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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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2
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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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Popovic M, Martin JH, Head RJ. COVID infection in 4 steps: Thermodynamic considerations reveal how viral mucosal diffusion, target receptor affinity and furin cleavage act in concert to drive the nature and degree of infection in human COVID-19 disease. Heliyon 2023; 9:e17174. [PMID: 37325453 PMCID: PMC10259165 DOI: 10.1016/j.heliyon.2023.e17174] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 06/04/2023] [Accepted: 06/09/2023] [Indexed: 06/17/2023] Open
Abstract
We have developed a mechanistic model of SARS-CoV-2 and SARS-CoV infection, exploring the relationship between the viral diffusion in the mucosa and viral affinity for the angiotensin converting enzyme 2 (ACE2) target. Utilising the structural similarity of SARS-CoV and SARS-CoV-2 and a shared viral target receptor (ACE2), but a dramatic difference in upper or lower respiratory tract infectivity, we were able to generate insights into the linkage of mucosal diffusion and target receptor affinity in determining the pathophysiological pathways of these two viruses. Our analysis reveals that for SARS-CoV-2 the higher affinity of ACE2 binding, the faster and more complete the mucosal diffusion in its transport from the upper airway to the region of the ACE2 target on the epithelium. This diffusional process is essential for the presentation of this virus to the furin catalysed highly efficient entry and infection process in the upper respiratory tract epithelial cells. A failure of SARS-CoV to follow this path is associated with lower respiratory tract infection and decreased infectivity. Thus, our analysis supports the view that through tropism SARS-CoV-2 has evolved a highly efficient membrane entry process that can act in concert with a high binding affinity of this virus and its variants for its ACE2 which in turn promotes enhanced movement of the virus from airway to epithelium. In this way ongoing mutations yielding higher affinities of SARS-CoV-2 for the ACE2 target becomes the basis for higher upper respiratory tract infectivity and greater viral spread. It is concluded that SARS-CoV-2 is constrained in the extent of its activities by the fundamental laws of physics and thermodynamics. Laws that describe diffusion and molecular binding. Moreover it can be speculated that the very earliest contact of this virus with the human mucosa defines the pathogenesis of this infection.
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Affiliation(s)
- Marko Popovic
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, 11000 Belgrade, Serbia
| | - Jennifer H Martin
- Centre for Drug Repurposing and Medicines Research, University of Newcastle and Hunter Medical Research Institute, Newcastle 2305, Australia
| | - Richard J Head
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
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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. 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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