiliation(s)
- Yunhan Jiang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Yulong Fu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Xiaojie Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Xiaoguang Guo
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Feiyu Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Xin Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Yao-Wei Huang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, PR China
| | - Jiyan Shi
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Chaofeng Shen
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, PR China.
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9
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Gu X, Cao T, Mou J, Liu J. Water bath is more efficient than hot air oven at thermal inactivation of coronavirus. Virol J 2023; 20:84. [PMID: 37131169 PMCID: PMC10153051 DOI: 10.1186/s12985-023-02038-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/11/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Thermal inactivation is a conventional and effective method of eliminating the infectivity of pathogens from specimens in clinical and biological laboratories, and reducing the risk of occupational exposure and environmental contamination. During the COVID-19 pandemic, specimens from patients and potentially infected individuals were heat treated and processed under BSL-2 conditions in a safe, cost-effective, and timely manner. The temperature and duration of heat treatment are optimized and standardized in the protocol according to the susceptibility of the pathogen and the impact on the integrity of the specimens, but the heating device is often undefined. Devices and medium transferring the thermal energy vary in heating rate, specific heat capacity, and conductivity, resulting in variations in efficiency and inactivation outcome that may compromise biosafety and downstream biological assays. METHODS We evaluated the water bath and hot air oven in terms of pathogen inactivation efficiency, which are the most commonly used inactivation devices in hospitals and biological laboratories. By evaluating the temperature equilibrium and viral titer elimination under various conditions, we studied the devices and their inactivation outcomes under identical treatment protocol, and to analyzed the factors, such as energy conductivity, specific heat capacity, and heating rate, underlying the inactivation efficiencies. RESULTS We compared thermal inactivation of coronavirus using different devices, and have found that the water bath was more efficient at reducing infectivity, with higher heat transfer and thermal equilibration than a forced hot air oven. In addition to the efficiency, the water bath showed relative consistency in temperature equilibration of samples of different volumes, reduced the need for prolonged heating, and eliminated the risk of pathogen spread by forced airflow. CONCLUSIONS Our data support the proposal to define the heating device in the thermal inactivation protocol and in the specimen management policy.
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Affiliation(s)
- Xinxia Gu
- Laboratory of Infectious Diseases and Vaccine, West China School of Medicine, West China Hospital, Sichuan University, 88 Keyuan S. Rd, Chengdu, 610041, China
| | - Ting Cao
- Laboratory of Infectious Diseases and Vaccine, West China School of Medicine, West China Hospital, Sichuan University, 88 Keyuan S. Rd, Chengdu, 610041, China
| | - Jun Mou
- Laboratory of Infectious Diseases and Vaccine, West China School of Medicine, West China Hospital, Sichuan University, 88 Keyuan S. Rd, Chengdu, 610041, China
| | - Jie Liu
- Laboratory of Infectious Diseases and Vaccine, West China School of Medicine, West China Hospital, Sichuan University, 88 Keyuan S. Rd, Chengdu, 610041, China.
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Domingo M, Faraudo J. Effect of surfactants on SARS-CoV-2: Molecular dynamics simulations. J Chem Phys 2023; 158:114107. [PMID: 36948819 DOI: 10.1063/5.0135251] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
Surfactants are commonly used as disinfection agents in personal care products against bacteria and viruses, including SARS-CoV-2. However, there is a lack of understanding of the molecular mechanisms of the inactivation of viruses by surfactants. Here, we employ coarse grain (CG) and all-atom (AA) molecular dynamics simulations to investigate the interaction between general families of surfactants and the SARS-CoV-2 virus. To this end, we considered a CG model of a full virion. Overall, we found that surfactants have only a small impact on the virus envelope, being inserted into the envelope without dissolving it or generating pores, at the conditions considered here. However, we found that surfactants may induce a deep impact on the spike protein of the virus (responsible for its infectivity), easily covering it and inducing its collapse over the envelope surface of the virus. AA simulations confirmed that both negatively and positively charged surfactants are able to extensively adsorb over the spike protein and get inserted into the virus envelope. Our results suggest that the best strategy for the design of surfactants as virucidal agents will be to focus on those strongly interacting with the spike protein.
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Affiliation(s)
- Marc Domingo
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Barcelona, Spain
| | - Jordi Faraudo
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Barcelona, Spain
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