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Wu G, Li Q, Dai J, Mao G, Ma Y. Design and Application of Biosafe Coronavirus Engineering Systems without Virulence. Viruses 2024; 16:659. [PMID: 38793541 PMCID: PMC11126016 DOI: 10.3390/v16050659] [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: 03/29/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
In the last twenty years, three deadly zoonotic coronaviruses (CoVs)-namely, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2-have emerged. They are considered highly pathogenic for humans, particularly SARS-CoV-2, which caused the 2019 CoV disease pandemic (COVID-19), endangering the lives and health of people globally and causing unpredictable economic losses. Experiments on wild-type viruses require biosafety level 3 or 4 laboratories (BSL-3 or BSL-4), which significantly hinders basic virological research. Therefore, the development of various biosafe CoV systems without virulence is urgently needed to meet the requirements of different research fields, such as antiviral and vaccine evaluation. This review aimed to comprehensively summarize the biosafety of CoV engineering systems. These systems combine virological foundations with synthetic genomics techniques, enabling the development of efficient tools for attenuated or non-virulent vaccines, the screening of antiviral drugs, and the investigation of the pathogenic mechanisms of novel microorganisms.
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Affiliation(s)
- Guoqiang Wu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (G.W.); (Q.L.); (J.D.)
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China
| | - Qiaoyu Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (G.W.); (Q.L.); (J.D.)
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (G.W.); (Q.L.); (J.D.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Guobin Mao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (G.W.); (Q.L.); (J.D.)
| | - Yingxin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (G.W.); (Q.L.); (J.D.)
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Abney SE, Higham CA, Wilson AM, Ijaz MK, McKinney J, Reynolds KA, Gerba CP. Transmission of Viruses from Restroom Use: A Quantitative Microbial Risk Assessment. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:65-78. [PMID: 38372960 DOI: 10.1007/s12560-023-09580-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/30/2023] [Indexed: 02/20/2024]
Abstract
Restroom use has been implicated in a number of viral outbreaks. In this study, we apply quantitative microbial risk assessment to quantify the risk of viral transmission by contaminated restroom fomites. We estimate risk from high-touch fomite surfaces (entrance/exit door, toilet seat) for three viruses of interest (SARS-CoV-2, adenovirus, norovirus) through eight exposure scenarios involving differing user behaviors, and the use of hand sanitizer following each scenario. We assessed the impacts of several sequences of fomite contacts in the restroom, reflecting the variability of human behavior, on infection risks for these viruses. Touching of the toilet seat was assumed to model adjustment of the seat (open vs. closed), a common touch point in single-user restrooms (home, small business, hospital). A Monte Carlo simulation was conducted for each exposure scenario (10,000 simulations each). Norovirus resulted in the highest probability of infection for all exposure scenarios with fomite surfaces. Post-restroom automatic-dispensing hand sanitizer use reduced the probability of infection for each virus by up to 99.75%. Handwashing within the restroom, an important risk-reduction intervention, was not found to be as effective as use of a non-touch hand sanitizer dispenser for reducing risk to near or below 1/1,000,000, a commonly used risk threshold for comparison.
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Affiliation(s)
- Sarah E Abney
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA
| | - Ciara A Higham
- EPSRC Centre for Doctoral Training in Fluid Dynamics, University of Leeds, Leeds, UK
| | - Amanda M Wilson
- Department of Community, Environment, & Policy, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - M Khalid Ijaz
- Global Research & Development for Lysol and Dettol, Reckitt Benckiser LLC, Montvale, NJ, USA
| | - Julie McKinney
- Global Research & Development for Lysol and Dettol, Reckitt Benckiser LLC, Montvale, NJ, USA
| | - Kelly A Reynolds
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA
- Department of Community, Environment, & Policy, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - Charles P Gerba
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA.
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Meyers G, Tews BA. Self-Replicating RNA Derived from the Genomes of Positive-Strand RNA Viruses. Methods Mol Biol 2024; 2786:25-49. [PMID: 38814389 DOI: 10.1007/978-1-0716-3770-8_2] [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: 05/31/2024]
Abstract
Self-replicating RNA derived from the genomes of positive-strand RNA viruses represents a powerful tool for both molecular studies on virus biology and approaches to novel safe and effective vaccines. The following chapter summarizes the principles how such RNAs can be established and used for design of vaccines. Due to the large variety of strategies needed to circumvent specific pitfalls in the design of such constructs the technical details of the experiments are not described here but can be found in the cited literature.
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Affiliation(s)
- Gregor Meyers
- Institut für Immunologie, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Birke Andrea Tews
- Institut für Infektionsmedizin, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany.
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Bello-Perez M, Hurtado-Tamayo J, Mykytyn AZ, Lamers MM, Requena-Platek R, Schipper D, Muñoz-Santos D, Ripoll-Gómez J, Esteban A, Sánchez-Cordón PJ, Enjuanes L, Haagmans BL, Sola I. SARS-CoV-2 ORF8 accessory protein is a virulence factor. mBio 2023; 14:e0045123. [PMID: 37623322 PMCID: PMC10653805 DOI: 10.1128/mbio.00451-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/04/2023] [Indexed: 08/26/2023] Open
Abstract
IMPORTANCE The relevance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ORF8 in the pathogenesis of COVID-19 is unclear. Virus natural isolates with deletions in ORF8 were associated with wild milder disease, suggesting that ORF8 might contribute to SARS-CoV-2 virulence. This manuscript shows that ORF8 is involved in inflammation and in the activation of macrophages in two experimental systems: humanized K18-hACE2 transgenic mice and organoid-derived human airway cells. These results identify ORF8 protein as a potential target for COVID-19 therapies.
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Affiliation(s)
- M. Bello-Perez
- Department of Molecular and Cell Biology, National Center for Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - J. Hurtado-Tamayo
- Department of Molecular and Cell Biology, National Center for Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - A. Z. Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - M. M. Lamers
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - R. Requena-Platek
- Department of Molecular and Cell Biology, National Center for Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - D. Schipper
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - D. Muñoz-Santos
- Department of Molecular and Cell Biology, National Center for Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - J. Ripoll-Gómez
- Department of Molecular and Cell Biology, National Center for Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - A. Esteban
- Department of Molecular and Cell Biology, National Center for Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - P. J. Sánchez-Cordón
- Veterinary Pathology Department, Animal Health Research Center (CISA), National Institute of Research, Agricultural and Food Technology, Valdeolmos, Spain
| | - L. Enjuanes
- Department of Molecular and Cell Biology, National Center for Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - B. L. Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - I. Sola
- Department of Molecular and Cell Biology, National Center for Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
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Javorsky A, Humbert PO, Kvansakul M. Viral manipulation of cell polarity signalling. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119536. [PMID: 37437846 DOI: 10.1016/j.bbamcr.2023.119536] [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: 03/08/2023] [Revised: 06/24/2023] [Accepted: 07/04/2023] [Indexed: 07/14/2023]
Abstract
Cell polarity refers to the asymmetric distribution of biomacromolecules that enable the correct orientation of a cell in a particular direction. It is thus an essential component for appropriate tissue development and function. Viral infections can lead to dysregulation of polarity. This is associated with a poor prognosis due to viral interference with core cell polarity regulatory scaffolding proteins that often feature PDZ (PSD-95, DLG, and ZO-1) domains including Scrib, Dlg, Pals1, PatJ, Par3 and Par6. PDZ domains are also promiscuous, binding to several different partners through their C-terminal region which contain PDZ-binding motifs (PBM). Numerous viruses encode viral effector proteins that target cell polarity regulators for their benefit and include papillomaviruses, flaviviruses and coronaviruses. A better understanding of the mechanisms of action utilised by viral effector proteins to subvert host cell polarity sigalling will provide avenues for future therapeutic intervention, while at the same time enhance our understanding of cell polarity regulation and its role tissue homeostasis.
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Affiliation(s)
- Airah Javorsky
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Patrick O Humbert
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia; Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria 3086, Australia; Department of Biochemistry & Pharmacology, University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Marc Kvansakul
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia; Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria 3086, Australia.
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Martinez JC, Ruiz-Sanz J, Resina MJ, Montero F, Camara-Artigas A, Luque I. A calorimetric and structural analysis of cooperativity in the thermal unfolding of the PDZ tandem of human Syntenin-1. Int J Biol Macromol 2023; 242:124662. [PMID: 37119899 DOI: 10.1016/j.ijbiomac.2023.124662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/10/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
Syntenin-1 is a multidomain protein containing a central tandem of two PDZ domains flanked by two unnamed domains. Previous structural and biophysical studies show that the two PDZ domains are functional both isolated and in tandem, occurring a gain in their respective binding affinities when joined through its natural short linker. To get insight into the molecular and energetic reasons of such a gain, here, the first thermodynamic characterization of the conformational equilibrium of Syntenin-1 is presented, with special focus on its PDZ domains. These studies include the thermal unfolding of the whole protein, the PDZ-tandem construct and the two isolated PDZ domains using circular dichroism, differential scanning fluorimetry and differential scanning calorimetry. The isolated PDZ domains show low stability (ΔG < 10 kJ·mol-1) and poor cooperativity compared to the PDZ-tandem, which shows higher stability (20-30 kJ·mol-1) and a fully cooperative behaviour, with energetics similar to that previously described for archetypical PDZ domains. The high-resolution structures suggest that this remarkable increase in cooperativity is associated to strong, water-mediated, interactions at the interface between the PDZ domains, associated to nine conserved hydration regions. The low Tm value (45 °C), the anomalously high unfolding enthalpy (>400 kJ·mol-1), and native heat capacity values (above 40 kJ·K-1·mol-1), indicate that these interfacial buried waters play a relevant role in Syntenin-1 folding energetics.
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Affiliation(s)
- Jose C Martinez
- Department of Physical Chemistry, Institute of Biotechnology and Excellence Unit in Chemistry Applied to Biomedicine and Environment, Faculty of Sciences, University of Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain.
| | - Javier Ruiz-Sanz
- Department of Physical Chemistry, Institute of Biotechnology and Excellence Unit in Chemistry Applied to Biomedicine and Environment, Faculty of Sciences, University of Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain.
| | - María J Resina
- Department of Physical Chemistry, Institute of Biotechnology and Excellence Unit in Chemistry Applied to Biomedicine and Environment, Faculty of Sciences, University of Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain.
| | - Fernando Montero
- Department of Physical Chemistry, Institute of Biotechnology and Excellence Unit in Chemistry Applied to Biomedicine and Environment, Faculty of Sciences, University of Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain.
| | - Ana Camara-Artigas
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain.
| | - Irene Luque
- Department of Physical Chemistry, Institute of Biotechnology and Excellence Unit in Chemistry Applied to Biomedicine and Environment, Faculty of Sciences, University of Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain.
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Malek A, Hoque A. Impact of vaccination on the entire population and dose-response relation of COVID-19. VACUNAS 2023:S1576-9887(23)00032-8. [PMID: 37362834 PMCID: PMC10156990 DOI: 10.1016/j.vacun.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/19/2023] [Indexed: 06/28/2023]
Abstract
Objective The objective of this study is to develop a mathematical model for the COVID-19 pandemic including vaccination, the transmissibility of the virus-pathogen dose-response relationship, vaccine efficiency, and vaccination rate. Methods The Runge-Kutta (RK-45) method was applied to solve the proposed model with MATLAB code and the calculated results show the dynamics of the individuals in each compartment. The data of total death due to the COVID-19 pandemic in the case of the USA were collected from GitHub and the re-use of this data needs no ethical clearance. The control reproduction number was used to assess the dose-response relationship and critical vaccination coverage. Results We have calculated the probability of infection and the infection risk against the different exposure doses and the virus copies, respectively. The results show that the probability of infection increases with the increasing exposure dose for certain virus copies and the risk of infection decreases with the increasing of virus copies for a certain exposure dose. The results also show that the critical vaccination coverage demands increase with an increase in transmission rate and decrease with increasing vaccine efficacy. Conclusions It was seen that the critical vaccination coverage corresponding to an increased transmission rate rise sharply in the beginning and then reached a threshold. Moreover, the real data of the total death cases in the USA were compared with the fitted curved of the model which validated the proposed model. Vaccination against COVID-19 is essential to control the pandemic, and achieving high vaccine uptake in the population can reduce the pandemic as fast as possible.
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Affiliation(s)
- Abdul Malek
- Department of Mathematics, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Ashabul Hoque
- Department of Mathematics, University of Rajshahi, Rajshahi 6205, Bangladesh
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Vita G, Woolf D, Avery-Hickmott T, Rowsell R. A CFD-based framework to assess airborne infection risk in buildings. BUILDING AND ENVIRONMENT 2023; 233:110099. [PMID: 36815961 PMCID: PMC9925846 DOI: 10.1016/j.buildenv.2023.110099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/31/2023] [Accepted: 02/12/2023] [Indexed: 06/18/2023]
Abstract
The COVID-19 pandemic has prompted huge efforts to further the scientific knowledge of indoor ventilation and its relationship to airborne infection risk. Exhaled infectious aerosols are spread and inhaled as a result of room airflow characteristics. Many calculation methods and assertions on risk assume 'well-mixed' flow conditions. However, ventilation in buildings is complex and often not showing well-mixed conditions. Ventilation guidance is typically based on the provision of generic minimum ventilation flow rates for a given space, irrespective of the effectiveness in the delivery of the supply air. Furthermore, the airflow might be heavily affected by the season, the HVAC ventilation, or the opening of windows, which would potentially generate draughts and non-uniform conditions. As a result, fresh air concentration would be variable depending upon a susceptible receptor's position in a room and, therefore, associated airborne infection risk. A computational fluid dynamics (CFD) and dynamic thermal modelling (DTM) framework is proposed to assess the influence of internal airflow characteristics on airborne infection risk. A simple metric is proposed, the hourly airborne infection rate (HAI) which can easily help designers to stress-test the ventilation within a building under several conditions. A case study is presented, and the results clearly demonstrate the importance of understanding detailed indoor airflow characteristics and associated concentration patterns in order to provide detailed design guidance, e.g. occupancy, supply air diffusers and furniture layouts, to reduce airborne infection risk.
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Affiliation(s)
- Giulio Vita
- Wirth Research Ltd, Charlotte Avenue, Bicester, OX27 8BL, United Kingdom
- University of Birmingham School of Engineering Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Darren Woolf
- Wirth Research Ltd, Charlotte Avenue, Bicester, OX27 8BL, United Kingdom
| | | | - Rob Rowsell
- Wirth Research Ltd, Charlotte Avenue, Bicester, OX27 8BL, United Kingdom
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Advances in Molecular Genetics Enabling Studies of Highly Pathogenic RNA Viruses. Viruses 2022; 14:v14122682. [PMID: 36560685 PMCID: PMC9784166 DOI: 10.3390/v14122682] [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: 10/24/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
Experimental work with viruses that are highly pathogenic for humans and animals requires specialized Biosafety Level 3 or 4 facilities. Such pathogens include some spectacular but also rather seldomly studied examples such as Ebola virus (requiring BSL-4), more wide-spread and commonly studied viruses such as HIV, and the most recent example, SARS-CoV-2, which causes COVID-19. A common characteristic of these virus examples is that their genomes consist of single-stranded RNA, which requires the conversion of their genomes into a DNA copy for easy manipulation; this can be performed to study the viral life cycle in detail, develop novel therapies and vaccines, and monitor the disease course over time for chronic virus infections. We summarize the recent advances in such new genetic applications for RNA viruses in Switzerland over the last 25 years, from the early days of the HIV/AIDS epidemic to the most recent developments in research on the SARS-CoV-2 coronavirus. We highlight game-changing collaborative efforts between clinical and molecular disciplines in HIV research on the path to optimal clinical disease management. Moreover, we summarize how the modern technical evolution enabled the molecular studies of emerging RNA viruses, confirming that Switzerland is at the forefront of SARS-CoV-2 research and potentially other newly emerging viruses.
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Surya W, Queralt-Martin M, Mu Y, Aguilella VM, Torres J. SARS-CoV-2 accessory protein 7b forms homotetramers in detergent. Virol J 2022; 19:193. [PMID: 36414943 PMCID: PMC9680129 DOI: 10.1186/s12985-022-01920-0] [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: 09/21/2022] [Accepted: 11/04/2022] [Indexed: 11/23/2022] Open
Abstract
A global pandemic is underway caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 genome, like its predecessor SARS-CoV, contains open reading frames that encode accessory proteins involved in virus-host interactions active during infection and which likely contribute to pathogenesis. One of these accessory proteins is 7b, with only 44 (SARS-CoV) and 43 (SARS-CoV-2) residues. It has one predicted transmembrane domain fully conserved, which suggests a functional role, whereas most variability is contained in the predicted cytoplasmic C-terminus. In SARS-CoV, 7b protein is expressed in infected cells, and the transmembrane domain was necessary and sufficient for Golgi localization. Also, anti-p7b antibodies have been found in the sera of SARS-CoV convalescent patients. In the present study, we have investigated the hypothesis that SARS-2 7b protein forms oligomers with ion channel activity. We show that in both SARS viruses 7b is almost completely α-helical and has a single transmembrane domain. In SDS, 7b forms various oligomers, from monomers to tetramers, but only monomers when exposed to reductants. Combination of SDS gel electrophoresis and analytical ultracentrifugation (AUC) in both equilibrium and velocity modes suggests a dimer-tetramer equilibrium, but a monomer-dimer-tetramer equilibrium in the presence of reductant. This data suggests that although disulfide-linked dimers may be present, they are not essential to form tetramers. Inclusion of pentamers or higher oligomers in the SARS-2 7b model were detrimental to fit quality. Preliminary models of this association was generated with AlphaFold2, and two alternative models were exposed to a molecular dynamics simulation in presence of a model lipid membrane. However, neither of the two models provided any evident pathway for ions. To confirm this, SARS-2 p7b was studied using Planar Bilayer Electrophysiology. Addition of p7b to model membranes produced occasional membrane permeabilization, but this was not consistent with bona fide ion channels made of a tetrameric assembly of α-helices.
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Affiliation(s)
- Wahyu Surya
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Maria Queralt-Martin
- grid.9612.c0000 0001 1957 9153Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12080 Castelló, Spain
| | - Yuguang Mu
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Vicente M. Aguilella
- grid.9612.c0000 0001 1957 9153Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12080 Castelló, Spain
| | - Jaume Torres
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
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Madi N, Sadeq M, Essa S, Safar HA, Al-Adwani A, Al-Khabbaz M. Strain Variation Based on Spike Glycoprotein Gene of SARS-CoV-2 in Kuwait from 2020 to 2021. Pathogens 2022; 11:pathogens11090985. [PMID: 36145416 PMCID: PMC9505955 DOI: 10.3390/pathogens11090985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 11/18/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19), which was first identified in Wuhan, China, in December 2019. With the global transmission of the virus, many SARS-CoV-2 variants have emerged due to the alterations of the spike glycoprotein. Therefore, the S glycoprotein encoding gene has widely been used for the molecular analysis of SARS-Co-2 due to its features affecting antigenicity and immunogenicity. We analyzed the S gene sequences of 35 SARS-CoV-2 isolates in Kuwait from March 2020 to February 2021 using the Sanger method and MinION nanopore technology to confirm novel nucleotide alterations. Our results show that the Kuwaiti strains from clade 19A and B were the dominant variants early in the pandemic, while clade 20I (Alpha, V1) was the dominant variant from February 2021 onward. Besides the known mutations, 21 nucleotide deletions in the S glycoprotein in one Kuwaiti strain were detected, which might reveal a recombinant SARS-CoV-2 with the defective viral genome (DVG). This study emphasizes the importance of closely perceiving the emerging clades with these mutations during this continuous pandemic as some may influence the specificity of diagnostic tests, such as RT-PCR and even vaccine design directing these positions.
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Affiliation(s)
- Nada Madi
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait
- Correspondence: ; Tel.: +965-99736265; Fax: +965-25332719
| | - Mohammad Sadeq
- Jaber Al-Ahmad Armed Forces Hospital, Sabhan 91710, Kuwait
| | - Sahar Essa
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait
| | - Hussain A. Safar
- Research Core Facility and OMICS Research Unit, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait
| | - Anfal Al-Adwani
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait
| | - Marwa Al-Khabbaz
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait
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Iddon C, Jones B, Sharpe P, Cevik M, Fitzgerald S. A population framework for predicting the proportion of people infected by the far-field airborne transmission of SARS-CoV-2 indoors. BUILDING AND ENVIRONMENT 2022; 221:109309. [PMID: 35757305 PMCID: PMC9212805 DOI: 10.1016/j.buildenv.2022.109309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
The number of occupants in a space influences the risk of far-field airborne transmission of SARS-CoV-2 because the likelihood of having infectious and susceptible people both correlate with the number of occupants. This paper explores the relationship between occupancy and the probability of infection, and how this affects an individual person and a population of people. Mass-balance and dose-response models determine far-field transmission risks for an individual person and a population of people after sub-dividing a large reference space into 10 identical comparator spaces. For a single infected person, the dose received by an individual person in the comparator space is 10 times higher because the equivalent ventilation rate per infected person is lower when the per capita ventilation rate is preserved. However, accounting for population dispersion, such as the community prevalence of the virus, the probability of an infected person being present and uncertainty in their viral load, shows the transmission probability increases with occupancy and the reference space has a higher transmission risk. Also, far-field transmission is likely to be a rare event that requires a high emission rate, and there are a set of Goldilocks conditions that are just right when equivalent ventilation is effective at mitigating against transmission. These conditions depend on the viral load, because when they are very high or low, equivalent ventilation has little effect on transmission risk. Nevertheless, resilient buildings should deliver the equivalent ventilation rate required by standards as minimum.
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Affiliation(s)
- Christopher Iddon
- Department of Architecture and Built Environment, University of Nottingham, Nottingham, UK
| | - Benjamin Jones
- Department of Architecture and Built Environment, University of Nottingham, Nottingham, UK
| | - Patrick Sharpe
- Department of Architecture and Built Environment, University of Nottingham, Nottingham, UK
| | - Muge Cevik
- Department of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
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13
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Diamond MS, Lambris JD, Ting JP, Tsang JS. Considering innate immune responses in SARS-CoV-2 infection and COVID-19. Nat Rev Immunol 2022; 22:465-470. [PMID: 35788185 PMCID: PMC9252555 DOI: 10.1038/s41577-022-00744-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2022] [Indexed: 12/22/2022]
Abstract
During the COVID-19 pandemic, much of the media focus has been on adaptive immunity, particularly antibody levels and memory T cells. However, immunologists have been striving to decipher how SARS-CoV-2 infection impacts our first line of defence, namely the innate immune system. In early 2022, Program staff from the NIAID at the NIH organized a workshop focusing on the innate immune response to SARS-CoV-2 infection and during COVID-19, which was chaired by Ralph Baric, Jenny Ting and John Lambris. Following the meeting, Nature Reviews Immunology invited some of the organizers and speakers to share their thoughts on the key discussion points.
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Affiliation(s)
- Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St Louis, MO, USA.
| | - John D Lambris
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jenny P Ting
- Departments of Genetics, Microbiology and Immunology, Lineberger Comprehensive Cancer Center, Center for Translational Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA.
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA.
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14
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Goławski M, Lewandowski P, Jabłońska I, Delijewski M. The Reassessed Potential of SARS-CoV-2 Attenuation for COVID-19 Vaccine Development—A Systematic Review. Viruses 2022; 14:v14050991. [PMID: 35632736 PMCID: PMC9146402 DOI: 10.3390/v14050991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
Live-attenuated SARS-CoV-2 vaccines received relatively little attention during the COVID-19 pandemic. Despite this, several methods of obtaining attenuated coronaviruses are known. In this systematic review, the strategies of coronavirus attenuation, which may potentially be applied to SARS-CoV-2, were identified. PubMed, Scopus, Web of Science and Embase databases were searched to identify relevant articles describing attenuating mutations tested in vivo. In case of coronaviruses other than SARS-CoV-2, sequence alignment was used to exclude attenuating mutations that cannot be applied to SARS-CoV-2. Potential immunogenicity, safety and efficacy of the attenuated SARS-CoV-2 vaccine were discussed based on animal studies data. A total of 27 attenuation strategies, used to create 101 different coronaviruses, have been described in 56 eligible articles. The disruption of the furin cleavage site in the SARS-CoV-2 spike protein was identified as the most promising strategy. The replacement of core sequences of transcriptional regulatory signals, which prevents recombination with wild-type viruses, also appears particularly advantageous. Other important attenuating mutations encompassed mostly the prevention of evasion of innate immunity. Sufficiently attenuated coronaviruses typically caused no meaningful disease in susceptible animals and protected them from challenges with virulent virus. This indicates that attenuated COVID-19 vaccines may be considered as a potential strategy to fight the threat posed by SARS-CoV-2.
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Affiliation(s)
- Marcin Goławski
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland; (P.L.); (M.D.)
- Correspondence:
| | - Piotr Lewandowski
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland; (P.L.); (M.D.)
| | - Iwona Jabłońska
- Department of Biophysics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland;
| | - Marcin Delijewski
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland; (P.L.); (M.D.)
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15
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Virucidal efficacy of laundry sanitizers against SARS-CoV-2 and other coronaviruses and influenza viruses. Sci Rep 2022; 12:5247. [PMID: 35347149 PMCID: PMC8960219 DOI: 10.1038/s41598-022-08259-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/03/2022] [Indexed: 11/25/2022] Open
Abstract
The clothes laundering process affords numerous opportunities for dissemination of infectious virus from contaminated clothing to appliance surfaces and other household surfaces and eventually to launderer’s hands. We have explored the efficacy of laundry sanitizers for inactivating coronaviruses and influenza viruses. Virucidal efficacy was tested using standardized suspension inactivation methods (EN 14476) or hard-surface inactivation methods (ASTM E1053-20) against SARS-CoV-2, human coronavirus 229E (HCoV 229E), influenza A virus (2009-H1N1 A/Mexico), or influenza B virus (B/Hong Kong). Efficacy was measured in terms of log10 reduction in infectious virus titer, after 15 min contact time (suspension studies) or 5 min contact time (hard surface studies) at 20 ± 1 °C. In liquid suspension studies, laundry sanitizers containing p-chloro-m-xylenol (PCMX) or quaternary ammonium compounds (QAC) caused complete inactivation (≥ 4 log10) of HCoV 229E and SARS-CoV-2 within 15 min contact time at 20 ± 1 °C. In hard surface studies, complete inactivation (≥ 4 log10) of each coronavirus or influenza virus, including SARS-CoV-2, was observed following a 5-min contact time at 20 ± 1 °C. Respiratory viruses may remain infectious on clothing/fabrics and environmental surfaces for hours to days. The use of a laundry sanitizer containing microbicidal actives may afford mitigation of the risk of contamination of surfaces during handling of the laundry and washing appliances (i.e., washer/dryer or basin), adjacent surfaces, the waste water stream, and the hands of individuals handling clothes contaminated with SARS-CoV-2, influenza viruses, or other emerging enveloped viruses.
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16
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Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) and the closely related SARS-CoV-2 are emergent highly pathogenic human respiratory viruses causing acute lethal disease associated with lung damage and dysregulated inflammatory responses. SARS-CoV envelope protein (E) is a virulence factor involved in the activation of various inflammatory pathways. Here, we study the contribution of host miRNAs to the virulence mediated by E protein. Small RNAseq analysis of infected mouse lungs identified miRNA-223 as a potential regulator of pulmonary inflammation, since it was significantly increased in SARS-CoV-WT virulent infection compared to the attenuated SARS-CoV-ΔE infection. In vivo inhibition of miRNA-223-3p increased mRNA levels of pro-inflammatory cytokines and NLRP3 inflammasome, suggesting that during lung infection, miRNA-223 might contribute to restrict an excessive inflammatory response. Interestingly, miRNA-223-3p inhibition also increased the levels of the CFTR transporter, which is involved in edema resolution and was significantly downregulated in the lungs of mice infected with the virulent SARS-CoV-WT virus. At the histopathological level, a decrease in the pulmonary edema was observed when miR-223-3p was inhibited, suggesting that miRNA-223-3p was involved in the regulation of the SARS-CoV-induced inflammatory pathology. These results indicate that miRNA-223 participates in the regulation of E protein-mediated inflammatory response during SARS-CoV infection by targeting different host mRNAs involved in the pulmonary inflammation, and identify miRNA-223 as a potential therapeutic target in SARS-CoV infection.
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17
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Wang Z, Yang W, Hua P, Zhang J, Krebs P. Transmission risk of SARS-CoV-2 in the watershed triggered by domestic wastewater discharge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150888. [PMID: 34634348 PMCID: PMC8501193 DOI: 10.1016/j.scitotenv.2021.150888] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 05/23/2023]
Abstract
The outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has already become an unprecedented global pandemic. However, the transmission of SARS-CoV-2, especially the protected SARS-CoV-2 RNA (pRNA) with infectious particles in waterways, is still largely unexplored. In this study, we developed a model to estimate SARS-CoV-2 transmission from the risk source in the excretion of patients to the final exposure in surface water. The model simulated the spatial and temporal distribution of the viral pRNA concentrations in the surface water of the Elbe watershed from March 2020 to January 2021. The results show that the WWTPs with the maximum capacity of >10,000 population equivalents were responsible for 95% of the viral load discharged into the surface water. We estimated the pRNA concentrations in surface water to be 1.33 × 10-2 copies·L-1 on average in the watershed based on the model simulation on viral transmission. It had considerable variations in spatial and temporal scales, which are dominantly controlled by epidemic situations and virus transport with decay in water, respectively. A quantitative microbial risk assessment was conducted to estimate the viral infection probability from surface water ingestion with consideration of the influence of toilet usage frequency and gender/age population groups. All the infection probabilities in the study period were lower than the reference risk levels of 10-4 and 10-5. The individuals aged 15-34 years had the highest infection probability of 4.86 × 10-9 on average from surface water ingestion during swimming activities. The data provided herein suggest that the low pRNA concentrations and infection probability reflected that the waterways were unlikely to be a significant transmission route for SARS-CoV-2.
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Affiliation(s)
- Zhenyu Wang
- Institute of Urban and Industrial Water Management, Technische Universität Dresden, 01062 Dresden, Germany
| | - Wenyu Yang
- Institute of Urban and Industrial Water Management, Technische Universität Dresden, 01062 Dresden, Germany
| | - Pei Hua
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, China; School of Environment, South China Normal University, University Town, Guangzhou, China.
| | - Jin Zhang
- Department of Ecology and Institute of Hydrobiology, Jinan University, 510632 Guangzhou, China
| | - Peter Krebs
- Institute of Urban and Industrial Water Management, Technische Universität Dresden, 01062 Dresden, Germany
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18
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Kalamvoki M, Norris V. A Defective Viral Particle Approach to COVID-19. Cells 2022; 11:302. [PMID: 35053418 PMCID: PMC8774189 DOI: 10.3390/cells11020302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/03/2021] [Accepted: 01/13/2022] [Indexed: 12/10/2022] Open
Abstract
The novel coronavirus SARS-CoV-2 has caused a pandemic resulting in millions of deaths worldwide. While multiple vaccines have been developed, insufficient vaccination combined with adaptive mutations create uncertainty for the future. Here, we discuss novel strategies to control COVID-19 relying on Defective Interfering Particles (DIPs) and related particles that arise naturally during an infection. Our intention is to encourage and to provide the basis for the implementation of such strategies by multi-disciplinary teams. We therefore provide an overview of SARS-CoV-2 for a multi-disciplinary readership that is specifically tailored to these strategies, we identify potential targets based on the current knowledge of the properties and functions of coronaviruses, and we propose specific strategies to engineer DIPs and other interfering or therapeutic nanoparticles.
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Affiliation(s)
- Maria Kalamvoki
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Vic Norris
- Laboratory of Microbiology Signals and Microenvironment, University of Rouen, 76821 Mont Saint Aignan, France;
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19
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Tyagi N, Gurian PL, Kumar A. Using QMRA to understand possible exposure risks of SARS-CoV-2 from the water environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:7240-7253. [PMID: 34467495 PMCID: PMC8408015 DOI: 10.1007/s11356-021-16188-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
This study investigated the human risk of infection due to inadvertent ingestion of water during swimming in a river that receives SARS-CoV-2-containing effluent from a wastewater treatment plant (WWTP). A quantitative microbial risk assessment (QMRA) approach was applied for risk estimation using dose-response models (DRM) of different surrogate coronaviruses (SARS-CoV-1, MERS-CoV) and the virus responsible for most infectious respiratory illnesses (i.e., influenza A H5N1) due to the unavailability of DRM for SARS-CoV-2. The ratio of infectious concentration to genomic copies of SARS-CoV-2 is unknown and also unavailable for other coronaviruses. Therefore, literature-based information on enteric viruses was used for formulating the ratio used for QMRA, although it is acknowledged that identifying this information for SARS-CoV-2 is a priority, and in the absence of information specific to SARS-CoV-2, another coronavirus would be a preferable surrogate to the enteric viruses used here. The calculated concentration of ingested SARS-CoV-2 ranged between 4.6 × 10-7 and 80.5 genomic copies/dip (one swim = 32 mL). The risk of infection (> 9 × 10-12 to 5.8 × 10-1) was found to be > 1/10,000 annual risk of infection. Moreover, the study revealed that the risk estimation was largely dependent on the value of the molecular concentration of SARS-CoV-2 (gc/mL). Overall immediate attention is required for obtaining information on the (i) ratio of infectious virus to genomic copies, (ii) DRM for SARS-CoV-2, and (iii) virus reduction rate after treatment in the WWTPs. The QMRA structure used in present findings is helpful in analyzing and prioritizing upcoming health risks due to swimming performed in contaminated rivers during the COVID-19 outbreak.
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Affiliation(s)
- Neha Tyagi
- Department of Civil Engineering, Indian Institute of Technology Delhi, New Delhi, 110016 India
| | - Patrick L. Gurian
- Department of Civil, Architectural and Environmental Engineering, Drexel University, Philadelphia, PA USA
| | - Arun Kumar
- Department of Civil Engineering, Indian Institute of Technology Delhi, New Delhi, 110016 India
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20
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The importance of accessory protein variants in the pathogenicity of SARS-CoV-2. Arch Biochem Biophys 2022; 717:109124. [PMID: 35085577 PMCID: PMC8785432 DOI: 10.1016/j.abb.2022.109124] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/15/2022] [Accepted: 01/17/2022] [Indexed: 01/16/2023]
Abstract
The coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS- CoV-2) with an estimated fatality rate of less than 1%. The SARS-CoV-2 accessory proteins ORF3a, ORF6, ORF7a, ORF7b, ORF8, and ORF10 possess putative functions to manipulate host immune mechanisms. These involve interferons, which appear as a consensus function, immune signaling receptor NLRP3 (NLR family pyrin domain-containing 3) inflammasome, and inflammatory cytokines such as interleukin 1β (IL-1β) and are critical in COVID-19 pathology. Outspread variations of each of the six accessory proteins were observed across six continents of all complete SARS-CoV-2 proteomes based on the data reported before November 2020. A decreasing order of percentage of unique variations in the accessory proteins was determined as ORF3a > ORF8 > ORF7a > ORF6 > ORF10 > ORF7b across all continents. The highest and lowest unique variations of ORF3a were observed in South America and Oceania, respectively. These findings suggest that the wide variations in accessory proteins seem to affect the pathogenicity of SARS-CoV-2.
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21
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Hiroki CH, Sarden N, Hassanabad MF, Yipp BG. Innate Receptors Expression by Lung Nociceptors: Impact on COVID-19 and Aging. Front Immunol 2021; 12:785355. [PMID: 34975876 PMCID: PMC8716370 DOI: 10.3389/fimmu.2021.785355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/16/2021] [Indexed: 12/14/2022] Open
Abstract
The lungs are constantly exposed to non-sterile air which carries harmful threats, such as particles and pathogens. Nonetheless, this organ is equipped with fast and efficient mechanisms to eliminate these threats from the airways as well as prevent pathogen invasion. The respiratory tract is densely innervated by sensory neurons, also known as nociceptors, which are responsible for the detection of external stimuli and initiation of physiological and immunological responses. Furthermore, expression of functional innate receptors by nociceptors have been reported; however, the influence of these receptors to the lung function and local immune response is poorly described. The COVID-19 pandemic has shown the importance of coordinated and competent pulmonary immunity for the prevention of pathogen spread as well as prevention of excessive tissue injury. New findings suggest that lung nociceptors can be a target of SARS-CoV-2 infection; what remains unclear is whether innate receptor trigger sensory neuron activation during SARS-CoV-2 infection and what is the relevance for the outcomes. Moreover, elderly individuals often present with respiratory, neurological and immunological dysfunction. Whether aging in the context of sensory nerve function and innate receptors contributes to the disorders of these systems is currently unknown. Here we discuss the expression of innate receptors by nociceptors, particularly in the lungs, and the possible impact of their activation on pulmonary immunity. We then demonstrate recent evidence that suggests lung sensory neurons as reservoirs for SARS-CoV-2 and possible viral recognition via innate receptors. Lastly, we explore the mechanisms by which lung nociceptors might contribute to disturbance in respiratory and immunological responses during the aging process.
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Affiliation(s)
- Carlos H. Hiroki
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Nicole Sarden
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Mortaza F. Hassanabad
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Bryan G. Yipp
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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22
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Bakhtazad A, Garmabi B, Joghataei MT. Neurological manifestations of coronavirus infections, before and after COVID-19: a review of animal studies. J Neurovirol 2021; 27:864-884. [PMID: 34727365 PMCID: PMC8561685 DOI: 10.1007/s13365-021-01014-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 07/15/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This virus, which was first identified in December 2019 in China, has resulted in a yet ongoing viral pandemic. Coronaviridae could potentially cause several disorders in a wide range of hosts such as birds and mammals. Although infections caused by this family of viruses are predominantly limited to the respiratory tract, Betacoronaviruses are potentially able to invade the central nervous system (CNS) as well as many other organs, thereby inducing neurological damage ranging from mild to lethal in both animals and humans. Over the past two decades, three novel CoVs, SARS-CoV-1, MERS-CoV, and SARS-CoV-2, emerging from animal reservoirs have exhibited neurotropic properties causing severe and even fatal neurological diseases. The pathobiology of these neuroinvasive viruses has yet to be fully known. Both clinical features of the previous CoV epidemics (SARS-CoV-1 and MERS-CoV) and lessons from animal models used in studying neurotropic CoVs, especially SARS and MERS, constitute beneficial tools in comprehending the exact mechanisms of virus implantation and in illustrating pathogenesis and virus dissemination pathways in the CNS. Here, we review the animal research which assessed CNS infections with previous more studied neurotropic CoVs to demonstrate how experimental studies with appliable animal models can provide scientists with a roadmap in the CNS impacts of SARS-CoV-2. Indeed, animal studies can finally help us discover the underlying mechanisms of damage to the nervous system in COVID-19 patients and find novel therapeutic agents in order to reduce mortality and morbidity associated with neurological complications of SARS-CoV-2 infection.
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Affiliation(s)
- Atefeh Bakhtazad
- Cellular and Molecular Research Center (CMRC), Iran University of Medical Sciences, 1449614535 Tehran, Iran
| | - Behzad Garmabi
- School of Medicine, Shahroud University of Medical Sciences, Haft-Tir Sq, University Blv, 3614773947 Shahroud, Iran
| | - Mohammad Taghi Joghataei
- Cellular and Molecular Research Center (CMRC), Iran University of Medical Sciences, 1449614535 Tehran, Iran
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23
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Prates-Syed WA, Chaves LCS, Crema KP, Vuitika L, Lira A, Côrtes N, Kersten V, Guimarães FEG, Sadraeian M, Barroso da Silva FL, Cabral-Marques O, Barbuto JAM, Russo M, Câmara NOS, Cabral-Miranda G. VLP-Based COVID-19 Vaccines: An Adaptable Technology against the Threat of New Variants. Vaccines (Basel) 2021; 9:1409. [PMID: 34960155 PMCID: PMC8708688 DOI: 10.3390/vaccines9121409] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 12/23/2022] Open
Abstract
Virus-like particles (VLPs) are a versatile, safe, and highly immunogenic vaccine platform. Recently, there are developmental vaccines targeting SARS-CoV-2, the causative agent of COVID-19. The COVID-19 pandemic affected humanity worldwide, bringing out incomputable human and financial losses. The race for better, more efficacious vaccines is happening almost simultaneously as the virus increasingly produces variants of concern (VOCs). The VOCs Alpha, Beta, Gamma, and Delta share common mutations mainly in the spike receptor-binding domain (RBD), demonstrating convergent evolution, associated with increased transmissibility and immune evasion. Thus, the identification and understanding of these mutations is crucial for the production of new, optimized vaccines. The use of a very flexible vaccine platform in COVID-19 vaccine development is an important feature that cannot be ignored. Incorporating the spike protein and its variations into VLP vaccines is a desirable strategy as the morphology and size of VLPs allows for better presentation of several different antigens. Furthermore, VLPs elicit robust humoral and cellular immune responses, which are safe, and have been studied not only against SARS-CoV-2 but against other coronaviruses as well. Here, we describe the recent advances and improvements in vaccine development using VLP technology.
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Affiliation(s)
- Wasim A. Prates-Syed
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
- Institute of Research and Education in Child Health (PENSI), São Paulo 01228200, SP, Brazil
| | - Lorena C. S. Chaves
- Department of Microbiology and Immunology, School of Medicine, Emory University, Claudia Nance Rollins Building, Atlanta, GA 30329, USA;
| | - Karin P. Crema
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
- Institute of Research and Education in Child Health (PENSI), São Paulo 01228200, SP, Brazil
| | - Larissa Vuitika
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
| | - Aline Lira
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
- Institute of Research and Education in Child Health (PENSI), São Paulo 01228200, SP, Brazil
| | - Nelson Côrtes
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
- Institute of Research and Education in Child Health (PENSI), São Paulo 01228200, SP, Brazil
| | - Victor Kersten
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
| | | | - Mohammad Sadraeian
- São Carlos Institute of Physics, IFSC-USP, São Carlos 13566590, SP, Brazil; (F.E.G.G.); (M.S.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology, Sydney, NSW 2007, Australia
| | - Fernando L. Barroso da Silva
- Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040903, SP, Brazil;
- Department of Chemical and Biomolecular Engeneering, North Carolina State University, Raleigh, NC 27695, USA
| | - Otávio Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508000, SP, Brazil
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Children’s Medical Center, Tehran 1419733151, Iran
| | - José A. M. Barbuto
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
- Laboratory of Medical Investigation in Pathogenesis and Targeted Therapy in Onco-Immuno-Hematology (LIM-31), Department of Hematology, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 0124690, SP, Brazil
| | - Momtchilo Russo
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
| | - Niels O. S. Câmara
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
| | - Gustavo Cabral-Miranda
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
- Institute of Research and Education in Child Health (PENSI), São Paulo 01228200, SP, Brazil
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Mahmood TB, Saha A, Hossan MI, Mizan S, Arman SMAS, Chowdhury AS. A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100065. [PMID: 34841355 PMCID: PMC8610355 DOI: 10.1016/j.crmicr.2021.100065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 01/08/2023] Open
Abstract
48 SNPs were identified from the genome-wide analysis of 410 South Asian SARS-CoV-2 sequences. About 85% SNPs are packaged in ORF1ab, spike protein, and nucleocapsid. South Asian strains are highly related to the South American and European strains according to the phylogenetic analysis. Unlike other countries, frequency of 1163A>T missense mutation is very high (78.80%) in Bangladeshi samples.
Counts for SARS-CoV-2 associated infections and fatalities are on the rise globally even in regions which contained the spread momentarily. The pattern of infections has been found to be controlled by the distinctive selection pressures exerted by fluctuating environmental nature and hosts. A total of 410 whole-genome sequences submitted by the South Asian countries were retrieved from the GISAID database and analyzed to assess the impact and pattern of mutations in this region. Most common and frequent mutations in the South Asian countries are 241C > T, 3037C > T, 14408C > T, and 23403A > G and about 85% SNPs are localized in ORF1ab, spike protein, and nucleocapsid. Among the identified mutations, the proportion of missense type (54.17%) was highest, followed by the synonymous (41.66%) and the non-coding types (4.17%). While analyzing transmission source in terms of geolocation, the largest clustered group from the South Asian countries was based on the G-clade (D614G) (81.7%; 335/410 samples), tracing the inception and transmission of SARS-CoV-2 infections in the South Asian countries from European regions. Phylogenetic analysis also revealed that the South Asian strains are highly related to the South American and European strains. We found that G-clade mutations are more prevalent (96.19%) in the samples of Bangladesh which were also prevalent in the European isolates. Surprisingly, one missense mutation (1163A > T) in ORF1ab gene became dominant only in Bangladesh (78.8%), which led to debates regarding effects on the pathogenicity and transmissibility of the virus. Overall, the findings of this study highlight the frequently mutated SARS-CoV-2 variants among the COVID-19 patients in the South Asian countries which might ease containment of the disease in this region through investigating the virulence reducing factors as the identified mutations are strongly correlated with low infection and mortality rate.
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Affiliation(s)
- Tousif Bin Mahmood
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Ayan Saha
- Department of Genetic Engineering and Biotechnology, East West University, Dhaka 1212, Bangladesh.,Faculty of Medicine, Children's Cancer Institute, University of New South Wales, Australia
| | - Mohammad Imran Hossan
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Shagufta Mizan
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram 4331, Bangladesh
| | - S M Abu Sufian Arman
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Afrin Sultana Chowdhury
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
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Sobolik JS, Sajewski ET, Jaykus LA, Cooper DK, Lopman BA, Kraay ANM, Ryan PB, Leon JS. Controlling risk of SARS-CoV-2 infection in essential workers of enclosed food manufacturing facilities. Food Control 2021; 133:108632. [PMID: 34703082 PMCID: PMC8532033 DOI: 10.1016/j.foodcont.2021.108632] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/23/2022]
Abstract
The SARS-CoV-2 global pandemic poses significant health risks to workers who are essential to maintaining the food supply chain. Using a quantitative risk assessment model, this study characterized the impact of risk reduction strategies for controlling SARS-CoV-2 transmission (droplet, aerosol, fomite-mediated) among front-line workers in a representative indoor fresh fruit and vegetable manufacturing facility. We simulated: 1) individual and cumulative SARS-CoV-2 infection risks from close contact (droplet and aerosols at 1–3 m), aerosol, and fomite-mediated exposures to a susceptible worker following exposure to an infected worker during an 8 h-shift; and 2) the relative reduction in SARS-CoV-2 infection risk attributed to infection control interventions (physical distancing, mask use, ventilation, surface disinfection, hand hygiene, vaccination). Without mitigation measures, the SARS-CoV-2 infection risk was largest for close contact (droplet and aerosol) at 1 m (0.96, 5th – 95th percentile: 0.67–1.0). In comparison, risk associated with fomite (0.26, 5th – 95th percentile: 0.10–0.56) or aerosol exposure alone (0.05, 5th – 95th percentile: 0.01–0.13) at 1 m distance was substantially lower (73–95%). At 1 m, droplet transmission predominated over aerosol and fomite-mediated transmission, however, this changed by 3 m, with aerosols comprising the majority of the exposure dose. Increasing physical distancing reduced risk by 84% (1–2 m) and 91% (1–3 m). Universal mask use reduced infection risk by 52–88%, depending on mask type. Increasing ventilation (from 0.1 to 2–8 air changes/hour) resulted in risk reductions of 14–54% (1 m) and 55–85% (2 m). Combining these strategies, together with handwashing and surface disinfection, resulted in <1% infection risk. Partial or full vaccination of the susceptible worker resulted in risk reductions of 73–92% (1 m risk range: 0.08–0.26). However, vaccination paired with other interventions (ACH 2, mask use, or distancing) was necessary to achieve infection risks <1%. Current industry SARS-CoV-2 risk reduction strategies, particularly when bundled, provide significant protection to essential food workers.
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Affiliation(s)
- Julia S Sobolik
- Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | | | - Lee-Ann Jaykus
- Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - D Kane Cooper
- Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Ben A Lopman
- Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Alicia N M Kraay
- Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - P Barry Ryan
- Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Juan S Leon
- Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
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Mohammad T, Choudhury A, Habib I, Asrani P, Mathur Y, Umair M, Anjum F, Shafie A, Yadav DK, Hassan MI. Genomic Variations in the Structural Proteins of SARS-CoV-2 and Their Deleterious Impact on Pathogenesis: A Comparative Genomics Approach. Front Cell Infect Microbiol 2021; 11:765039. [PMID: 34722346 PMCID: PMC8548870 DOI: 10.3389/fcimb.2021.765039] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022] Open
Abstract
A continual rise in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection causing coronavirus disease (COVID-19) has become a global threat. The main problem comes when SARS-CoV-2 gets mutated with the rising infection and becomes more lethal for humankind than ever. Mutations in the structural proteins of SARS-CoV-2, i.e., the spike surface glycoprotein (S), envelope (E), membrane (M) and nucleocapsid (N), and replication machinery enzymes, i.e., main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) creating more complexities towards pathogenesis and the available COVID-19 therapeutic strategies. This study analyzes how a minimal variation in these enzymes, especially in S protein at the genomic/proteomic level, affects pathogenesis. The structural variations are discussed in light of the failure of small molecule development in COVID-19 therapeutic strategies. We have performed in-depth sequence- and structure-based analyses of these proteins to get deeper insights into the mechanism of pathogenesis, structure-function relationships, and development of modern therapeutic approaches. Structural and functional consequences of the selected mutations on these proteins and their association with SARS-CoV-2 virulency and human health are discussed in detail in the light of our comparative genomics analysis.
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Affiliation(s)
- Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Arunabh Choudhury
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Insan Habib
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Purva Asrani
- Department of Microbiology, University of Delhi, New Delhi, India
| | - Yash Mathur
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Mohd Umair
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Dharmendra Kumar Yadav
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Incheon, South Korea
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Cotman ZJ, Bowden MJ, Richter BP, Phelps JH, Dibble CJ. Factors affecting aerosol SARS-CoV-2 transmission via HVAC systems; a modeling study. PLoS Comput Biol 2021; 17:e1009474. [PMID: 34662342 PMCID: PMC8553169 DOI: 10.1371/journal.pcbi.1009474] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 10/28/2021] [Accepted: 09/23/2021] [Indexed: 12/11/2022] Open
Abstract
The role of heating, ventilation, and air-conditioning (HVAC) systems in the transmission of SARS-CoV-2 is unclear. To address this gap, we simulated the release of SARS-CoV-2 in a multistory office building and three social gathering settings (bar/restaurant, nightclub, wedding venue) using a well-mixed, multi-zone building model similar to those used by Wells, Riley, and others. We varied key factors of HVAC systems, such as the Air Changes Per Hour rate (ACH), Fraction of Outside Air (FOA), and Minimum Efficiency Reporting Values (MERV) to examine their effect on viral transmission, and additionally simulated the protective effects of in-unit ultraviolet light decontamination (UVC) and separate in-room air filtration. In all building types, increasing the ACH reduced simulated infections, and the effects were seen even with low aerosol emission rates. However, the benefits of increasing the fraction of outside air and filter efficiency rating were greatest when the aerosol emission rate was high. UVC filtration improved the performance of typical HVAC systems. In-room filtration in an office setting similarly reduced overall infections but worked better when placed in every room. Overall, we found little evidence that HVAC systems facilitate SARS-CoV-2 transmission; most infections in the simulated office occurred near the emission source, with some infections in individuals temporarily visiting the release zone. HVAC systems only increased infections in one scenario involving a marginal increase in airflow in a poorly ventilated space, which slightly increased the likelihood of transmission outside the release zone. We found that improving air circulation rates, increasing filter MERV rating, increasing the fraction of outside air, and applying UVC radiation and in-room filtration may reduce SARS-CoV-2 transmission indoors. However, these mitigation measures are unlikely to provide a protective benefit unless SARS-CoV-2 aerosol emission rates are high (>1,000 Plaque-forming units (PFU) / min).
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Affiliation(s)
- Zachary J. Cotman
- Battelle Memorial Institute, Columbus, Ohio, United States of America
| | - Michael J. Bowden
- Battelle Memorial Institute, Columbus, Ohio, United States of America
| | | | - Joseph H. Phelps
- Battelle Memorial Institute, Columbus, Ohio, United States of America
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Sobolik JS, Sajewski ET, Jaykus LA, Cooper DK, Lopman BA, Kraay ANM, Ryan PB, Guest JL, Webb-Girard A, Leon JS. Low risk of SARS-CoV-2 transmission via fomite, even in cold-chain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.08.23.21262477. [PMID: 34462753 PMCID: PMC8404890 DOI: 10.1101/2021.08.23.21262477] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Countries continue to debate the need for decontamination of cold-chain food packaging to reduce possible SARS-CoV-2 fomite transmission among workers. While laboratory-based studies demonstrate persistence of SARS-CoV-2 on surfaces, the likelihood of fomite-mediated transmission under real-life conditions is uncertain. METHODS Using a quantitative risk assessment model, we simulated in a frozen food packaging facility 1) SARS-CoV-2 fomite-mediated infection risks following worker exposure to contaminated plastic packaging; and 2) reductions in these risks attributed to masking, handwashing, and vaccination. FINDINGS In a representative facility with no specific interventions, SARS-CoV-2 infection risk to a susceptible worker from contact with contaminated packaging was 2·8 × 10 -3 per 1h-period (95%CI: 6·9 × 10 -6 , 2·4 × 10 -2 ). Implementation of standard infection control measures, handwashing and masks (9·4 × 10 -6 risk per 1h-period, 95%CI: 2·3 × 10 -8 , 8·1 × 10 -5 ), substantially reduced risk (99·7%). Vaccination of the susceptible worker (two doses Pfizer/Moderna, vaccine effectiveness: 86-99%) combined with handwashing and masking reduced risk to less than 1·0 × 10 -6 . Simulating increased infectiousness/transmissibility of new variants (2-, 10-fold viral shedding) among a fully vaccinated workforce, handwashing and masks continued to mitigate risk (2·0 × 10 -6 -1·1 × 10 -5 risk per 1h-period). Decontamination of packaging in addition to these interventions reduced infection risks to below the 1·0 × 10 -6 risk threshold. INTERPRETATION Fomite-mediated SARS-CoV-2 infection risks were very low under cold-chain conditions. Handwashing and masking provide significant protection to workers, especially when paired with vaccination. FUNDING U.S. Department of Agriculture.
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Affiliation(s)
- Julia S. Sobolik
- Rollins School of Public Health, Emory University, Atlanta, GA, USA, 30322
| | | | - Lee-Ann Jaykus
- Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA, 27695
| | - D. Kane Cooper
- Rollins School of Public Health, Emory University, Atlanta, GA, USA, 30322
| | - Ben A. Lopman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA, 30322
| | - Alicia NM. Kraay
- Rollins School of Public Health, Emory University, Atlanta, GA, USA, 30322
| | - P. Barry Ryan
- Rollins School of Public Health, Emory University, Atlanta, GA, USA, 30322
| | - Jodie L. Guest
- Rollins School of Public Health, Emory University, Atlanta, GA, USA, 30322
| | - Amy Webb-Girard
- Rollins School of Public Health, Emory University, Atlanta, GA, USA, 30322
| | - Juan S. Leon
- Rollins School of Public Health, Emory University, Atlanta, GA, USA, 30322
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29
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Biochemical composition, transmission and diagnosis of SARS-CoV-2. Biosci Rep 2021; 41:229295. [PMID: 34291285 PMCID: PMC8350435 DOI: 10.1042/bsr20211238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a life-threatening respiratory infection caused by severe acute respiratory syndrome virus (SARS-CoV-2), a novel human coronavirus. COVID-19 was declared a pandemic by World Health Organization in March 2020 for its continuous and rapid spread worldwide. Rapidly emerging COVID-19 epicenters and mutants of concerns have created mammoth chaos in healthcare sectors across the globe. With over 185 million infections and approximately 4 million deaths globally, COVID-19 continues its unchecked spread despite all mitigation measures. Until effective and affordable antiretroviral drugs are made available and the population at large is vaccinated, timely diagnosis of the infection and adoption of COVID-appropriate behavior remains major tool available to curtail the still escalating COVID-19 pandemic. This review provides an updated overview of various techniques of COVID-19 testing in human samples and also discusses, in brief, the biochemical composition and mode of transmission of the SARS-CoV-2. Technological advancement in various molecular, serological and immunological techniques including mainly the reverse-transcription polymerase chain reaction (RT-PCR), CRISPR, lateral flow assays (LFAs), and immunosensors are reviewed.
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30
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Zhang X, Wang J. Dose-response Relation Deduced for Coronaviruses From Coronavirus Disease 2019, Severe Acute Respiratory Syndrome, and Middle East Respiratory Syndrome: Meta-analysis Results and its Application for Infection Risk Assessment of Aerosol Transmission. Clin Infect Dis 2021; 73:e241-e245. [PMID: 33119733 PMCID: PMC7665418 DOI: 10.1093/cid/ciaa1675] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND A comprehensive understanding of the transmission routes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is of great importance to effectively control the spread of coronavirus disease 2019 (COVID-19). However, the fundamental dose-response relation is missing for evaluation of the infection risk. METHODS We developed a simple framework to integrate the a priori dose-response relation for SARS-CoV-2 based on mice experiments, the recent data on infection risk from a meta-analysis, and respiratory virus shedding in exhaled breath to shed light on the dose-response relation for humans. The aerosol transmission infection risk was evaluated based on the dose-response model for a typical indoor environment. RESULTS The developed dose-response relation is an exponential function with a constant k in the range of about 6.4 × 104 to 9.8 × 105 virus copies, which means that the infection risk caused by 1 virus copy in viral shedding is on the order of 10-6 to 10-5. The median infection risk via aerosol transmission with 1-hour exposure (10-6 to 10-4) was significantly lower than the risk caused by close contact (10-1) in a room with an area of 10 to 400 m2 with 1 infected individual in it and with a typical ventilation rate of 1 air change per hour. CONCLUSIONS The infection risk caused by aerosol transmission was significantly lower than the risk caused by close contact. It is still necessary to be cautious for the potential aerosol transmission risk in small rooms with prolonged exposure duration.
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Affiliation(s)
- Xiaole Zhang
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatics Engineering, Swiss Federal Institute of Technology Zürich (ETH Zürich), Zürich, Switzerland.,Laboratory for Advanced Analytical Technologies, Department of Mobility, Energy and Environment, Swiss Federal Laboratories for Materials Science and Technology (Empa), Dübendorf, Switzerland
| | - Jing Wang
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatics Engineering, Swiss Federal Institute of Technology Zürich (ETH Zürich), Zürich, Switzerland.,Laboratory for Advanced Analytical Technologies, Department of Mobility, Energy and Environment, Swiss Federal Laboratories for Materials Science and Technology (Empa), Dübendorf, Switzerland
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31
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Pandey K, Acharya A, Mohan M, Ng CL, Reid SP, Byrareddy SN. Animal models for SARS-CoV-2 research: A comprehensive literature review. Transbound Emerg Dis 2021; 68:1868-1885. [PMID: 33128861 PMCID: PMC8085186 DOI: 10.1111/tbed.13907] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 10/09/2020] [Accepted: 10/28/2020] [Indexed: 12/13/2022]
Abstract
Emerging and re-emerging viral diseases can create devastating effects on human lives and may also lead to economic crises. The ongoing COVID-19 pandemic due to the novel coronavirus (nCoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which originated in Wuhan, China, has caused a global public health emergency. To date, the molecular mechanism of transmission of SARS-CoV-2, its clinical manifestations and pathogenesis is not completely understood. The global scientific community has intensified its efforts in understanding the biology of SARS-CoV-2 for development of vaccines and therapeutic interventions to prevent the rapid spread of the virus and to control mortality and morbidity associated with COVID-19. To understand the pathophysiology of SARS-CoV-2, appropriate animal models that mimic the biology of human SARS-CoV-2 infection are urgently needed. In this review, we outline animal models that have been used to study previous human coronaviruses (HCoVs), including severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV). Importantly, we discuss models that are appropriate for SARS-CoV-2 as well as the advantages and disadvantages of various available methods.
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Affiliation(s)
- Kabita Pandey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Mahesh Mohan
- Texas Biomedical Research Institute, Southwest National Primate Research Center, San Antonio, TX, USA
| | - Caroline L Ng
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - St Patrick Reid
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Centre, Omaha, NE, USA
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Centre, Omaha, NE, USA
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Wilson AM, Jones RM, Lugo Lerma V, Abney SE, King MF, Weir MH, Sexton JD, Noakes CJ, Reynolds KA. Respirators, face masks, and their risk reductions via multiple transmission routes for first responders within an ambulance. JOURNAL OF OCCUPATIONAL AND ENVIRONMENTAL HYGIENE 2021; 18:345-360. [PMID: 34129448 DOI: 10.1080/15459624.2021.1926468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
First responders may have high SARS-CoV-2 infection risks due to working with potentially infected patients in enclosed spaces. The study objective was to estimate infection risks per transport for first responders and quantify how first responder use of N95 respirators and patient use of cloth masks can reduce these risks. A model was developed for two Scenarios: an ambulance transport with a patient actively emitting a virus in small aerosols that could lead to airborne transmission (Scenario 1) and a subsequent transport with the same respirator or mask use conditions, an uninfected patient; and remaining airborne SARS-CoV-2 and contaminated surfaces due to aerosol deposition from the previous transport (Scenario 2). A compartmental Monte Carlo simulation model was used to estimate the dispersion and deposition of SARS-CoV-2 and subsequent infection risks for first responders, accounting for variability and uncertainty in input parameters (i.e., transport duration, transfer efficiencies, SARS-CoV-2 emission rates from infected patients, etc.). Infection risk distributions and changes in concentration on hands and surfaces over time were estimated across sub-Scenarios of first responder respirator use and patient cloth mask use. For Scenario 1, predicted mean infection risks were reduced by 69%, 48%, and 85% from a baseline risk (no respirators or face masks used) of 2.9 × 10-2 ± 3.4 × 10-2 when simulated first responders wore respirators, the patient wore a cloth mask, and when first responders and the patient wore respirators or a cloth mask, respectively. For Scenario 2, infection risk reductions for these same Scenarios were 69%, 50%, and 85%, respectively (baseline risk of 7.2 × 10-3 ± 1.0 × 10-2). While aerosol transmission routes contributed more to viral dose in Scenario 1, our simulations demonstrate the ability of face masks worn by patients to additionally reduce surface transmission by reducing viral deposition on surfaces. Based on these simulations, we recommend the patient wear a face mask and first responders wear respirators, when possible, and disinfection should prioritize high use equipment.
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Affiliation(s)
- Amanda M Wilson
- Rocky Mountain Center for Occupational and Environmental Health, University of Utah, Salt Lake City, Utah
- Department of Family and Preventive Medicine, School of Medicine, University of Utah, Salt Lake City, Utah
| | - Rachael M Jones
- Rocky Mountain Center for Occupational and Environmental Health, University of Utah, Salt Lake City, Utah
- Department of Family and Preventive Medicine, School of Medicine, University of Utah, Salt Lake City, Utah
| | - Veronica Lugo Lerma
- Department of Community, Environment, and Policy, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona
| | - Sarah E Abney
- Department of Community, Environment, and Policy, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona
- Department of Environmental Science, College of Agriculture and Life Sciences, University of Arizona, Tucson, Arizona
| | | | - Mark H Weir
- Divison of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, Ohio
| | - Jonathan D Sexton
- Department of Community, Environment, and Policy, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona
| | | | - Kelly A Reynolds
- Department of Community, Environment, and Policy, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona
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Gorkhali R, Koirala P, Rijal S, Mainali A, Baral A, Bhattarai HK. Structure and Function of Major SARS-CoV-2 and SARS-CoV Proteins. Bioinform Biol Insights 2021; 15:11779322211025876. [PMID: 34220199 PMCID: PMC8221690 DOI: 10.1177/11779322211025876] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 05/25/2021] [Indexed: 01/20/2023] Open
Abstract
SARS-CoV-2 virus, the causative agent of COVID-19 pandemic, has a genomic organization consisting of 16 nonstructural proteins (nsps), 4 structural proteins, and 9 accessory proteins. Relative of SARS-CoV-2, SARS-CoV, has genomic organization, which is very similar. In this article, the function and structure of the proteins of SARS-CoV-2 and SARS-CoV are described in great detail. The nsps are expressed as a single or two polyproteins, which are then cleaved into individual proteins using two proteases of the virus, a chymotrypsin-like protease and a papain-like protease. The released proteins serve as centers of virus replication and transcription. Some of these nsps modulate the host’s translation and immune systems, while others help the virus evade the host immune system. Some of the nsps help form replication-transcription complex at double-membrane vesicles. Others, including one RNA-dependent RNA polymerase and one exonuclease, help in the polymerization of newly synthesized RNA of the virus and help minimize the mutation rate by proofreading. After synthesis of the viral RNA, it gets capped. The capping consists of adding GMP and a methylation mark, called cap 0 and additionally adding a methyl group to the terminal ribose called cap1. Capping is accomplished with the help of a helicase, which also helps remove a phosphate, two methyltransferases, and a scaffolding factor. Among the structural proteins, S protein forms the receptor of the virus, which latches on the angiotensin-converting enzyme 2 receptor of the host and N protein binds and protects the genomic RNA of the virus. The accessory proteins found in these viruses are small proteins with immune modulatory roles. Besides functions of these proteins, solved X-ray and cryogenic electron microscopy structures related to the function of the proteins along with comparisons to other coronavirus homologs have been described in the article. Finally, the rate of mutation of SARS-CoV-2 residues of the proteome during the 2020 pandemic has been described. Some proteins are mutated more often than other proteins, but the significance of these mutation rates is not fully understood.
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Affiliation(s)
- Ritesh Gorkhali
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
| | | | - Sadikshya Rijal
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
| | - Ashmita Mainali
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
| | - Adesh Baral
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
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Sobolik JS, Sajewski ET, Jaykus LA, Cooper DK, Lopman BA, Kraay ANM, Ryan PB, Leon JS. Controlling risk of SARS-CoV-2 infection in essential workers of enclosed food manufacturing facilities. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.05.14.21257244. [PMID: 34031667 PMCID: PMC8142669 DOI: 10.1101/2021.05.14.21257244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The SARS-CoV-2 global pandemic poses significant health risks to workers who are essential to maintaining the food supply chain. Using a quantitative risk assessment model, this study characterized the impact of risk reduction strategies for controlling SARS-CoV-2 transmission (droplet, aerosol, fomite-mediated) among front-line workers in a representative enclosed food manufacturing facility. We simulated: 1) individual and cumulative SARS-CoV-2 infection risks from close contact (droplet and aerosols at 1-3m), aerosol, and fomite-mediated exposures to a susceptible worker following exposure to an infected worker during an 8h-shift; and 2) the relative reduction in SARS-CoV-2 infection risk attributed to infection control interventions (physical distancing, mask use, ventilation, surface disinfection, hand hygiene). Without mitigation measures, the SARS-CoV-2 infection risk was largest for close contact (droplet and aerosol) at 1m (0.96, 95%CI: 0.67-1.0). In comparison, risk associated with fomite (0.26, 95%CI: 0.10-0.56) or aerosol exposure alone (0.05, 95%CI: 0.01-0.13) at 1m distance was substantially lower (73-95%). At 1m, droplet transmission predominated over aerosol and fomite-mediated transmission, however, this changed by 3m, with aerosols comprising the majority of the exposure dose. Increasing physical distancing reduced risk by 84% (1 to 2m) and 91% (1 to 3m). Universal mask use reduced infection risk by 52-88%, depending on mask type. Increasing ventilation (from 0.1 to 2-8 air changes/hour) resulted in risk reductions of 14-54% (1m) and 55-85% (2m). Combining these strategies, together with handwashing and surface disinfection, resulted in <1% infection risk. Current industry SARS-CoV-2 risk reduction strategies, particularly when bundled, provide significant protection to essential food workers. SIGNIFICANCE STATEMENT Using mathematical modeling, we find that workers in enclosed food manufacturing facilities are at higher risk of SARS-CoV-2 infection from close contact transmission (exposure to large droplets and small aerosol particles) than fomite transmission. Thus, strategies protecting workers should prioritize close contact transmission pathways, such as physical distancing, universal mask use, and room air changes, with surface disinfection (reducing fomite transmission) and handwashing of secondary importance. Our work supports current international (EU-OSHA), domestic (FDA, OSHA), and food industry-standard guidance for managing COVID-19 transmission in essential workers in the food manufacturing sector. Although our model was designed for an indoor food manufacturing setting, it can be readily adapted to other indoor environments and infectious respiratory pathogens.
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Affiliation(s)
- Julia S. Sobolik
- Rollins School of Public Health, Emory University, Atlanta, GA USA
| | | | - Lee-Ann Jaykus
- Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695
| | - D. Kane Cooper
- Rollins School of Public Health, Emory University, Atlanta, GA USA
| | - Ben A. Lopman
- Rollins School of Public Health, Emory University, Atlanta, GA USA
| | - Alicia NM. Kraay
- Rollins School of Public Health, Emory University, Atlanta, GA USA
| | - P. Barry Ryan
- Rollins School of Public Health, Emory University, Atlanta, GA USA
| | - Juan S. Leon
- Rollins School of Public Health, Emory University, Atlanta, GA USA
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35
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Shi KW, Huang YH, Quon H, Ou-Yang ZL, Wang C, Jiang SC. Quantifying the risk of indoor drainage system in multi-unit apartment building as a transmission route of SARS-CoV-2. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 762:143056. [PMID: 33268249 PMCID: PMC7560110 DOI: 10.1016/j.scitotenv.2020.143056] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/08/2020] [Accepted: 10/10/2020] [Indexed: 05/05/2023]
Abstract
The COVID-19 pandemic has had a profound impact on human society. The isolation of SARS-CoV-2 from patients' feces on human cell line raised concerns of possible transmission through human feces including exposure to aerosols generated by toilet flushing and through the indoor drainage system. Currently, routes of transmission, other than the close contact droplet transmission, are still not well understood. A quantitative microbial risk assessment was conducted to estimate the health risks associated with two aerosol exposure scenarios: 1) toilet flushing, and 2) faulty connection of a floor drain with the building's main sewer pipe. SARS-CoV-2 data were collected from the emerging literature. The infectivity of the virus in feces was estimated based on a range of assumption between viral genome equivalence and infectious unit. The human exposure dose was calculated using Monte Carlo simulation of viral concentrations in aerosols under each scenario and human breathing rates. The probability of COVID-19 illness was generated using the dose-response model for SARS-CoV-1, a close relative of SARS-CoV-2, that was responsible for the SARS outbreak in 2003. The results indicate the median risks of developing COVID-19 for a single day exposure is 1.11 × 10-10 and 3.52 × 10-11 for toilet flushing and faulty drain scenario, respectively. The worst case scenario predicted the high end of COVID-19 risk for the toilet flushing scenario was 5.78 × 10-4 (at 95th percentile). The infectious viral loads in human feces are the most sensitive input parameter and contribute significantly to model uncertainty.
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Affiliation(s)
- Kuang-Wei Shi
- School of Environment, Tsinghua University, Beijing, China
| | - Yen-Hsiang Huang
- Civil and Environmental Engineering, University of California, Irvine, USA
| | - Hunter Quon
- Civil and Environmental Engineering, University of California, Irvine, USA
| | - Zi-Lu Ou-Yang
- School of Environment, Tsinghua University, Beijing, China
| | - Chengwen Wang
- School of Environment, Tsinghua University, Beijing, China.
| | - Sunny C Jiang
- Civil and Environmental Engineering, University of California, Irvine, USA.
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36
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Ijaz MK, Nims RW, Zhou SS, Whitehead K, Srinivasan V, Kapes T, Fanuel S, Epstein JH, Daszak P, Rubino JR, McKinney J. Microbicidal actives with virucidal efficacy against SARS-CoV-2 and other beta- and alpha-coronaviruses and implications for future emerging coronaviruses and other enveloped viruses. Sci Rep 2021; 11:5626. [PMID: 33707476 PMCID: PMC7952405 DOI: 10.1038/s41598-021-84842-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/18/2021] [Indexed: 12/12/2022] Open
Abstract
Mitigating the risk of acquiring coronaviruses including SARS-CoV-2 requires awareness of the survival of virus on high-touch environmental surfaces (HITES) and skin, and frequent use of targeted microbicides with demonstrated efficacy. The data on stability of infectious SARS-CoV-2 on surfaces and in suspension have been put into perspective, as these inform the need for hygiene. We evaluated the efficacies of formulated microbicidal actives against alpha- and beta-coronaviruses, including SARS-CoV-2. The coronaviruses SARS-CoV, SARS-CoV-2, human coronavirus 229E, murine hepatitis virus-1, or MERS-CoV were deposited on prototypic HITES or spiked into liquid matrices along with organic soil loads. Alcohol-, quaternary ammonium compound-, hydrochloric acid-, organic acid-, p-chloro-m-xylenol-, and sodium hypochlorite-based microbicidal formulations were evaluated per ASTM International and EN standard methodologies. All evaluated formulated microbicides inactivated SARS-CoV-2 and other coronaviruses in suspension or on prototypic HITES. Virucidal efficacies (≥ 3 to ≥ 6 log10 reduction) were displayed within 30 s to 5 min. The virucidal efficacy of a variety of commercially available formulated microbicides against SARS-CoV-2 and other coronaviruses was confirmed. These microbicides should be useful for targeted surface and hand hygiene and disinfection of liquids, as part of infection prevention and control for SARS-CoV-2 and emerging mutational variants, and other emerging enveloped viruses.
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Affiliation(s)
- M Khalid Ijaz
- Reckitt Benckiser LLC, Global Research and Development for Lysol and Dettol, One Philips Parkway, Montvale, NJ, 07645, USA.
- Medgar Evers College of the City University of New York (CUNY), 1650 Bedford Ave, Brooklyn, NY, 11225, USA.
| | - Raymond W Nims
- RMC Pharmaceutical Solutions, Inc, 1851 Lefthand Circle, Suite A, Longmont, CO, 80501, USA
| | - Sifang Steve Zhou
- Microbac Laboratories, Inc, 105 Carpenter Drive, Sterling, VA, 20164, USA
| | - Kelly Whitehead
- Reckitt Benckiser LLC, Global Research and Development for Lysol and Dettol, One Philips Parkway, Montvale, NJ, 07645, USA
| | - Vanita Srinivasan
- Reckitt Benckiser LLC, Global Research and Development for Lysol and Dettol, One Philips Parkway, Montvale, NJ, 07645, USA
| | - Tanya Kapes
- Microbac Laboratories, Inc, 105 Carpenter Drive, Sterling, VA, 20164, USA
| | - Semhar Fanuel
- Microbac Laboratories, Inc, 105 Carpenter Drive, Sterling, VA, 20164, USA
| | - Jonathan H Epstein
- EcoHealth Alliance, 520 Eighth Avenue, Suite 1200, New York, NY, 10018-6507, USA
| | - Peter Daszak
- EcoHealth Alliance, 520 Eighth Avenue, Suite 1200, New York, NY, 10018-6507, USA
| | - Joseph R Rubino
- Reckitt Benckiser LLC, Global Research and Development for Lysol and Dettol, One Philips Parkway, Montvale, NJ, 07645, USA
| | - Julie McKinney
- Reckitt Benckiser LLC, Global Research and Development for Lysol and Dettol, One Philips Parkway, Montvale, NJ, 07645, USA
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37
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Pitol AK, Julian TR. Community Transmission of SARS-CoV-2 by Surfaces: Risks and Risk Reduction Strategies. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2021; 8:263-269. [PMID: 37566313 PMCID: PMC7805599 DOI: 10.1021/acs.estlett.0c00966] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 05/19/2023]
Abstract
SARS-CoV-2, the virus responsible for the COVID-19 pandemic, is perceived to be primarily transmitted via person-to-person contact through droplets produced while talking, coughing, and sneezing. Transmission may also occur through other routes, including contaminated surfaces; nevertheless, the role that surfaces have on the spread of the disease remains contested. Here, we use the Quantitative Microbial Risk Assessment framework to examine the risks of community transmission of SARS-CoV-2 through surfaces and to evaluate the effectiveness of hand and surface disinfection as potential interventions. Using conservative assumptions on input parameters of the model (e.g., dose-response relationship, ratio of genome copies to infective virus), the average of the median risks for single hand-to-surface contact followed by hand-to-face contact range from 1.6 × 10-4 to 5.6 × 10-9 for modeled prevalence rates of 0.2%-5%. For observed prevalence rates (0.2%, 1%), this corresponds to a low risk of infection (<10-6). Hand disinfection substantially reduces risks of transmission independently of the disease's prevalence and contact frequency. In contrast, the effectiveness of surface disinfection is highly dependent on the prevalence and the frequency of contacts. The work supports the current perception that contaminated surfaces are not a primary mode of transmission of SARS-CoV-2 and affirms the benefits of making hand disinfectants widely available.
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Affiliation(s)
- Ana K. Pitol
- Department of Civil and Environmental Engineering,
Imperial College London, London SW7 2AZ, United
Kingdom
| | - Timothy R. Julian
- Eawag, Swiss Federal Institute of Aquatic
Science and Technology, Dübendorf CH-8600,
Switzerland
- Swiss Tropical and Public Health
Institute, Basel CH-4051, Switzerland
- University of Basel, Basel
CH-4055, Switzerland
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38
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Pohl MO, Busnadiego I, Kufner V, Glas I, Karakus U, Schmutz S, Zaheri M, Abela I, Trkola A, Huber M, Stertz S, Hale BG. SARS-CoV-2 variants reveal features critical for replication in primary human cells. PLoS Biol 2021; 19:e3001006. [PMID: 33760807 PMCID: PMC8021179 DOI: 10.1371/journal.pbio.3001006] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/05/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
Abstract
Since entering the human population, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2; the causative agent of Coronavirus Disease 2019 [COVID-19]) has spread worldwide, causing >100 million infections and >2 million deaths. While large-scale sequencing efforts have identified numerous genetic variants in SARS-CoV-2 during its circulation, it remains largely unclear whether many of these changes impact adaptation, replication, or transmission of the virus. Here, we characterized 14 different low-passage replication-competent human SARS-CoV-2 isolates representing all major European clades observed during the first pandemic wave in early 2020. By integrating viral sequencing data from patient material, virus stocks, and passaging experiments, together with kinetic virus replication data from nonhuman Vero-CCL81 cells and primary differentiated human bronchial epithelial cells (BEpCs), we observed several SARS-CoV-2 features that associate with distinct phenotypes. Notably, naturally occurring variants in Orf3a (Q57H) and nsp2 (T85I) were associated with poor replication in Vero-CCL81 cells but not in BEpCs, while SARS-CoV-2 isolates expressing the Spike D614G variant generally exhibited enhanced replication abilities in BEpCs. Strikingly, low-passage Vero-derived stock preparation of 3 SARS-CoV-2 isolates selected for substitutions at positions 5/6 of E and were highly attenuated in BEpCs, revealing a key cell-specific function to this region. Rare isolate-specific deletions were also observed in the Spike furin cleavage site during Vero-CCL81 passage, but these were rapidly selected against in BEpCs, underscoring the importance of this site for SARS-CoV-2 replication in primary human cells. Overall, our study uncovers sequence features in SARS-CoV-2 variants that determine cell-specific replication and highlights the need to monitor SARS-CoV-2 stocks carefully when phenotyping newly emerging variants or potential variants of concern.
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Affiliation(s)
- Marie O. Pohl
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Idoia Busnadiego
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Irina Glas
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, ETH and University of Zurich, Zurich, Switzerland
| | - Umut Karakus
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Irene Abela
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Silke Stertz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Benjamin G. Hale
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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39
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Singh R, Kang A, Luo X, Jeyanathan M, Gillgrass A, Afkhami S, Xing Z. COVID-19: Current knowledge in clinical features, immunological responses, and vaccine development. FASEB J 2021; 35:e21409. [PMID: 33577115 PMCID: PMC7898934 DOI: 10.1096/fj.202002662r] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 01/08/2023]
Abstract
The COVID-19 pandemic has unfolded to be the most challenging global health crisis in a century. In 11 months since its first emergence, according to WHO, the causative infectious agent SARS-CoV-2 has infected more than 100 million people and claimed more than 2.15 million lives worldwide. Moreover, the world has raced to understand the virus and natural immunity and to develop vaccines. Thus, within a short 11 months a number of highly promising COVID-19 vaccines were developed at an unprecedented speed and are now being deployed via emergency use authorization for immunization. Although a considerable number of review contributions are being published, all of them attempt to capture only a specific aspect of COVID-19 or its therapeutic approaches based on ever-expanding information. Here, we provide a comprehensive overview to conceptually thread together the latest information on global epidemiology and mitigation strategies, clinical features, viral pathogenesis and immune responses, and the current state of vaccine development.
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Affiliation(s)
- Ramandeep Singh
- McMaster Immunology Research CentreM. G. DeGroote Institute for Infectious Disease Research & Department of MedicineMcMaster UniversityHamiltonONCanada
| | - Alisha Kang
- McMaster Immunology Research CentreM. G. DeGroote Institute for Infectious Disease Research & Department of MedicineMcMaster UniversityHamiltonONCanada
| | - Xiangqian Luo
- McMaster Immunology Research CentreM. G. DeGroote Institute for Infectious Disease Research & Department of MedicineMcMaster UniversityHamiltonONCanada
- Department of Pediatric OtolaryngologyShenzhen HospitalSouthern Medical UniversityShenzhenChina
| | - Mangalakumari Jeyanathan
- McMaster Immunology Research CentreM. G. DeGroote Institute for Infectious Disease Research & Department of MedicineMcMaster UniversityHamiltonONCanada
| | - Amy Gillgrass
- McMaster Immunology Research CentreM. G. DeGroote Institute for Infectious Disease Research & Department of MedicineMcMaster UniversityHamiltonONCanada
| | - Sam Afkhami
- McMaster Immunology Research CentreM. G. DeGroote Institute for Infectious Disease Research & Department of MedicineMcMaster UniversityHamiltonONCanada
| | - Zhou Xing
- McMaster Immunology Research CentreM. G. DeGroote Institute for Infectious Disease Research & Department of MedicineMcMaster UniversityHamiltonONCanada
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40
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Harvey AP, Fuhrmeister ER, Cantrell ME, Pitol AK, Swarthout JM, Powers JE, Nadimpalli ML, Julian TR, Pickering AJ. Longitudinal Monitoring of SARS-CoV-2 RNA on High-Touch Surfaces in a Community Setting. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2021; 8:168-175. [PMID: 34192125 PMCID: PMC7927285 DOI: 10.1021/acs.estlett.0c00875] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 05/19/2023]
Abstract
Environmental surveillance of surface contamination is an unexplored tool for understanding transmission of SARS-CoV-2 in community settings. We conducted longitudinal swab sampling of high-touch non-porous surfaces in a Massachusetts town during a COVID-19 outbreak from April to June 2020. Twenty-nine of 348 (8.3%) surface samples were positive for SARS-CoV-2 RNA, including crosswalk buttons, trash can handles, and door handles of essential business entrances (grocery store, liquor store, bank, and gas station). The estimated risk of infection from touching a contaminated surface was low (less than 5 in 10,000) by quantitative microbial risk assessment, suggesting fomites play a minimal role in SARS-CoV-2 community transmission. The weekly percentage of positive samples (out of n = 33 unique surfaces per week) best predicted variation in city-level COVID-19 cases with a 7-day lead time. Environmental surveillance of SARS-CoV-2 RNA on high-touch surfaces may be a useful tool to provide early warning of COVID-19 case trends.
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Affiliation(s)
- Abigail P. Harvey
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | | | - Molly E. Cantrell
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | - Ana K. Pitol
- Department of Civil and Environmental Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Jenna M. Swarthout
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | - Julie E. Powers
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | - Maya L. Nadimpalli
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | - Timothy R. Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dubendorf CH-8600, Switzerland
- Swiss Tropical and Public Health Institute, Basel CH-4051, Switzerland
- University of Basel, Basel CH-4055, Switzerland
| | - Amy J. Pickering
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
- Department of Civil and Environmental Engineering, University of California, Berkeley, 94720
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41
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Mizukoshi A, Nakama C, Okumura J, Azuma K. Assessing the risk of COVID-19 from multiple pathways of exposure to SARS-CoV-2: Modeling in health-care settings and effectiveness of nonpharmaceutical interventions. ENVIRONMENT INTERNATIONAL 2021; 147:106338. [PMID: 33401172 PMCID: PMC7758024 DOI: 10.1016/j.envint.2020.106338] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/10/2020] [Accepted: 12/14/2020] [Indexed: 05/07/2023]
Abstract
We assessed the risk of COVID-19 infection in a healthcare worker (HCW) from multiple pathways of exposure to SARS-CoV-2 in a health-care setting of short distance of 0.6 m between the HCW and a patient while caring, and evaluated the effectiveness of a face mask and a face shield using a model that combined previous infection-risk models. The multiple pathways of exposure included hand contact via contaminated surfaces and an HCW's fingers with droplets, droplet spray, and inhalation of inspirable and respirable particles. We assumed a scenario of medium contact time (MCT) and long contact time (LCT) over 1 day of care by an HCW. SARS-CoV-2 in the particles emitted by coughing, breathing, and vocalization (only in the LCT scenario) by the patient were considered. The contribution of the risk of infection of an HCW by SARS-CoV-2 from each pathway to the sum of the risks from all pathways depended on virus concentration in the saliva of the patient. At a virus concentration in the saliva of 101-105 PFU mL-1 concentration in the MCT scenario and 101-104 PFU mL-1 concentration in the LCT scenario, droplet spraying was the major pathway (60%-86%) of infection, followed by hand contact via contaminated surfaces (9%-32%). At a high virus concentration in the saliva (106-108 PFU mL-1 in the MCT scenario and 105-108 PFU mL-1 in the LCT scenario), hand contact via contaminated surfaces was the main contributor (41%-83%) to infection. The contribution of inhalation of inspirable particles was 4%-10% in all assumed cases. The contribution of inhalation of respirable particles increased as the virus concentration in the saliva increased, and reached 5%-27% at the high saliva concentration (107 and 108 PFU mL-1) in the assumed scenarios using higher dose-response function parameter (0.246) and comparable to other pathways, although these were worst and rare cases. Regarding the effectiveness of nonpharmaceutical interventions, the relative risk (RR) of an overall risk for an HCW with an intervention vs. an HCW without intervention was 0.36-0.37, 0.02-0.03, and <4.0 × 10-4 for a face mask, a face shield, and a face mask plus shield, respectively, in the likely median virus concentration in the saliva (102-104 PFU mL-1), suggesting that personal protective equipment decreased the infection risk by 63%->99.9%. In addition, the RR for a face mask worn by the patient, and a face mask worn by the patient plus increase of air change rate from 2 h-1 to 6 h-1 was <1.0 × 10-4 and <5.0 × 10-5, respectively in the same virus concentration in the saliva. Therefore, by modeling multiple pathways of exposure, the contribution of the infection risk from each pathway and the effectiveness of nonpharmaceutical interventions for COVID-19 were indicated quantitatively, and the importance of the use of a face mask and shield was confirmed.
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Affiliation(s)
- Atsushi Mizukoshi
- Department of Environmental Medicine and Behavioral Science, Kindai University Faculty of Medicine, Osakasayama 589-8511, Japan.
| | - Chikako Nakama
- Department of Environmental Medicine and Behavioral Science, Kindai University Faculty of Medicine, Osakasayama 589-8511, Japan.
| | - Jiro Okumura
- Department of Environmental Medicine and Behavioral Science, Kindai University Faculty of Medicine, Osakasayama 589-8511, Japan.
| | - Kenichi Azuma
- Department of Environmental Medicine and Behavioral Science, Kindai University Faculty of Medicine, Osakasayama 589-8511, Japan.
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42
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Nizamudeen ZA, Xu ER, Karthik V, Halawa M, Arkill KP, Jackson AM, Bates DO, Emsley J. Structural assessment of SARS-CoV2 accessory protein ORF7a predicts LFA-1 and Mac-1 binding potential. Biosci Rep 2021; 41:BSR20203837. [PMID: 33305306 PMCID: PMC7796194 DOI: 10.1042/bsr20203837] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 01/17/2023] Open
Abstract
ORF7a is an accessory protein common to SARS-CoV1 and the recently discovered SARS-CoV2, which is causing the COVID-19 pandemic. The ORF7a protein has a structural homology with ICAM-1 which binds to the T lymphocyte integrin receptor LFA-1. As COVID-19 has a strong immune component as part of the disease, we sought to determine whether SARS-CoV2 would have a similar structural interaction with LFA-1. Using molecular docking simulations, we found that SARS-CoV2 ORF7a has the key structural determinants required to bind LFA-1 but also the related leukocyte integrin Mac-1, which is also known to be expressed by macrophages. Our study shows that SARS-CoV2 ORF7a protein has a conserved Ig immunoglobulin-like fold containing an integrin binding site that provides a mechanistic hypothesis for SARS-CoV2's interaction with the human immune system. This suggests that experimental investigation of ORF7a-mediated effects on immune cells such as T lymphocytes and macrophages (leukocytes) could help understand the disease further and develop effective treatments.
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Affiliation(s)
- Zubair Ahmed Nizamudeen
- Division of Cancer and Stem Cells, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Emma-Ruoqi Xu
- School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Vivin Karthik
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, U.S.A
| | - Mohamed Halawa
- School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Kenton P. Arkill
- Division of Cancer and Stem Cells, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Andrew M. Jackson
- Division of Cancer and Stem Cells, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, U.K
| | - David O. Bates
- Division of Cancer and Stem Cells, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Jonas Emsley
- School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, U.K
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Sengupta A, Hassan SS, Choudhury PP. Clade GR and clade GH isolates of SARS-CoV-2 in Asia show highest amount of SNPs. INFECTION GENETICS AND EVOLUTION 2021; 89:104724. [PMID: 33476804 PMCID: PMC7816605 DOI: 10.1016/j.meegid.2021.104724] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 02/06/2023]
Abstract
Clades are monophyletic groups composed of a common ancestor and all its lineal descendants. As the propensity of virulence of a disease depends upon the type of clade the virus belongs to and it causes different fatality rates of disease in different countries, so the clade-wise analysis of SARS-CoV-2 isolates collected from different countries can illuminate the actual evolutionary relationships between them. In this study, 1566 SARS-CoV-2 genome sequences across ten Asian countries are collected, clustered, and characterized based on the clade they belong to. The isolates are compared to the Wuhan reference sequence” hCoV-19/Wuhan/WIV04/19″ to identify the mutations that occurred at different protein regions. Structural changes in amino acids due to mutations lead to functional instability of the proteins. Detailed clade-wise functional assessments are carried out to quantify the stability and vulnerability of the mutations occurring in SARS-CoV-2 genomes which can shade light on personalized prevention and treatment of the disease and encourage towards the invention of clade-specific vaccines.
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Affiliation(s)
- Antara Sengupta
- Department of Computer Science and Engineering, University of Calcutta, West Bengal, India.
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, West Bengal, India
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Kumar BK, Rohit A, Prithvisagar KS, Rai P, Karunasagar I, Karunasagar I. Deletion in the C-terminal region of the envelope glycoprotein in some of the Indian SARS-CoV-2 genome. Virus Res 2021; 291:198222. [PMID: 33166565 PMCID: PMC7645280 DOI: 10.1016/j.virusres.2020.198222] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 11/17/2022]
Abstract
The envelope glycoprotein (E) is the smallest structural component of SARS-CoVs; plays an essential role in the viral replication starting from envelope formation to assembly. The in silico analysis of 2086 whole genome sequences from India performed in this study provides the first observation on the extensive deletion of amino acid residues in the C-terminal region of the envelope glycoprotein in 34 Indian SARS-CoV-2 genomes. These amino acid deletions map to the homopentameric interface and PDZ binding motif (PBM) present in the C-terminal region of E protein as well as immediately after the reverse primer binding region as per Charité protocol in 26 of these genomes, hence, their detection through RT-qPCR may not be hampered and therefore E gene-based RT-qPCR would still detect these isolates. Eight genomes from the State of Odisha had deletion even in the primer binding site. It is possible that the deletions in the C-terminal region of E protein of these genomes are a result of adapting to a newer geographical area and host. The information on the clinical status was available only for 9 out of 34 cases and these were asymptomatic. However, further studies are indispensable to understand the functional consequences of amino acid deletion in the C terminal region of SARS-CoV-2 envelope protein in the viral pathogenesis and host adaptation.
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Affiliation(s)
- Ballamoole Krishna Kumar
- Division of Infectious Diseases, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Anusha Rohit
- Department of Microbiology, The Madras Medical Mission, 4-A, Dr, Mogappair, Chennai, Tamil Nadu, 600037, India
| | - Kattapuni Suresh Prithvisagar
- Division of Infectious Diseases, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Praveen Rai
- Division of Infectious Diseases, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Indrani Karunasagar
- Division of Infectious Diseases, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Iddya Karunasagar
- Nitte (Deemed to be University), University Enclave, Medical Sciences Complex, Deralakatte, Mangaluru, 575018, India.
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Shahrajabian MH, Sun W, Cheng Q. Product of natural evolution (SARS, MERS, and SARS-CoV-2); deadly diseases, from SARS to SARS-CoV-2. Hum Vaccin Immunother 2021; 17:62-83. [PMID: 32783700 PMCID: PMC7872062 DOI: 10.1080/21645515.2020.1797369] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/24/2020] [Accepted: 07/10/2020] [Indexed: 12/13/2022] Open
Abstract
SARS-CoV-2, the virus causing COVID-19, is a single-stranded RNA virus belonging to the order Nidovirales, family Coronaviridae, and subfamily Coronavirinae. SARS-CoV-2 entry to cellsis initiated by the binding of the viral spike protein (S) to its cellular receptor. The roles of S protein in receptor binding and membrane fusion makes it a prominent target for vaccine development. SARS-CoV-2 genome sequence analysis has shown that this virus belongs to the beta-coronavirus genus, which includes Bat SARS-like coronavirus, SARS-CoV and MERS-CoV. A vaccine should induce a balanced immune response to elicit protective immunity. In this review, we compare and contrast these three important CoV diseases and how they inform on vaccine development.
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Affiliation(s)
| | - Wenli Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China
- Global Alliance of HeBAU-CLS&HeQiS for BioAl-Manufacturing, Baoding, Hebei, China
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46
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Viral PDZ Binding Motifs Influence Cell Behavior Through the Interaction with Cellular Proteins Containing PDZ Domains. Methods Mol Biol 2021; 2256:217-236. [PMID: 34014525 DOI: 10.1007/978-1-0716-1166-1_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Viruses have evolved to interact with their hosts. Some viruses such as human papilloma virus, dengue virus, SARS-CoV, or influenza virus encode proteins including a PBM that interact with cellular proteins containing PDZ domains. There are more than 400 cellular protein isoforms with these domains in the human genome, indicating that viral PBMs have a high potential to influence the behavior of the cell. In this review we analyze the most relevant cellular processes known to be affected by viral PBM-cellular PDZ interactions including the establishment of cell-cell interactions and cell polarity, the regulation of cell survival and apoptosis and the activation of the immune system. Special attention has been provided to coronavirus PBM conservation throughout evolution and to the role of the PBMs of human coronaviruses SARS-CoV and MERS-CoV in pathogenesis.
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47
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Rahman MS, Hoque MN, Islam MR, Islam I, Mishu ID, Rahaman MM, Sultana M, Hossain MA. Mutational insights into the envelope protein of SARS-CoV-2. GENE REPORTS 2020; 22:100997. [PMID: 33319124 PMCID: PMC7723457 DOI: 10.1016/j.genrep.2020.100997] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/23/2020] [Accepted: 12/02/2020] [Indexed: 01/03/2023]
Abstract
The ongoing mutations in the structural proteins of SARS-CoV-2 are the major impediment for prevention and control of the COVID-19 disease. Presently we focused on evolution of the envelope (E) protein, one of the most enigmatic and less studied protein among the four structural proteins (S, E, M and N) associated with multitude of immunopathological functions of SARS-CoV-2. In the present study, we comprehensively analyzed 81,818 high quality E protein sequences of SARS-CoV-2 globally available in the GISAID database as of 20 August 2020. Compared to Wuhan reference strain, our mutational analysis explored only 1.2 % (982/81818) mutant strains undergoing a total of 115 unique amino acid (aa) substitutions in the E protein, highlighting the fact that most (98.8 %) of the E protein of SARS-CoV-2 strains are highly conserved. Moreover, we found 58.77 % (134 of 228) nucleotides (nt) positions of SARS-CoV-2 E gene encountering a total of 176 unique nt-level mutations globally, which may affect the efficacy of real time RT-PCR-based molecular detection of COVID-19. Importantly, higher aa variations observed in the C-terminal domain (CTD) of the E protein, particularly at Ser55-Phe56, Arg69 and the C-terminal end (DLLV: 72–75) may alter the binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 and thus could play a key role in COVID-19 pathogenesis. Furthermore, this study revealed the V25A mutation in the transmembrane domain which is a key factor for the homopentameric conformation of E protein. Our analysis also observed a triple cysteine motif harboring mutation (L39M, A41S, A41V, C43F, C43R, C43S, C44Y, N45R) which may hinder the binding of E protein with spike glycoprotein. These results therefore suggest the continuous monitoring of the structural proteins including the envelope protein of SARS-CoV-2 since the number of genome sequences from across the world are continuously increasing.
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Key Words
- CTD, C-terminal domain
- E, envelope
- Envelope protein
- M, membrane
- Mutations
- N, nucleocapsid
- NC, negatively charged
- NP, non-polar
- PC, positively charged
- S, spike
- SARS-CoV-2
- SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus-2
- TMD, transmembrane domain
- Transmembrane domain
- Triple cysteine motif
- aa, amino acid
- nt, nucleotide
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Affiliation(s)
- M Shaminur Rahman
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - M Nazmul Hoque
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | | | | | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
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Hassan SS, Choudhury PP, Uversky VN, Dayhoff GW, Aljabali AAA, Uhal BD, Lundstrom K, Rezaei N, Seyran M, Pizzol D, Adadi P, Lal A, Soares A, Abd El-aziz TM, Kandimalla R, Tambuwala M, Azad GK, Sherchan SP, Baetas-da-cruz W, Takayama K, Serrano-aroca Á, Chauhan G, Palu G, Brufsky AM. Variability of Accessory Proteins Rules the SARS-CoV-2 Pathogenicity.. [DOI: 10.1101/2020.11.06.372227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
AbstractThe coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) which is pandemic with an estimated fatality rate less than 1% is ongoing. SARS-CoV-2 accessory proteins ORF3a, ORF6, ORF7a, ORF7b, ORF8, and ORF10 with putative functions to manipulate host immune mechanisms such as interferons, immune signaling receptor NLRP3 (NOD-, LRR-, and pyrin domain-containing 3) inflammasome, inflammatory cytokines such as interleukin 1β(IL-1β) are critical in COVID-19 pathology. Outspread variations of each of the six accessory proteins of all complete proteomes (available as of October 26, 2020, in the National Center for Biotechnology Information depository) of SARS-CoV-2, were observed across six continents. Across all continents, the decreasing order of percentage of unique variations in the accessory proteins was found to be ORF3a>ORF8>ORF7a>ORF6>ORF10>ORF7b. The highest and lowest unique variations of ORF3a were observed in South America and Oceania, respectively. This finding suggests that the wide variations of accessory proteins seem to govern the pathogenicity of SARS-CoV-2, and consequently, certain propositions and recommendations can be made in the public interest.
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Hassan SS, Choudhury PP, Roy B. SARS-CoV2 envelope protein: non-synonymous mutations and its consequences. Genomics 2020; 112:3890-3892. [PMID: 32640274 PMCID: PMC7335631 DOI: 10.1016/j.ygeno.2020.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 01/09/2023]
Abstract
In the NCBI database, as on June 6, 2020, total number of available complete genome sequences of SARS-CoV2 across the world is 3617. The envelope (E) protein of SARS-CoV2 possesses several non-synonymous mutations over the transmembrane and C-terminus domains in 15 (0.414%) genomes among 3617 SARS-CoV2 genomes, analyzed. More precisely, 10(0.386%) out of 2588 genomes from the USA, 3(0.806%) from Asia, 1 (0.348%) from Europe and 1 (0.274%) from Oceania contained the missense mutations over the E-protein of SARS-CoV2 genomes. The C-terminus motif DLLV has been to DFLV and YLLV in the proteins from QJR88103 (Australia: Victoria) and QKI36831 (China: Guangzhou) respectively, which might affect the binding of this motif with the host protein PALS1.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India.
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India.
| | - Bidyut Roy
- Human Genetics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India.
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50
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Harvey AP, Fuhrmeister ER, Cantrell M, Pitol AK, Swarthout JM, Powers JE, Nadimpalli ML, Julian TR, Pickering AJ. Longitudinal monitoring of SARS-CoV-2 RNA on high-touch surfaces in a community setting. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.10.27.20220905. [PMID: 33140065 PMCID: PMC7605577 DOI: 10.1101/2020.10.27.20220905] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Environmental surveillance of surface contamination is an unexplored tool for understanding transmission of SARS-CoV-2 in community settings. We conducted longitudinal swab sampling of high-touch non-porous surfaces in a Massachusetts town during a COVID-19 outbreak from April to June 2020. Twenty-nine of 348 (8.3 %) surface samples were positive for SARS-CoV-2, including crosswalk buttons, trash can handles, and door handles of essential business entrances (grocery store, liquor store, bank, and gas station). The estimated risk of infection from touching a contaminated surface was low (less than 5 in 10,000), suggesting fomites play a minimal role in SARS-CoV-2 community transmission. The weekly percentage of positive samples (out of n=33 unique surfaces per week) best predicted variation in city-level COVID-19 cases using a 7-day lead time. Environmental surveillance of SARS-CoV-2 RNA on high-touch surfaces could be a useful tool to provide early warning of COVID-19 case trends.
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Affiliation(s)
- Abigail P. Harvey
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | | | - Molly Cantrell
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | - Ana K. Pitol
- Department of Civil and Environmental Engineering, Imperial College London, United Kingdom
| | - Jenna M. Swarthout
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | - Julie E. Powers
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | - Maya L. Nadimpalli
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | - Timothy R. Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dubendorf CH-8600, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Amy J. Pickering
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
- Department of Civil and Environmental Engineering, University of California, Berkeley
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