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Popović ME. Animal bioenergetics: Thermodynamic and kinetic analysis of growth and metabolism of Anguilla anguilla. ZOOLOGY 2024; 163:126158. [PMID: 38428123 DOI: 10.1016/j.zool.2024.126158] [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: 03/01/2023] [Revised: 02/05/2024] [Accepted: 02/18/2024] [Indexed: 03/03/2024]
Abstract
Bioenergetics and biothermodynamics are valuable tools in research on growth and metabolic processes of a wide range of organisms, including viruses, bacteria, fungi, algae and plants, as is shown by the many publications on this topic in the literature. These studies provide insight into growth and metabolism of individual species, as well as interactions between species, like the virus-host interaction (infection) and virus-virus interaction (competition). However, this approach has not yet been applied to animal species. The universality of biothermodynamics and bioenergetics provides a good motive to apply them in analysis of animals. In this research, we made a bioenergetic, biothermodynamic and kinetic characterization for the first time for an animal species - Anguilla anguilla L. (European eel). We made a comparative analysis on yellow (young adult) and silver (mature adult) phases. Metabolic processes were modeled as chemical reactions with characteristic thermodynamic properties: enthalpy, entropy and Gibbs energy. Moreover, Gibbs energy explained growth rates, through phenomenological equations. This analysis of animal metabolism and growth explained metabolic properties of yellow and silver A. anguilla, including the bioenergetic aspect of life history. Moreover, we compared thermodynamic properties of A. anguilla with those of its main macromolecular components and other organisms. The thermodynamic properties were explained by the structural properties of organisms. This research extends the bioenergetic and biothermodynamic approaches to zoology, which should allow analysis of the energetic aspect of animal metabolic processes, interactions with their environment and interactions with other organisms. Furthermore, it connects the macroscopic perspective of zoology with the microscopic perspectives of biochemistry, bioenergetics and biothermodynamics. This will provide a basis for development of mechanistic models of animal growth and metabolism.
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Affiliation(s)
- Marko E Popović
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, Njegoševa 12, Belgrade 11000, Serbia.
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Popovic M. SARS-CoV-2 strain wars continues: Chemical and thermodynamic characterization of live matter and biosynthesis of Omicron BN.1, CH.1.1 and XBC variants. MICROBIAL RISK ANALYSIS 2023; 24:100260. [PMID: 36974134 PMCID: PMC10032061 DOI: 10.1016/j.mran.2023.100260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 06/11/2023]
Abstract
SARS-CoV-2 has during the last 3 years mutated several dozen times. Most mutations in the newly formed variants have been chemically and thermodynamically characterized. New variants have been declared as variants under monitoring. The European Centre for Disease Prevention and Control has suggested the hypothesis that the new BN.1, CH.1.1 and XBC variants could have properties similar to those of VOC. Thermodynamic properties of new variants have been reported in this manuscript for the first time. Gibbs energy of biosynthesis, as the driving force for viral multiplication, is less negative for the new variants than for the earlier variants. This indicates that the virus has evolved towards decrease in pathogenicity, which leads to less severe forms of COVID-19.
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Affiliation(s)
- Marko Popovic
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, 11000 Belgrade, Serbia
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Popovic M, Pantović Pavlović M, Pavlović M. Ghosts of the past: Elemental composition, biosynthesis reactions and thermodynamic properties of Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2. MICROBIAL RISK ANALYSIS 2023; 24:100263. [PMID: 37234934 PMCID: PMC10199755 DOI: 10.1016/j.mran.2023.100263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/07/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]
Abstract
From the perspectives of molecular biology, genetics and biothermodynamics, SARS-CoV-2 is the among the best characterized viruses. Research on SARS-CoV-2 has shed a new light onto driving forces and molecular mechanisms of viral evolution. This paper reports results on empirical formulas, biosynthesis reactions and thermodynamic properties of biosynthesis (multiplication) for the Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2. Thermodynamic analysis has shown that the physical driving forces for evolution of SARS-CoV-2 are Gibbs energy of biosynthesis and Gibbs energy of binding. The driving forces have led SARS-CoV-2 through the evolution process from the original Hu-1 to the newest variants in accordance with the expectations of the evolution theory.
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Affiliation(s)
- Marko Popovic
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, 11000 Belgrade, Serbia
| | - Marijana Pantović Pavlović
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, 11000 Belgrade, Serbia
- University of Belgrade, Centre of Excellence in Chemistry and Environmental Engineering - ICTM, Belgrade, Serbia
| | - Miroslav Pavlović
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, 11000 Belgrade, Serbia
- University of Belgrade, Centre of Excellence in Chemistry and Environmental Engineering - ICTM, Belgrade, Serbia
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Fahim M, Abu ElSood H, AbdElGawad B, Deghedy O, Naguib A, Roshdy WH, Showky S, Kamel R, Elguindy N, Abdel Fattah M, Afifi S, Kandeel A, Abdelghaffar K. Adapting an integrated acute respiratory infections sentinel surveillance to the COVID-19 pandemic requirements, Egypt, 2020-2022. PUBLIC HEALTH IN PRACTICE 2023; 5:100358. [PMID: 36686982 PMCID: PMC9846875 DOI: 10.1016/j.puhip.2023.100358] [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: 08/06/2022] [Revised: 12/14/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
Objectives In Egypt, an integrated surveillance for acute respiratory infections (ARIs) was established in 2016 to identify the causes of ARIs. The surveillance system includes 19 governmental hospitals. In response to the coronavirus disease 2019 (COVID-19) pandemic, the World Health Organisation (WHO) requested surveillance adaptation to address the emerging challenges. This study aims to describe the experience in Egypt of adapting ARI surveillance to the COVID-19 pandemic. Methods WHO case definitions were used to identify patients with ARIs. Nasopharyngeal/oropharyngeal swabs were collected for SARS-CoV-2 and influenza testing. Demographic and clinical information were obtained by interviewing patients at the hospitals. During the COVID-19 pandemic, the first two outpatients daily and every fifth admitted patient were enrolled in the study. To determine the status of ARIs in Egypt during the pandemic, patient demographic, clinical and laboratory data from 2020 to 2022 were obtained and descriptive analyses were performed. Results Overall, 18,160 patients were enrolled in the study, including 7923 (43.6%) seen at outpatient clinics and 10,237 (56.4%) inpatients. Of the study participants, 6453 (35.5%) tested positive for ARIs, including 5620 (87.1%) for SARS-CoV-2, 781 (12.1%) for influenza and 52 (0.8%) for SARS-CoV-2/influenza coinfection. SARS-CoV-2 was the cause for 95.3% of admitted patients and 65.4% of outpatients. Influenza subtypes included A/H3 (55.7%), Influenza-B (29.1%) and H1/pdm09 (14.2%). Compared with influenza, SARS-CoV-2 tended to infect the elderly, in warm weather and in urban governorates, and resulted in more hospitalisations, longer hospital stays and higher case fatalities (16.3% vs 6.6%, p < 0.001). Conclusions ARI surveillance in Egypt was successfully adapted to the COVID-19 pandemic and effectively described the clinical characteristics and severity of circulating viruses. Surveillance reported the re-emergence of influenza with a severe course and high fatality. Surveillance is essential for monitoring the activity of respiratory viruses with the aim of guiding clinical management, including preventative and control measures.
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Affiliation(s)
- Manal Fahim
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, 3 Magles ElShaab Street, Kasr Alainy, Cairo, Egypt
| | - Hanaa Abu ElSood
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, 3 Magles ElShaab Street, Kasr Alainy, Cairo, Egypt
| | - Basma AbdElGawad
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, 3 Magles ElShaab Street, Kasr Alainy, Cairo, Egypt
| | - Ola Deghedy
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, 3 Magles ElShaab Street, Kasr Alainy, Cairo, Egypt
| | - Amel Naguib
- Central Public Health Laboratory, Ministry of Health and Population, Elsheikh Rehan Street, Cairo, Egypt
| | - Wael H. Roshdy
- Central Public Health Laboratory, Ministry of Health and Population, Elsheikh Rehan Street, Cairo, Egypt
| | - Shymaa Showky
- Central Public Health Laboratory, Ministry of Health and Population, Elsheikh Rehan Street, Cairo, Egypt
| | - Reham Kamel
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, 3 Magles ElShaab Street, Kasr Alainy, Cairo, Egypt
| | - Nancy Elguindy
- Central Public Health Laboratory, Ministry of Health and Population, Elsheikh Rehan Street, Cairo, Egypt
| | - Mohammad Abdel Fattah
- Preventive Sector, Ministry of Health and Population, 3 Magles ElShaab Street, Kasr Alainy, Cairo, Egypt
| | - Salma Afifi
- Ministry of Health and Population Consultant, 3 Magles ElShaab Street, Kasr Alainy, Cairo, Egypt
| | - Amr Kandeel
- Preventive Sector, Ministry of Health and Population, 3 Magles ElShaab Street, Kasr Alainy, Cairo, Egypt
| | - Khaled Abdelghaffar
- Ministry of Health and Population, 3 Magles ElShaab Street, Kasr Alainy, Cairo, Egypt
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Popovic ME. XBB.1.5 Kraken cracked: Gibbs energies of binding and biosynthesis of the XBB.1.5 variant of SARS-CoV-2. Microbiol Res 2023; 270:127337. [PMID: 36804126 PMCID: PMC9928726 DOI: 10.1016/j.micres.2023.127337] [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: 01/22/2023] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023]
Abstract
The SARS-CoV-2 Hydra with many heads (variants) has been causing the COVID-19 pandemic for 3 years. The appearance of every new head (SARS-CoV-2 variant) causes a new pandemic wave. The last in the series is the XBB.1.5 "Kraken" variant. In the general public (social media) and in the scientific community (scientific journals), during the last several weeks since the variant has appeared, the question was raised of whether the infectivity of the new variant will be greater. This article attempts to provide the answer. Analysis of thermodynamic driving forces of binding and biosynthesis leads to the conclusion that infectivity of the XBB.1.5 variant could be increased to a certain extent. The pathogenicity of the XBB.1.5 variant seems to be unchanged compared to the other Omicron variants.
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Affiliation(s)
- Marko E Popovic
- School of Life Sciences, Technical University of Munich, 85354 Freising, Germany.
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Popovic M. The SARS-CoV-2 Hydra, a tiny monster from the 21st century: Thermodynamics of the BA.5.2 and BF.7 variants. MICROBIAL RISK ANALYSIS 2023; 23:100249. [PMID: 36777924 PMCID: PMC9898946 DOI: 10.1016/j.mran.2023.100249] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/01/2023] [Accepted: 02/01/2023] [Indexed: 06/01/2023]
Abstract
SARS-CoV-2 resembles the ancient mythical creature Hydra. Just like with the Hydra, when one head is cut, it is followed by appearance of two more heads, suppression of one SARS-CoV-2 variant causes appearance of newer variants. Unlike Hydra that grows identical heads, newer SARS-CoV-2 variants are usually more infective, which can be observed as time evolution of the virus at hand, which occurs through acquisition of mutations during time. The appearance of new variants is followed by appearance of new COVID-19 pandemic waves. With the appearance of new pandemic waves and determining of sequences, in the scientific community and general public the question is always raised of whether the new variant will be more virulent and more pathogenic. The two variants characterized in this paper, BA.5.2 and BF.7, have caused a pandemic wave during the late 2022. This paper gives full chemical and thermodynamic characterization of the BA.5.2 and BF.7 variants of SARS-CoV-2. Having in mind that Gibbs energy of binding and biosynthesis represent the driving forces for the viral life cycle, based on the calculated thermodynamic properties we can conclude that the newer variants are more infective than earlier ones, but that their pathogenicity has not changed.
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Affiliation(s)
- Marko Popovic
- School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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Popovic M. Never ending story? Evolution of SARS-CoV-2 monitored through Gibbs energies of biosynthesis and antigen-receptor binding of Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants. MICROBIAL RISK ANALYSIS 2023; 23:100250. [PMID: 36777740 PMCID: PMC9896887 DOI: 10.1016/j.mran.2023.100250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/01/2023] [Accepted: 02/01/2023] [Indexed: 06/01/2023]
Abstract
RNA viruses exhibit a great tendency to mutate. Mutations occur in the parts of the genome that encode the spike glycoprotein and less often in the rest of the genome. This is why Gibbs energy of binding changes more than that of biosynthesis. Starting from 2019, the wild type that was labeled Hu-1 has during the last 3 years evolved to produce several dozen new variants, as a consequence of mutations. Mutations cause changes in empirical formulas of new virus strains, which lead to change in thermodynamic properties of biosynthesis and binding. These changes cause changes in the rate of reactions of binding of virus antigen to the host cell receptor and the rate of virus multiplication in the host cell. Changes in thermodynamic and kinetic parameters lead to changes in biological parameters of infectivity and pathogenicity. Since the beginning of the COVID-19 pandemic, SARS-CoV-2 has been evolving towards increase in infectivity and maintaining constant pathogenicity, or for some variants a slight decrease in pathogenicity. In the case of Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants pathogenicity is identical as in the Omicron BA.2.75 variant. On the other hand, infectivity of the Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants is greater than those of previous variants. This will most likely result in the phenomenon of asymmetric coinfection, that is circulation of several variants in the population, some being dominant.
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Affiliation(s)
- Marko Popovic
- School of Life Sciences, Technical University of Munich, Freising, Germany
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Biothermodynamics of Viruses from Absolute Zero (1950) to Virothermodynamics (2022). Vaccines (Basel) 2022; 10:vaccines10122112. [PMID: 36560522 PMCID: PMC9784531 DOI: 10.3390/vaccines10122112] [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: 11/11/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Biothermodynamics of viruses is among the youngest but most rapidly developing scientific disciplines. During the COVID-19 pandemic, it closely followed the results published by molecular biologists. Empirical formulas were published for 50 viruses and thermodynamic properties for multiple viruses and virus variants, including all variants of concern of SARS-CoV-2, SARS-CoV, MERS-CoV, Ebola virus, Vaccinia and Monkeypox virus. A review of the development of biothermodynamics of viruses during the last several decades and intense development during the last 3 years is described in this paper.
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Popovic M. Why doesn't Ebola virus cause pandemics like SARS-CoV-2? MICROBIAL RISK ANALYSIS 2022; 22:100236. [PMID: 36312211 PMCID: PMC9597532 DOI: 10.1016/j.mran.2022.100236] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/22/2022] [Accepted: 10/22/2022] [Indexed: 06/01/2023]
Abstract
Ebola virus is among the most dangerous, contagious and deadly etiological causes of viral diseases. However, Ebola virus has never extensively spread in human population and never have led to a pandemic. Why? The mechanistic biophysical model revealing the biothermodynamic background of virus-host interaction) could help us to understand pathogenesis of Ebola virus disease (earlier known as the Ebola hemorrhagic fever). In this paper for the first time the empirical formula, thermodynamic properties of biosynthesis (including the driving force of virus multiplication in the susceptible host), binding constant and thermodynamic properties of binding are reported. Thermodynamic data for Ebola virus were compared with data for SARS-CoV-2 to explain why SARS-CoV-2 has caused a pandemic, while Ebola remains on local epidemic level. The empirical formula of the Ebola virus was found to be CH1.569O0.3281N0.2786P0.00173S0.00258. Standard Gibbs energy of biosynthesis of the Ebola virus nucleocapsid is -151.59 kJ/C-mol.
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Affiliation(s)
- Marko Popovic
- School of Life Sciences, Technical University of Munich, Freising, Germany
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Popovic M. Strain wars 3: Differences in infectivity and pathogenicity between Delta and Omicron strains of SARS-CoV-2 can be explained by thermodynamic and kinetic parameters of binding and growth. MICROBIAL RISK ANALYSIS 2022; 22:100217. [PMID: 35434234 PMCID: PMC9001013 DOI: 10.1016/j.mran.2022.100217] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/10/2022] [Accepted: 04/10/2022] [Indexed: 05/05/2023]
Abstract
In this paper, for the first time, empirical formulas have been reported of the Delta and Omicron strains of SARS-CoV-2. The empirical formula of the Delta strain entire virion was found to be CH1.6383O0.2844N0.2294P0.0064S0.0042, while its nucleocapsid has the formula CH1.5692O0.3431N0.3106P0.0060S0.0043. The empirical formula of the Omicron strain entire virion was found to be CH1.6404O0.2842N0.2299P0.0064S0.0038, while its nucleocapsid has the formula CH1.5734O0.3442N0.3122P0.0060S0.0033. Based on the empirical formulas, standard thermodynamic properties of formation and growth have been calculated and reported for the Delta and Omicron strains. Moreover, standard thermodynamic properties of binding have been reported for Wild type (Hu-1), Alpha, Beta, Gamma, Delta and Omicron strains. For all the strains, binding phenomenological coefficients and antigen-receptor (SGP-ACE2) binding rates have been determined and compared, which are proportional to infectivity. The results show that the binding rate of the Omicron strain is between 1.5 and 2.5 times greater than that of the Delta strain. The Omicron strain is characterized by a greater infectivity, based on the epidemiological data available in the literature. The increased infectivity was explained in this paper using Gibbs energy of binding. However, no indications exist for decreased pathogenicity of the Omicron strain. Pathogenicity is proportional to the virus multiplication rate, while Gibbs energies of multiplication are very similar for the Delta and Omicron strains. Thus, multiplication rate and pathogenicity are similar for the Delta and Omicron strains. The lower number of severe cases caused by the Omicron strain can be explained by increased number of immunized people. Immunization does not influence the possibility of occurrence of infection, but influences the rate of immune response, which is much more efficient in immunized people. This leads to prevention of more severe Omicron infection cases.
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Affiliation(s)
- Marko Popovic
- School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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Popovic M. Strain wars 5: Gibbs energies of binding of BA.1 through BA.4 variants of SARS-CoV-2. MICROBIAL RISK ANALYSIS 2022; 22:100231. [PMID: 36034590 PMCID: PMC9392893 DOI: 10.1016/j.mran.2022.100231] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 06/01/2023]
Abstract
This paper reports, for the first time, standard Gibbs energies of binding of the BA.1, BA.2, BA.3, BA.2.13, BA.2.12.1 and BA.4 Omicron variants of SARS-CoV-2, to the Human ACE2 receptor. Variants BA.1 through BA.3 exhibit a trend of decreasing standard Gibbs energy of binding and hence increased infectivity. The BA.4 variant exhibits a less negative standard Gibbs energy of binding, but also more efficient evasion of the immune response. Therefore, it was concluded that all the analyzed strains evolve in accordance with expectations of the theory of evolution, albeit using different strategies.
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Affiliation(s)
- Marko Popovic
- School of Life Sciences, Technical University of Munich, Freising, Germany
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Popovic M. Beyond COVID-19: Do biothermodynamic properties allow predicting the future evolution of SARS-CoV-2 variants? MICROBIAL RISK ANALYSIS 2022; 22:100232. [PMID: 36061411 PMCID: PMC9428117 DOI: 10.1016/j.mran.2022.100232] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 06/01/2023]
Abstract
During the COVID-19 pandemic, many statistical and epidemiological studies have been published, trying to predict the future development of the SARS-CoV-2 pandemic. However, it would be beneficial to have a specific, mechanistic biophysical model, based on the driving forces of processes performed during virus-host interactions and fundamental laws of nature, allowing prediction of future evolution of SARS-CoV-2 and other viruses. In this paper, an attempt was made to predict the development of the pandemic, based on biothermodynamic parameters: Gibbs energy of binding and Gibbs energy of growth. Based on analysis of biothermodynamic parameters of various variants of SARS-CoV-2, SARS-CoV and MERS-CoV that appeared during evolution, an attempt was made to predict the future directions of evolution of SARS-CoV-2 and potential occurrence of new strains that could lead to new pandemic waves. Possible new mutations that could appear in the future could lead to changes in chemical composition, biothermodynamic properties (driving forces of new virus strains) and biological properties of SARS CoV-2 that represent a risk for humanity.
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Affiliation(s)
- Marko Popovic
- School of Life Sciences, Technical University of Munich, Freising 85354 , Germany
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Omicron BA.2.75 Sublineage (Centaurus) Follows the Expectations of the Evolution Theory: Less Negative Gibbs Energy of Biosynthesis Indicates Decreased Pathogenicity. MICROBIOLOGY RESEARCH 2022. [DOI: 10.3390/microbiolres13040066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 belongs to the group of RNA viruses with a pronounced tendency to mutate. Omicron BA.2.75 is a subvariant believed to be able to suppress the currently dominant BA.5 and cause a new winter wave of the COVID-19 pandemic. Omicron BA.2.75 is characterized by a greater infectivity compared to earlier Omicron variants. However, the Gibbs energy of the biosynthesis of virus particles is slightly less negative compared to those of other variants. Thus, the multiplication rate of Omicron BA.2.75 is lower than that of other SARS-CoV-2 variants. This leads to slower accumulation of newly formed virions and less damage to host cells, indicating evolution of SARS-CoV-2 toward decreasing pathogenicity.
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Omicron BA.2.75 Subvariant of SARS-CoV-2 Is Expected to Have the Greatest Infectivity Compared with the Competing BA.2 and BA.5, Due to Most Negative Gibbs Energy of Binding. BIOTECH (BASEL (SWITZERLAND)) 2022; 11:biotech11040045. [PMID: 36278557 PMCID: PMC9589998 DOI: 10.3390/biotech11040045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Omicron BA.2.75 may become the next globally dominant strain of COVID-19 in 2022. The BA.2.75 sub-variant has acquired more mutations (9) in spike protein and other genes of SARS-CoV-2 than any other variant. Thus, its chemical composition and thermodynamic properties have changed compared with earlier variants. In this paper, the Gibbs energy of the binding and antigen-receptor binding rate was reported for the BA.2.75 variant. Gibbs energy of the binding of the Omicron BA.2.75 variant is more negative than that of the competing variants BA.2 and BA.5.
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Popovic M. Strain wars 4 - Darwinian evolution through Gibbs' glasses: Gibbs energies of binding and growth explain evolution of SARS-CoV-2 from Hu-1 to BA.2. Virology 2022; 575:36-42. [PMID: 36057159 DOI: 10.1016/j.virol.2022.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/21/2022] [Indexed: 01/07/2023]
Abstract
All processes in nature are driven by negative Gibbs energy. Gibbs energy is used by various viruses and their strains to hijack host cell metabolic machinery. The analysis was made by using the atom counting method to obtain elemental compositions and Gibbs energy of growth of the BA.2 strain of SARS-CoV-2. Moreover, Gibbs energy of binding was determined for the BA.2 strain. The properties of BA.2 were compared to those of Hu-1, Delta and Omicron strains. It is concluded that SARS-CoV-2 has evolved by making its Gibbs energy of binding more negative. Hence, it seems that the change in Gibbs energy of binding plays the major role in SARS-CoV-2 evolution. Therefore, Gibbs energy difference between various strains represents the possible mechanism of Darwinian evolution of viruses. In particular, a virus evolves through mutations, resulting in change in information content, elemental composition, increase in infectivity and decrease in pathogenicity.
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Affiliation(s)
- Marko Popovic
- School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.
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16
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Popovic M, Popovic M. Strain Wars: Competitive interactions between SARS-CoV-2 strains are explained by Gibbs energy of antigen-receptor binding. MICROBIAL RISK ANALYSIS 2022; 21:100202. [PMID: 35155724 PMCID: PMC8816792 DOI: 10.1016/j.mran.2022.100202] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 05/16/2023]
Abstract
Since the beginning of the COVID-19 pandemic, SARS-CoV-2 has mutated several times into new strains, with an increased infectivity. Infectivity of SARS-CoV-2 strains depends on binding affinity of the virus to its host cell receptor. In this paper, we quantified the binding affinity using Gibbs energy of binding and analyzed the competition between SARS-CoV-2 strains as an interference phenomenon. Gibbs energies of binding were calculated for several SARS-SoV-2 strains, including Hu-1 (wild type), B.1.1.7 (alpha), B.1.351 (beta), P.1 (Gamma), B.1.36 and B.1.617 (Delta). The least negative Gibbs energy of binding is that of Hu-1 strain, -37.97 kJ/mol. On the other hand, the most negative Gibbs energy of binding is that of the Delta strain, -49.50 kJ/mol. We used the more negative Gibbs energy of binding to explain the increased infectivity of newer SARS-CoV-2 strains compared to the wild type. Gibbs energies of binding was found to decrease chronologically, with appearance of new strains. The ratio of Gibbs energies of binding of mutated strains and wild type was used to define a susceptibility coefficient, which is an indicator of viral interference, where a virus can prevent or partially inhibit infection with another virus.
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Affiliation(s)
- Marko Popovic
- TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany
| | - Marta Popovic
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
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Gale P. Using thermodynamic equilibrium models to predict the effect of antiviral agents on infectivity: Theoretical application to SARS-CoV-2 and other viruses. MICROBIAL RISK ANALYSIS 2022; 21:100198. [PMID: 34901357 PMCID: PMC8642839 DOI: 10.1016/j.mran.2021.100198] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 05/21/2023]
Abstract
Thermodynamic equilibrium models predict the infectivity of novel and emerging viruses using molecular data including the binding affinity of the virus to the host cell (as represented by the association constant Ka_virus_T) and the probability, pvirogenesis, of the virus replicating after entry to the cell. Here those models are adapted based on the principles of ligand binding to macromolecules to assess the effect on virus infectivity of inhibitor molecules which target specific proteins of the virus. Three types of inhibitor are considered using the thermodynamic equilibrium model for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of the human lung with parameters for the strength and nature of the interaction between the target virus protein and the inhibitor molecule. The first is competitive inhibition of the SARS-CoV-2 spike glycoprotein (SGP) trimer binding to its human angiotensin converting enzyme 2 (ACE2) receptor by unfractionated heparin (UFH). Using a novel approach presented here, a value of Ka_virus_T = 3.53 × 1017 M-1 is calculated for SARS-CoV-2 from the IC50 for inhibition by UFH of SARS-CoV-2 plaque formation in cell culture together with the dissociation constant KVI of 0.73 × 10-10 M reported for heparin binding to SARS-CoV-2 SGP trimer. Such a high Ka_virus_T limits the effectiveness of competitive inhibitors such as UFH. The second is the attachment of a nanoparticle such as a zinc oxide tetrapod (ZnOT) to the virus shell as for herpes simplex virus (HSV). The increase in molecular weight through ZnOT attachment is predicted to decrease Ka_virus_T by orders of magnitude by making the entropy change (ΔSa_immob) on immobilisation of the ZnOT:virus complex on cell binding more negative than for the virus alone. According to the model, ZnOT acts synergistically with UFH at the IC50 of 33 μg/cm3 which together decrease viral infectivity by 61,000-fold compared to the two-fold and three-fold decreases predicted for UFH alone at the IC50 and for ZnOT alone respectively. According to the model here, UFH alone at its peak deliverable dose to the lung of 1,000 μg/cm3 only decreases infectivity by 31-fold. Practicable approaches to target and decrease ΔSa_immob for respiratory viruses should therefore be considered. The combination of decreasing ΔSa_immob together with blocking the interaction of virus surface protein with its host cell receptor may achieve synergistic effects for faecal-oral viruses and HSV. The third is reversible noncompetitive inhibition of the viral main protease (Mpro) for which the decrease in pvirogenesis is assumed to be proportional to the decrease in enzyme activity as predicted by enzyme kinetic equations for a given concentration of inhibitor which binds to Mpro with dissociation constant Ki. Virologists reporting viral inhibition studies are urged to report the concentration of cells in the cell culture experiment as this is a key parameter in estimating Ka_virus_T here.
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Affiliation(s)
- Paul Gale
- Independent Scientist, 15 Weare Close, Portland, Dorset, DT5 1JP, UK
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Strain wars 2: Binding constants, enthalpies, entropies, Gibbs energies and rates of binding of SARS-CoV-2 variants. Virology 2022; 570:35-44. [PMID: 35366482 PMCID: PMC8961312 DOI: 10.1016/j.virol.2022.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/04/2022] [Accepted: 03/24/2022] [Indexed: 12/30/2022]
Abstract
SARS-CoV-2 virus is the cause of COVID-19 pandemic and belongs to RNA viruses, showing great tendency to mutate. Several dozens of mutations have been observed on the SARS-CoV-2 virus, during the last two years. Some of the mutated strains show a greater infectivity and are capable of suppressing the earlier strains, through interference. In this work, kinetic and thermodynamic properties were calculated for strains characterized by various numbers and locations of mutations. It was shown that mutations lead to changes in chemical composition, thermodynamic properties and infectivity. Through competition, the phenomenon of interference of various SARS-CoV-2 strains was explained, which results in suppression of the wild type by mutant strains. Standard Gibbs energy of binding and binding constant for the Omicron (B.1.1.529) strain were found to be ΔBG⁰ = −45.96 kJ/mol and KB = 1.13 ∙ 10+8 M−1, respectively.
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Popovic M. Atom counting method for determining elemental composition of viruses and its applications in biothermodynamics and environmental science. Comput Biol Chem 2022; 96:107621. [PMID: 34998080 DOI: 10.1016/j.compbiolchem.2022.107621] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/28/2021] [Accepted: 12/31/2021] [Indexed: 01/01/2023]
Abstract
Quantitative physicochemical perspective on life processes has been a great asset, in bioengineering and biotechnology. The quantitative physicochemical approach can be applied to practically all organisms, including viruses, if their chemical composition and thermodynamic properties are known. In this paper, a new method is suggested for determining elemental composition of viruses, based on atom counting. The atom counting method requires knowledge of genetic sequence, protein sequences and protein copy numbers. An algorithm was suggested for a program that finds elemental composition of various viruses (DNA or RNA, enveloped or non-enveloped). Except for the nucleic acid, capsid proteins, lipid bilayer and carbohydrates, this method includes membrane proteins, as well as spike proteins. The atom counting method has been compared with the existing molecular composition and geometric methods on 5 viruses of different morphology, as well as experimentally determined composition of the poliovirus. The atom counting method was found to be more accurate in most cases. The three methods were found to be complementary, since they require different kind of input information. Moreover, since the 3 methods rest on different assumptions, results of one model can be compared to those of the other two.
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Affiliation(s)
- Marko Popovic
- School of Life Sciences, Technical University of Munich, Freising, Germany
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