Journal of Nuclear Science, Engineering and Technology (JONSAT)
In cooperation with the Iranian Nuclear Society

Investigation of electron beam irradiation effect on spikes of SARS-COV2, MERS-COV, UK variant, SARS-COV by Geant4-DNA toolkit

Document Type : Research Paper

Authors

M. Jalili Torkamani 1
F. Zolfagharpour 1
A. Asadi 2
P. Sayyahkoohi 1

1 Department of Physics, Faculty of Science, University of Mohaghegh Ardabili, P.O.BOX: 5619913131, Ardabil – Iran

2 Department of Biology, Faculty of Science, University of Mohaghegh Ardabili, P.O.BOX: 561991313, Ardabil, Iran

https://doi.org/10.24200/nst.2022.1003.1680
Abstract
Viruses pass cell walls and enter cells using their spikes, So one of the efficient ways to stop viral infections is to disturb their spikes functionality. In this research, the process of energy absorption and transfer by SARS-COV2, MERS-COV, UK-COV, and SARS-COV spikes was studied. In this research sample viruses exposed to radioactive radiations and results were compared by Geant4-DNA and analyzed. A strategy to reduce the virus life cycle is energy absorption. In this research, the response to viruses spikes to radiation was simulated. Samples were exposed to 10 eV–2 keV electron beams. The level of Energy absorption and its relation to the number of infected patients was studied. It was concluded there is an inverse relationship between absorbed energy level and patient death.

Highlights

  1. D.L. Roberts, J.S. Rossman, I. Jaric, Dating first cases of COVID-19, Plos Pathogens, 17(6), e1009620 (2021).

 

  1. A. Deslandes, et al., SARS-CoV-2 was already spreading in France in late December 2019, International Journal of Antimicrobial Agents, 55(6), 106006 (2020).

 

  1. M.A. Jorden, et al., Evidence for Limited Early spread of COVID-19 Within the United States, Morbidity and Mortality. US Department of Health and Human. 69(22), 680-684 (2020).

 

  1. S. Alsobaie, Understanding the Molecular Biology of SARS-CoV-2 and the COVID-19 Pandemic: A Review, Infection and Drug Resistance., 14, 2259-2268 (2021).

 

  1. R. Yan, et al., Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2, Science., 367(6485), 1444-1448 (2020).

 

  1. S.M. Gobeil, et al., Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and Antigenicity, Science., 373(641), 6226 (2021).

 

  1. R.N. Kirchdoerfer, et al., Stabilized oronavirus spikes are resistant to conformational changes induced by receptor recognition or roteolysis, Scientific Reports, 8, 15701 (2018).

 

  1. S.M. Gobeil, P. Acharya, UK (B.1.1.7) SARS-CoV-2 spike protein variant (S-GSAS- B.1.1.7) in the 1- RBD-up conformation, Full WWPDB EM Validation Report, 2-49 (2021).

 

  1. Y. Yuan, et al., Cryo-EM Structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains, Nature Communications., 8(15092), (2017).

 

  1. Z. Liu, et al., Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS-CoV2, Medical Virology., 92(6), 595-601 (2020).

 

  1. J. Lan, et al., Structure of the SARS-CoV-2 spike receptor- binding domain bound to the ACE2 receptor, Nature., 581, 215-220 (2020).

 

  1. A. Mittal, et al., COVID-19 pandemic: Insights into structure, function, and hACE2 receptor recognition by SARS-CoV-2, Plos Pathogens., 16(8), e1008762 (2020).

 

  1. T.N. Starr, et al., SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape, Nature., 597, 97-102 (2021).

 

  1. W.T. Harvey, et al., SARS- CoV-2 variants, spike mutations and immune escape, Nature Reviews Microbiology., 19, 409-424 (2021).

 

  1. L. Piccoli, et al., Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology, Cell., 183(4), 1024-1042 (2020).

 

  1. A. Bardane, et al., Monte Carlo Simulation Method Highlighting on the Electron Beam Irradiation on the Structure of SARS-CoV-2, Biophysics and Medical Physics., 75(6), 638-644 (2020).

 

  1. G. Feng, et al., Electron Beam Irradiation on Novel Coronavirus (COVID-19): via a Monte-Carlo Simulation, Chinese Physics, B., 134, 225 (2020).

 

  1. M. Durante, et al., Virus Irradiation and COVID-19 Disease, Frontiers in Physics., 8, 565861 (2020).

 

  1. P. Afaghi, et al., Denaturation of the SARS-CoV-2 spike protein under non-thermal microwave radiation, Nature Scientifc Reports., 11, 23373 (2021).

 

  1. L. Min, Q. Sun, Antibodies and Vaccines Target RBD of SARS-CoV-2, Frontiers in Molecular Biosciences, (8), 671633 (2021).

 

  1. R. Lu, et al., February 2020. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding, The Lancet. 395(10224), 565-574 (2020).

 

  1. A.R. Fehr, S. Perlman, Coronaviruses: An Overview of Their Replication and Pathogenesis, Methods in Molecular Biology, 1282, 1–23 (2015).

 

  1. X. Xiong, et al., A thermostable, closed SARS-CoV-2 spike protein trimer, Nature Structural & Molecular Biology, 27, 934–941 (2020).

 

  1. Z.O. Abu‐Faraj, Understanding COVID-19 and some Effective Means for Combating it, Linkedin 21. B.S. Chhikara et al. SARS-CoV-2 disease COVID-19: Infection, prevention and clinical advances of the prospective chemical drug therapeutics, Chemical Biology Letters, 7(1), 63‐72 (2020).

 

  1. J. Yang, et al., Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor, Nature Communications., 11, 4541 (2020).

 

  1. Molecular explorations through biology and Medicine, http://pdb101.rcsb.org/motm/246.

 

  1. X. Dong Wu, et al., The spike protein of severe acute respiratory syndrome (SARS) is cleaved in virus infected Vero-E6 cells, Cell Research, 14, 400-406 (2004).

 

  1. A.L. Alaofi, M. Shahid, Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency, Biomolecules, 11, 1273 (2021).

 

  1. J. Zhaoa, et al., Rapid generation of a mouse model for Middle East respiratory syndrome, Pnas, 111(13), 4970–4975 (2014).

 

  1. T. Biftu, R. SinhaRoy, DPP-4 Inhibitors, Comprehensive Medicinal Chemistry III., 7, 512-555 (2017).

 

  1. M.H. Shoaib, et al., A journey from SARS-CoV-2 to COVID-19 and Beyond: A Comprehensive Insight of Epidemiology, Diagnosis, Pathogenesis, and overview of the Progress into its Therapeutic management, Frontiers in Pharmacology., 26(12), 576448 (2021).

 

  1. Number of SARS-CoV-2 Alpha variant cases worldwide as of October 29, 2021 by country or territory, https://www.statista.com.

 

  1. B117 deadlier than other COVID-19 strains, more data affirm,https://www.cidrap.umn.edu.

 

  1. M.Ch. Yeung, R. Heng XU, SARS: epidemiology, Respirology, 8, S9–S14 (2003).

 

  1. Middle East respiratory syndrome, MERS situation update. October 2021, http://www.emro.who.int/ health-topics/mers- cov/mers-outbreaks.html.

Keywords

Geant4-DNA
SARS-COV2
MERS-COV
UK-COV
Electron beam
  1. D.L. Roberts, J.S. Rossman, I. Jaric, Dating first cases of COVID-19, Plos Pathogens, 17(6), e1009620 (2021).

 

  1. A. Deslandes, et al., SARS-CoV-2 was already spreading in France in late December 2019, International Journal of Antimicrobial Agents, 55(6), 106006 (2020).

 

  1. M.A. Jorden, et al., Evidence for Limited Early spread of COVID-19 Within the United States, Morbidity and Mortality. US Department of Health and Human. 69(22), 680-684 (2020).

 

  1. S. Alsobaie, Understanding the Molecular Biology of SARS-CoV-2 and the COVID-19 Pandemic: A Review, Infection and Drug Resistance., 14, 2259-2268 (2021).

 

  1. R. Yan, et al., Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2, Science., 367(6485), 1444-1448 (2020).

 

  1. S.M. Gobeil, et al., Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and Antigenicity, Science., 373(641), 6226 (2021).

 

  1. R.N. Kirchdoerfer, et al., Stabilized oronavirus spikes are resistant to conformational changes induced by receptor recognition or roteolysis, Scientific Reports, 8, 15701 (2018).

 

  1. S.M. Gobeil, P. Acharya, UK (B.1.1.7) SARS-CoV-2 spike protein variant (S-GSAS- B.1.1.7) in the 1- RBD-up conformation, Full WWPDB EM Validation Report, 2-49 (2021).

 

  1. Y. Yuan, et al., Cryo-EM Structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains, Nature Communications., 8(15092), (2017).

 

  1. Z. Liu, et al., Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS-CoV2, Medical Virology., 92(6), 595-601 (2020).

 

  1. J. Lan, et al., Structure of the SARS-CoV-2 spike receptor- binding domain bound to the ACE2 receptor, Nature., 581, 215-220 (2020).

 

  1. A. Mittal, et al., COVID-19 pandemic: Insights into structure, function, and hACE2 receptor recognition by SARS-CoV-2, Plos Pathogens., 16(8), e1008762 (2020).

 

  1. T.N. Starr, et al., SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape, Nature., 597, 97-102 (2021).

 

  1. W.T. Harvey, et al., SARS- CoV-2 variants, spike mutations and immune escape, Nature Reviews Microbiology., 19, 409-424 (2021).

 

  1. L. Piccoli, et al., Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology, Cell., 183(4), 1024-1042 (2020).

 

  1. A. Bardane, et al., Monte Carlo Simulation Method Highlighting on the Electron Beam Irradiation on the Structure of SARS-CoV-2, Biophysics and Medical Physics., 75(6), 638-644 (2020).

 

  1. G. Feng, et al., Electron Beam Irradiation on Novel Coronavirus (COVID-19): via a Monte-Carlo Simulation, Chinese Physics, B., 134, 225 (2020).

 

  1. M. Durante, et al., Virus Irradiation and COVID-19 Disease, Frontiers in Physics., 8, 565861 (2020).

 

  1. P. Afaghi, et al., Denaturation of the SARS-CoV-2 spike protein under non-thermal microwave radiation, Nature Scientifc Reports., 11, 23373 (2021).

 

  1. L. Min, Q. Sun, Antibodies and Vaccines Target RBD of SARS-CoV-2, Frontiers in Molecular Biosciences, (8), 671633 (2021).

 

  1. R. Lu, et al., February 2020. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding, The Lancet. 395(10224), 565-574 (2020).

 

  1. A.R. Fehr, S. Perlman, Coronaviruses: An Overview of Their Replication and Pathogenesis, Methods in Molecular Biology, 1282, 1–23 (2015).

 

  1. X. Xiong, et al., A thermostable, closed SARS-CoV-2 spike protein trimer, Nature Structural & Molecular Biology, 27, 934–941 (2020).

 

  1. Z.O. Abu‐Faraj, Understanding COVID-19 and some Effective Means for Combating it, Linkedin 21. B.S. Chhikara et al. SARS-CoV-2 disease COVID-19: Infection, prevention and clinical advances of the prospective chemical drug therapeutics, Chemical Biology Letters, 7(1), 63‐72 (2020).

 

  1. J. Yang, et al., Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor, Nature Communications., 11, 4541 (2020).

 

  1. Molecular explorations through biology and Medicine, http://pdb101.rcsb.org/motm/246.

 

  1. X. Dong Wu, et al., The spike protein of severe acute respiratory syndrome (SARS) is cleaved in virus infected Vero-E6 cells, Cell Research, 14, 400-406 (2004).

 

  1. A.L. Alaofi, M. Shahid, Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency, Biomolecules, 11, 1273 (2021).

 

  1. J. Zhaoa, et al., Rapid generation of a mouse model for Middle East respiratory syndrome, Pnas, 111(13), 4970–4975 (2014).

 

  1. T. Biftu, R. SinhaRoy, DPP-4 Inhibitors, Comprehensive Medicinal Chemistry III., 7, 512-555 (2017).

 

  1. M.H. Shoaib, et al., A journey from SARS-CoV-2 to COVID-19 and Beyond: A Comprehensive Insight of Epidemiology, Diagnosis, Pathogenesis, and overview of the Progress into its Therapeutic management, Frontiers in Pharmacology., 26(12), 576448 (2021).

 

  1. Number of SARS-CoV-2 Alpha variant cases worldwide as of October 29, 2021 by country or territory, https://www.statista.com.

 

  1. B117 deadlier than other COVID-19 strains, more data affirm,https://www.cidrap.umn.edu.

 

  1. M.Ch. Yeung, R. Heng XU, SARS: epidemiology, Respirology, 8, S9–S14 (2003).

 

  1. Middle East respiratory syndrome, MERS situation update. October 2021, http://www.emro.who.int/ health-topics/mers- cov/mers-outbreaks.html.

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