Evolutionary mechanisms of virus variability

Cover Page

Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription Access

Abstract

The evolutionary changes of viruses are primarily associated with the replication processes of viruses containing deoxyribonucleic and ribonucleic acids, which differ significantly. The genomes of most viruses containing ribonucleic acid are replicated with much less accuracy compared to the genomes of viruses containing deoxyribonucleic acid. Comparing the number of mutations in an infected cell reflects an inverse relationship between genome size and the frequency of mutations carried out by these two categories of viruses. Viruses with double-stranded deoxyribonucleic acid genomes have a low mutation rate compared to single-stranded genomes. The genome of viruses is not a stable unique structure, but rather an average, variable number of different amino acid sequences. It is in the virus population that a high mutation rate is maintained, and low variability is not beneficial for the preservation of viruses in nature. Some animal species may be intermediate hosts when new epidemic viruses appear. The introduction of non-viral nucleic acid into the viral genome can also contribute to the evolutionary changes of the virus, lead to the formation of defective genomes or to the emergence of hypervirulent strains. Viral genomes encode numerous molecules that modulate a wide range of protective immune mechanisms. The variability of viruses is also facilitated by the simultaneous integration of several proviral genomes into one cell, which activates the processes of recombination and genetic shift. An important evolutionary point may be the conversion of ribonucleic acid ribose into deoxyribose of deoxyribonucleic acid, which increases the stability of nucleic acids by more than 100 times. Horizontal gene transfer between viruses that infect different hosts is a central feature of the evolution of viruses containing ribonucleic acid. Eukaryote viruses with single-stranded deoxyribonucleic acid probably evolved from bacterial plasmids after they acquired capsid protein genes from the (+) ribonucleic acid chain of viruses. In addition to megaviruses and adenoviruses, polintons are likely precursors to bidnaviruses and virophages.

About the authors

Alexander V. Moskalev

Kirov Military Medical Academy

Author for correspondence.
Email: alexmav195223@yandex.ru
ORCID iD: 0000-0002-3403-3850
SPIN-code: 8227-2647

MD, Dr. Sci. (Med.), professor

Russian Federation, Saint Petersburg

Boris Yu. Gumilevsky

Kirov Military Medical Academy

Email: alexmav195223@yandex.ru
SPIN-code: 3428-7704
Scopus Author ID: 6602391269
ResearcherId: J-1841-2017

MD, Dr. Sci. (Med.), professor

Russian Federation, Saint Petersburg

Vasiliy Ya. Apchel

Kirov Military Medical Academy; A.I. Herzen Russian State Pedagogical University of the Ministry of Education and Science of the Russian Federation

Email: alexmav195223@yandex.ru
ORCID iD: 0000-0001-7658-4856
SPIN-code: 4978-0785
Scopus Author ID: 6507529350
ResearcherId: Е-8190-2019

MD, Dr. Sci. (Med.), professorciences

Russian Federation, Saint Petersburg; Saint Petersburg

Vasiliy N. Tsygan

Kirov Military Medical Academy

Email: alexmav195223@yandex.ru
ORCID iD: 0000-0003-1199-0911
SPIN-code: 7215-6206

MD, Dr. Sci. (Med.), professor

Russian Federation, Saint Petersburg

References

  1. Katze MG, Korth MJ, Law GL, et al. Viral pathogenesis: From basics to systems biology. San Diego: Academic Press, 2016. 422 p.
  2. Ahmad L, Mostowy S, Sancho-Shimizu S. Autophagy-virus interplay: From cell biology to human disease. Front Cell Dev Biol. 2018;19:155. doi: 10.3389/fcell.2018.00155
  3. Luoa LY, Hahnb WC. Oncogenic signaling adaptor proteins. J Genet Genomics. 2015;42(10):521–529. doi: 10.1016/j.jgg.2015.09.001
  4. Griffin DE. The immune response in measles: Virus control, clearance and protective immunity. Viruses. 2016;10(8):282–291. doi: 10.3390/v8100282
  5. Gong B-L, Mao R-Q, Xiao Y, et al. Improvement of enzyme activity and soluble expression of an alkaline protease isolated from oil-polluted mud flat metagenome by random mutagenesis. Enzyme Microb Technol. 2017;106:97–105. doi: 10.1016/j.enzmictec.2017.06.015
  6. Domingo E, Perales C. Quasispecies and virus. Eur Biophys J. 2018;4(47):443–457. doi: 10.1007/s00249-018-1282-6
  7. Guo Y-J, Pan W-W, Liu S-B, et al. ERK/MAPK signaling pathway and tumorigenesis. Exp Ther Med. 2020;19(3):1997–2007. doi: 10.3892/etm.2020.8454
  8. Takata MA, Gonçalves-Carneiro D, Zang TM, et al. CG dinucleotide suppression enables antiviral defence targeting non-self RNA. Nature. 2017;550(7674):124–127. doi: 10.1038/nature24039
  9. Thapa RJ, Ingram JP, Ragan KB, et al. DAI senses influenza a virus genomic RNA and activates RIPK3-Dependent cell death. Cell Host Microbe. 2016;20(5):674–681. doi: 10.1016/j.chom.2016.09.014
  10. Hemann EA, Green R, Turnbull JB, et al. Interferon-λ modulates dendritic cells to facilitate T cell immunity ion with influenza A virus. Nat Immunol. 2019;20:1035–1045. doi: 10.1038/s41590-019-0408-z
  11. Stecca B, Rovida E. Impact of ERK5 on the hallmarks of cancer. Int J Mol Sci. 2019;20(6):1426. doi: 10.3390/ijms20061426
  12. Yang L, Shi P, Zhao G, et al. Targeting cancer stem cell pathways for cancer therapy. Signal Transduct Target Ther. 2020;5(8):8. doi: 10.1038/s41392-020-0110-5
  13. Burrell C, Howard C, Murphy F. Fenner and White’s medical virology. 5th edition. San Diego: Academic Press, 2016. 454 p.
  14. Nash A, Dalziel R, Fitzgerald J. Mims’ pathogenesis of infectious disease. 6th edition. San Diego: Academic Press; 2015. 348 p.
  15. Maillard PV, van der Veen AG, Poirier EZ, et al. Slicing and dicing viruses: antiviral RNA interference in mammals. EMBO J. 2019;38(8):e100941. doi: 10.15252/embj.2018100941
  16. Hayward A. Origin of the retroviruses: when, where, and how? Curr Opin Virol. 2017;25:23–27. doi: 10.1016/j.coviro.2017.06.006
  17. Krupovic M, Koonin EV. Multiple origins of viral capsid proteins from cellular ancestors. PNAS USA. 2017;114(12):E2401–E2410. doi: 10.1073/pnas.1621061114
  18. Lee S, Liu H, Wilen CB, et al. A secreted viral nonstructural protein deters intestinal norovirus pathogenesis. Cell Host Microbe. 2019;25(6):179–187. doi: 10.1016/j.chom.2019.04.005845–857
  19. Horie M. The biological significance of bornavirus-derived genes in mammals. Curr Opin Virol. 2017;25:1–6. doi: 10.1016/j.coviro.2017.06.004
  20. Hadjidj R, Badis A, Mechri S, et al. Purification, biochemical, and molecular characterization of novel protease from Bacillus licheniformis strain K7A. Int J Biol Macromol. 2018;114:1033–1048. doi: 10.1016/j.ijbiomac.2018.03.167
  21. Jeong YJ, Baek SC, Kim H. Cloning and characterization of a novel intracellular serine protease (IspK) from Bacillus megaterium with a potential additive for detergents. Int J Biol Macromol. 2018;108:808–816. doi: 10.1016/j.ijbiomac.2017.10.173
  22. Ashraf NM, Krishnagopal A, Hussain A, et al. Engineering of serine protease for improved thermostability and catalytic activity using rational design. Int J Biol Macromol. 2019;126:229–237. doi: 10.1016/j.ijbiomac.2018.12.218
  23. Ashraf NM, Krishnagopal A, Hussain A, et al. Engineering of serine protease for improved thermo stability and catalytic activity using rational design. Int J Biol Macromol. 2019;126:229–237. doi: 10.1016/j.ijbiomac.2018
  24. Ho SYW, Lanfear R, Bromham L, et al. Time-dependent rates of molecular evolution. Mol Ecol. 2011;20(15):3087–3101. doi: 10.1111/j.1365-294X.2011.05178.x
  25. Katzourakis A, Gifford RJ. Endogenous viral elements in animal genomes. PLoS Genet. 2010;11(6):e1001191. doi: 10.1371/journal.pgen.1001191
  26. Aiewsakun P, Katzourakis A. Endogenous viruses: Connecting recent and ancient viral evolution. Virology. 2015;479-480:26–37. doi: 10.1016/j.virol.2015.02.011
  27. Parrish NF, Tomonaga K. Endogenized viral sequences in mammals. Curr Opin Microbiol. 2016;31:176–183. doi: 10.1016/j.mib.2016.03.002
  28. Frank JA, Feschotte C. Co-option of endogenous viral sequences for host cell function. Curr Opin Virol. 2017;25:81–89. doi: 10.1016/j.coviro.2017.07.021
  29. Garcia-Sastre A. Ten strategies of interferon evasion by viruses. Cell Host Microbe. 2017;22(2):176–184. doi: 10.1016/j.chom.2017.07.012
  30. Diner BA, Lum KK, Javitt A, et al. Interactions of the antiviral factor interferon gamma-inducible protein 16. NIFI16 mediate immune signaling and herpes simplex virus-1 immunosuppression. Mol Cell Proteomics. 2015;14(9):2341–2356. doi: 10.1074/mcp.M114.047068
  31. Stoye JP. Studies of endogenous retroviruses reveal a continuing evolutionary saga. Nat Rev Microbiol. 2012;6(10):395–406. doi: 10.1038/nrmicro2783
  32. Hemann EA, Green R, Turnbull JB, et al. Interferon-λ modulates dendritic cells to facilitate T cell immunity ion with influenza A virus. Nat Immunol. 2019;20:1035–1045. doi: 10.1038/s41590-019-0408-z
  33. Enard D, Cai L, Gwennap C, Petrov DA. Viruses are a dominant driver of protein adaptation in mammals. Elife. 2016;5:e12469. doi: 10.7554/eLife.12469
  34. Xu X, Zhang M, Xu F, Jiang S. Wnt signaling in breast cancer: biological mechanisms, challenges and opportunities. Mol Cancer. 2020;19(165):165. doi: 10.1186/s12943-020-01276-5
  35. Wang B, Li X, Liu L, Wang M. β-Catenin: oncogenic role and therapeutic target in cervical cancer. Biol Res. 2020;53:33. doi: 10.1186/s40659-020-00301-7
  36. Ma Z, Damania B. The cGAS-STING defense pathway and its counteraction by viruses. Cell Host Microbe. 2016;19(2):150–158. doi: 10.1016/j.chom.2016.01.010

Supplementary files

Supplementary Files
Action
1. JATS XML
Download
2. Fig. 1. Appearance and transmission of distinct serotypes of influenza A virus in human pandemics in the 20th century (оn J. Flint, V. Racaniello, G. Rall et al. Principles of Virology. Fifth edition. Vol. II. 2020)

Download (392KB)
Indexing metadata
3. Fig. 2. Phylogeny of reverse transcriptases in retroviruses and pararetroviruses: env — envelope genes; gag — group-specific antigen; IN — integrase; LTR — long terminal repeat; MA — matrix protein; MP — motion protein; NC — nucleocapsid; nef tat, rev, vif, vpr, vpu — human immunodeficiency virus type 1 genes that express regulatory proteins via mRNA; P — polymerase; pol — polymerase genes; PR — protease; PreS — pre-surface protein (shell); PX/TA — activator of protein X/transcription; RH — RNase H; RT — reverse transcriptase; SU — surface glycoprotein; TM — transmembrane glycoprotein; TP — RNase H; TT/SR — translational transactivator/suppressor of RNA interference; VAP — virion-associated protein (аdapted from M. Krupovic et al. 2018. J. Virol 92:e00515-18)

Download (694KB)
Indexing metadata
4. Fig. 3. Genetic maps of selected (–) strand RNA viral genomes (on J. Flint, V. Racaniello, G. Rall et al. Principles of Virology. Fifth edition. Vol. II. 2020)

Download (510KB)
Indexing metadata
5. Fig. 4. RNA virus genomes and evolution (оn J. Flint, V. Racaniello, G. Rall et al. Principles of Virology. Fifth edition. Vol. II. 2020)

Download (413KB)
Indexing metadata

Copyright (c) 2023 Eco-Vector

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies