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D'Arco A, Di Fabrizio M, Mancini T, Mosetti R, Macis S, Tranfo G, Della Ventura G, Marcelli A, Petrarca M, Lupi S. Secondary Structures of MERS-CoV, SARS-CoV, and SARS-CoV-2 Spike Proteins Revealed by Infrared Vibrational Spectroscopy. Int J Mol Sci 2023; 24:ijms24119550. [PMID: 37298500 DOI: 10.3390/ijms24119550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/28/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
All coronaviruses are characterized by spike glycoproteins whose S1 subunits contain the receptor binding domain (RBD). The RBD anchors the virus to the host cellular membrane to regulate the virus transmissibility and infectious process. Although the protein/receptor interaction mainly depends on the spike's conformation, particularly on its S1 unit, their secondary structures are poorly known. In this paper, the S1 conformation was investigated for MERS-CoV, SARS-CoV, and SARS-CoV-2 at serological pH by measuring their Amide I infrared absorption bands. The SARS-CoV-2 S1 secondary structure revealed a strong difference compared to those of MERS-CoV and SARS-CoV, with a significant presence of extended β-sheets. Furthermore, the conformation of the SARS-CoV-2 S1 showed a significant change by moving from serological pH to mild acidic and alkaline pH conditions. Both results suggest the capability of infrared spectroscopy to follow the secondary structure adaptation of the SARS-CoV-2 S1 to different environments.
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Affiliation(s)
- Annalisa D'Arco
- Laboratori Nazionali Frascati, National Institute for Nuclear Physics (INFN-LNF), Via E. Fermi 54, 00044 Frascati, Italy
- Department of Physics, University of Rome 'La Sapienza', P.le A. Moro 2, 00185 Rome, Italy
| | - Marta Di Fabrizio
- Laboratory of Biological Electron Microscopy, School of Basic Sciences, Institute of Physics, EPFL & Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, 1015 Lausanne, Switzerland
| | - Tiziana Mancini
- Department of Physics, University of Rome 'La Sapienza', P.le A. Moro 2, 00185 Rome, Italy
| | - Rosanna Mosetti
- Department of Physics, University of Rome 'La Sapienza', P.le A. Moro 2, 00185 Rome, Italy
| | - Salvatore Macis
- Department of Physics, University of Rome 'La Sapienza', P.le A. Moro 2, 00185 Rome, Italy
| | - Giovanna Tranfo
- Department of Occupational and Environmental Medicine, Epidemiology and Hygiene, INAIL, Monte Porzio Catone, 00078 Rome, Italy
| | - Giancarlo Della Ventura
- Laboratori Nazionali Frascati, National Institute for Nuclear Physics (INFN-LNF), Via E. Fermi 54, 00044 Frascati, Italy
- Department of Science, University Rome Tre, Largo San Leonardo Murialdo 1, 00146 Rome, Italy
| | - Augusto Marcelli
- Laboratori Nazionali Frascati, National Institute for Nuclear Physics (INFN-LNF), Via E. Fermi 54, 00044 Frascati, Italy
- Rome International Centre for Materials Science Superstipes, Via dei Sabelli 119A, 00185 Rome, Italy
| | - Massimo Petrarca
- National Institute for Nuclear Physics Section Rome1, P.le A. Moro 2, 00185 Rome, Italy
- Department of Basic and Applied Sciences for Engineering (SBAI), University of Rome 'La Sapienza', Via Scarpa 16, 00161 Rome, Italy
| | - Stefano Lupi
- Department of Physics, University of Rome 'La Sapienza', P.le A. Moro 2, 00185 Rome, Italy
- National Institute for Nuclear Physics Section Rome1, P.le A. Moro 2, 00185 Rome, Italy
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Campi G, Perali A, Marcelli A, Bianconi A. Sars-Cov2 world pandemic recurrent waves controlled by variants evolution and vaccination campaign. Sci Rep 2022; 12:18108. [PMID: 36302922 PMCID: PMC9612611 DOI: 10.1038/s41598-022-22816-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 10/19/2022] [Indexed: 12/30/2022] Open
Abstract
While understanding the time evolution of Covid-19 pandemic is needed to plan economics and tune sanitary policies, a quantitative information of the recurrent epidemic waves is elusive. This work describes a statistical physics study of the subsequent waves in the epidemic spreading of Covid-19 and disclose the frequency components of the epidemic waves pattern over two years in United States, United Kingdom and Japan. These countries have been taken as representative cases of different containment policies such as "Mitigation" (USA and UK) and "Zero Covid" (Japan) policies. The supercritical phases in spreading have been identified by intervals with RIC-index > 0. We have used the wavelet transform of infection and fatality waves to get the spectral analysis showing a dominant component around 130 days. Data of the world dynamic clearly indicates also the crossover to a different phase due to the enforcement of vaccination campaign. In Japan and United Kingdom, we observed the emergence in the infection waves of a long period component (~ 170 days) during vaccination campaign. These results indicate slowing down of the epidemic spreading dynamics due to the vaccination campaign. Finally, we find an intrinsic difference between infection and fatality waves pointing to a non-trivial variation of the lethality due to different gene variants.
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Affiliation(s)
- Gaetano Campi
- Institute of Crystallography, Consiglio Nazionale delle Ricerche CNR, Via Salaria Km 29.300, Monterotondo Roma, 00015, Rome, Italy.
- Rome International Centre Materials Science, Superstripes RICMASS, Via dei Sabelli 119A, 00185, Rome, Italy.
| | - Andrea Perali
- Physics Unit, School of Pharmacy, University of Camerino, 62032, Camerino, MC, Italy.
| | - Augusto Marcelli
- INFN-Laboratori Nazionali di Frascati, Via E. Fermi 54, 00044, Frascati, RM, Italy
| | - Antonio Bianconi
- Institute of Crystallography, Consiglio Nazionale delle Ricerche CNR, Via Salaria Km 29.300, Monterotondo Roma, 00015, Rome, Italy.
- Rome International Centre Materials Science, Superstripes RICMASS, Via dei Sabelli 119A, 00185, Rome, Italy.
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Moscow, Russian Federation, 115409.
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Cereda G, Viscardi C, Baccini M. Combining and comparing regional SARS-CoV-2 epidemic dynamics in Italy: Bayesian meta-analysis of compartmental models and global sensitivity analysis. Front Public Health 2022; 10:919456. [PMID: 36187637 PMCID: PMC9523586 DOI: 10.3389/fpubh.2022.919456] [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: 04/13/2022] [Accepted: 08/10/2022] [Indexed: 01/22/2023] Open
Abstract
During autumn 2020, Italy faced a second important SARS-CoV-2 epidemic wave. We explored the time pattern of the instantaneous reproductive number, R 0(t), and estimated the prevalence of infections by region from August to December calibrating SIRD models on COVID-19-related deaths, fixing at values from literature Infection Fatality Rate (IFR) and average infection duration. A Global Sensitivity Analysis (GSA) was performed on the regional SIRD models. Then, we used Bayesian meta-analysis and meta-regression to combine and compare the regional results and investigate their heterogeneity. The meta-analytic R 0(t) curves were similar in the Northern and Central regions, while a less peaked curve was estimated for the South. The maximum R 0(t) ranged from 2.15 (South) to 2.61 (North) with an increase following school reopening and a decline at the end of October. The predictive performance of the regional models, assessed through cross validation, was good, with a Mean Absolute Percentage Error of 7.2% and 10.9% when considering prediction horizons of 7 and 14 days, respectively. Average temperature, urbanization, characteristics of family medicine and healthcare system, economic dynamism, and use of public transport could partly explain the regional heterogeneity. The GSA indicated the robustness of the regional R 0(t) curves to different assumptions on IFR. The infectious period turned out to have a key role in determining the model results, but without compromising between-region comparisons.
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Affiliation(s)
- Giulia Cereda
- Department of Statistics, Computer Science, Applications, University of Florence, Florence, Italy,Florence Center for Data Science, University of Florence, Florence, Italy,*Correspondence: Giulia Cereda
| | - Cecilia Viscardi
- Department of Statistics, Computer Science, Applications, University of Florence, Florence, Italy,Florence Center for Data Science, University of Florence, Florence, Italy,Cecilia Viscardi
| | - Michela Baccini
- Department of Statistics, Computer Science, Applications, University of Florence, Florence, Italy,Florence Center for Data Science, University of Florence, Florence, Italy,Michela Baccini
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Campi G, Bianconi A. Periodic recurrent waves of Covid-19 epidemics and vaccination campaign. CHAOS, SOLITONS, AND FRACTALS 2022; 160:112216. [PMID: 35601116 PMCID: PMC9114150 DOI: 10.1016/j.chaos.2022.112216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/11/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
While understanding of periodic recurrent waves of Covid-19 epidemics would aid to combat the pandemics, quantitative analysis of data over a two years period from the outbreak, is lacking. The complexity of Covid-19 recurrent waves is related with the concurrent role of i) the containment measures enforced to mitigate the epidemics spreading ii) the rate of viral gene mutations, and iii) the variable immune response of the host implemented by vaccination. This work focuses on the effect of massive vaccination and gene variants on the recurrent waves in a representative case of countries enforcing mitigation and vaccination strategy. The spreading rate is measured by the ratio between the reproductive number Rt(t) and the doubling time Td(t) called RIC-index and the daily fatalities number. The dynamics of the Covid-19 epidemics have been studied by wavelet analysis and represented by a non-linear helicoid vortex in a 3D space where both RIC-index and fatalities change with time. The onset of periodic recurrent waves has been identified by the transition from convergent to divergent trajectories on the helicoid vortex. We report a main period of recurrent waves of 120 days and the elongation of this period after the vaccination campaign.
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Affiliation(s)
- Gaetano Campi
- Institute of Crystallography, Consiglio Nazionale delle Ricerche CNR, via Salaria Km 29.300, Monterotondo, Roma I-00015, Italy
- Rome International Centre Materials Science Superstripes RICMASS, via dei Sabelli 119A, 00185 Rome, Italy
| | - Antonio Bianconi
- Institute of Crystallography, Consiglio Nazionale delle Ricerche CNR, via Salaria Km 29.300, Monterotondo, Roma I-00015, Italy
- Rome International Centre Materials Science Superstripes RICMASS, via dei Sabelli 119A, 00185 Rome, Italy
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Hassan J, Haigh C, Ahmed T, Uddin MJ, Das DB. Potential of Microneedle Systems for COVID-19 Vaccination: Current Trends and Challenges. Pharmaceutics 2022; 14:1066. [PMID: 35631652 PMCID: PMC9144974 DOI: 10.3390/pharmaceutics14051066] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/27/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022] Open
Abstract
To prevent the coronavirus disease 2019 (COVID-19) pandemic and aid restoration to prepandemic normality, global mass vaccination is urgently needed. Inducing herd immunity through mass vaccination has proven to be a highly effective strategy for preventing the spread of many infectious diseases, which protects the most vulnerable population groups that are unable to develop immunity, such as people with immunodeficiencies or weakened immune systems due to underlying medical or debilitating conditions. In achieving global outreach, the maintenance of the vaccine potency, transportation, and needle waste generation become major issues. Moreover, needle phobia and vaccine hesitancy act as hurdles to successful mass vaccination. The use of dissolvable microneedles for COVID-19 vaccination could act as a major paradigm shift in attaining the desired goal to vaccinate billions in the shortest time possible. In addressing these points, we discuss the potential of the use of dissolvable microneedles for COVID-19 vaccination based on the current literature.
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Affiliation(s)
- Jasmin Hassan
- Drug Delivery & Therapeutics Lab, Dhaka 1212, Bangladesh; (J.H.); (T.A.)
| | - Charlotte Haigh
- Department of Chemical Engineering, Loughborough University, Epinal Way, Loughborough LE11 3TU, UK;
| | - Tanvir Ahmed
- Drug Delivery & Therapeutics Lab, Dhaka 1212, Bangladesh; (J.H.); (T.A.)
| | - Md Jasim Uddin
- Drug Delivery & Therapeutics Lab, Dhaka 1212, Bangladesh; (J.H.); (T.A.)
- Faculty of Engineering and Science, University of Greenwich, Chatham Maritime, Kent ME4 4TB, UK
- Department of Pharmacy, Brac University, 66 Mohakhali, Dhaka 1212, Bangladesh
| | - Diganta B. Das
- Department of Chemical Engineering, Loughborough University, Epinal Way, Loughborough LE11 3TU, UK;
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Grinchuk P, Fisenko S. Power-law multi-wave model for COVID-19 propagation in countries with nonuniform population density. QUANTITATIVE BIOLOGY 2022. [DOI: 10.15302/j-qb-022-0301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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