The SARS-CoV-2 Hydra, a Tiny Monster from the 21st Century: Thermodynamics of the BA.5.2 and BF.7 Variants

Overview

Journal Microb Risk Anal

Specialty Microbiology

Date 2023 Feb 13

PMID 36777924

Authors

Marko Popovic

Affiliations

Soon will be listed here.

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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References

Tkhilaishvili T, Lombardi L, Klatt A, Trampuz A, Di Luca M . Bacteriophage Sb-1 enhances antibiotic activity against biofilm, degrades exopolysaccharide matrix and targets persisters of Staphylococcus aureus. Int J Antimicrob Agents. 2018; 52(6):842-853. DOI: 10.1016/j.ijantimicag.2018.09.006. View

Aladag A, Hoffmann S, Stoldt M, Bosing C, Willbold D, Schwarten M . Hepatitis C virus NS5A is able to competitively displace c-Myc from the Bin1 SH3 domain in vitro. J Pept Sci. 2014; 20(5):334-40. DOI: 10.1002/psc.2618. View

Noble C, Pheng Lim S, Arora R, Yokokawa F, Nilar S, Seh C . A Conserved Pocket in the Dengue Virus Polymerase Identified through Fragment-based Screening. J Biol Chem. 2016; 291(16):8541-8. PMC: 4861426. DOI: 10.1074/jbc.M115.710731. View

Wang L, Tkhilaishvili T, Bernal Andres B, Trampuz A, Gonzalez Moreno M . Bacteriophage-antibiotic combinations against ciprofloxacin/ceftriaxone-resistant Escherichia coli in vitro and in an experimental Galleria mellonella model. Int J Antimicrob Agents. 2020; 56(6):106200. DOI: 10.1016/j.ijantimicag.2020.106200. View

Morowitz H, Kostelnik J, Yang J, Cody G . The origin of intermediary metabolism. Proc Natl Acad Sci U S A. 2000; 97(14):7704-8. PMC: 16608. DOI: 10.1073/pnas.110153997. View

Maassen S, Huskens J, Cornelissen J . Elucidating the Thermodynamic Driving Forces of Polyanion-Templated Virus-like Particle Assembly. J Phys Chem B. 2019; 123(46):9733-9741. PMC: 6875872. DOI: 10.1021/acs.jpcb.9b06258. View

Von Bertalanffy L . The theory of open systems in physics and biology. Science. 1950; 111(2872):23-9. DOI: 10.1126/science.111.2872.23. View

Byrn R, Jones S, Bennett H, Bral C, Clark M, Jacobs M . Preclinical activity of VX-787, a first-in-class, orally bioavailable inhibitor of the influenza virus polymerase PB2 subunit. Antimicrob Agents Chemother. 2014; 59(3):1569-82. PMC: 4325764. DOI: 10.1128/AAC.04623-14. View

von Stockar U, Liu J . Does microbial life always feed on negative entropy? Thermodynamic analysis of microbial growth. Biochim Biophys Acta. 1999; 1412(3):191-211. DOI: 10.1016/s0005-2728(99)00065-1. View

10.

Du X, Li Y, Xia Y, Ai S, Liang J, Sang P . Insights into Protein-Ligand Interactions: Mechanisms, Models, and Methods. Int J Mol Sci. 2016; 17(2). PMC: 4783878. DOI: 10.3390/ijms17020144. View

11.

Degueldre C . Single virus inductively coupled plasma mass spectroscopy analysis: A comprehensive study. Talanta. 2021; 228:122211. DOI: 10.1016/j.talanta.2021.122211. View

12.

Guosheng L, Yi L, Xiangdong C, Peng L, Ping S, Songsheng Q . Study on interaction between T4 phage and Escherichia coli B by microcalorimetric method. J Virol Methods. 2003; 112(1-2):137-43. DOI: 10.1016/s0166-0934(03)00214-3. View

13.

Tkhilaishvili T, Di Luca M, Abbandonato G, Maiolo E, Klatt A, Reuter M . Real-time assessment of bacteriophage T3-derived antimicrobial activity against planktonic and biofilm-embedded Escherichia coli by isothermal microcalorimetry. Res Microbiol. 2018; 169(9):515-521. DOI: 10.1016/j.resmic.2018.05.010. View

14.

Liu T, Sae-Ueng U, Li D, Lander G, Zuo X, Jonsson B . Solid-to-fluid-like DNA transition in viruses facilitates infection. Proc Natl Acad Sci U S A. 2014; 111(41):14675-80. PMC: 4205597. DOI: 10.1073/pnas.1321637111. View

15.

Morowitz H, Heinz B, Deamer D . The chemical logic of a minimum protocell. Orig Life Evol Biosph. 1988; 18(3):281-7. DOI: 10.1007/BF01804674. View

16.

Scialo F, Daniele A, Amato F, Pastore L, Matera M, Cazzola M . ACE2: The Major Cell Entry Receptor for SARS-CoV-2. Lung. 2020; 198(6):867-877. PMC: 7653219. DOI: 10.1007/s00408-020-00408-4. View

17.

Ozilgen M, Yilmaz B . COVID-19 disease causes an energy supply deficit in a patient. Int J Energy Res. 2020; 45(2):1157-1160. PMC: 7537131. DOI: 10.1002/er.5883. View

18.

Popovic M . Strain wars 2: Binding constants, enthalpies, entropies, Gibbs energies and rates of binding of SARS-CoV-2 variants. Virology. 2022; 570:35-44. PMC: 8961312. DOI: 10.1016/j.virol.2022.03.008. View

19.

Gale P . Using thermodynamic equilibrium models to predict the effect of antiviral agents on infectivity: Theoretical application to SARS-CoV-2 and other viruses. Microb Risk Anal. 2021; 21:100198. PMC: 8642839. DOI: 10.1016/j.mran.2021.100198. View

20.

Kawahara T, Akiba I, Sakou M, Sakaguchi T, Taniguchi H . Inactivation of human and avian influenza viruses by potassium oleate of natural soap component through exothermic interaction. PLoS One. 2018; 13(9):e0204908. PMC: 6160177. DOI: 10.1371/journal.pone.0204908. View