Cellular and Natural Viral Engineering in Cognition-Based Evolution

References

• Zhang YZ, Chen YM, Wang W, et al. Expanding the RNA virosphere by unbiased metagenomics. Annu Rev Virol. 2019;6:119–33.
   PubMed Web of Science ®Google Scholar
• Rohwer F, Thurber RV. Viruses manipulate the marine environment. Nature. 2009;459(7244):207–212.
   PubMed Web of Science ®Google Scholar
• Adachi A. Grand challenge in human/animal virology: unseen, smallest replicative entities shape the whole globe. Front Microbiol. 2020;11:431.
   PubMed Web of Science ®Google Scholar
• Karsenti E, Acinas SG, Bork P, et al. A holistic approach to marine eco-systems biology. PLoS Biol. 2011;9(10):e1001177.
   PubMed Web of Science ®Google Scholar
• Endo H, Blanc-Mathieu R, Li Y, et al. Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions. Nat Ecol Evol. 2020;4(12):1639–1649.
   PubMed Web of Science ®Google Scholar
• Dinsdale EA, Edwards RA, Hall D, et al. Functional metagenomic profiling of nine biomes. Nature. 2008;452(7187):629–632.
   PubMed Web of Science ®Google Scholar
• Baluška F. Cell‐cell channels, viruses, and evolution: via infection, parasitism, and symbiosis toward higher levels of biological complexity. Ann NY Acad Sci. 2009;1178(1):106–119.
   PubMedGoogle Scholar
• Forterre P, Prangishvili D. The great billion‐year war between ribosome‐and capsid‐encoding organisms (cells and viruses) as the major source of evolutionary novelties. Ann NY Acad Sci. 2009;1178(1):65–77.
   PubMedGoogle Scholar
• Koonin EV, Wolf YI. Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Front Cell Infect Microbiol. 2012;2:119.
   PubMed Web of Science ®Google Scholar
• Ryan F. Virolution. London, UK: William Collins; 2009.
   Google Scholar
• Villarreal LP. Viruses and the evolution of life. Wash. D.C: ASM press; 2005.
   Google Scholar
• Villarreal LP, Witzany G. Viruses are essential agents within the roots and stem of the tree of life. J Theor Biol. 2010;262(4):698–710.
   PubMed Web of Science ®Google Scholar
• Moelling K. Viruses more friends than foes. Electroanalysis. 2016;32(4):669–673.
   Google Scholar
• Roossinck MJ. Symbiosis, mutualism and symbiogenesis. In: Plant virus evolution. Berlin, Heidelberg: Springer; 2008. pp. 157–164.
   Google Scholar
• Roossinck MJ, Bazán ER. Symbiosis: viruses as intimate partners. Annu Rev Virol. 2017;4:123–139.
   PubMed Web of Science ®Google Scholar
• Ryan FP. Viral symbiosis and the holobiontic nature of the human genome. APMIS. 2016;124(1–2):11–19.
   PubMed Web of Science ®Google Scholar
• Villarreal LP. Virus-host symbiosis mediated by persistence. Symbiosis. 2007;44(1/3):1–9.
   Web of Science ®Google Scholar
• Baluška F, Miller WB, Reber AS. Biomolecular basis of cellular consciousness via subcellular nanobrains. Int J Mol Sci. 2021;22(5):2545.
   PubMed Web of Science ®Google Scholar
• Lyon P. The cognitive cell: bacterial behavior reconsidered. Front Microbiol. 2015;6:264.
   PubMedGoogle Scholar
• Miller WB. Cognition, information fields and hologenomic entanglement: evolution in light and shadow. Biology (Basel). 2016;5(2):21.
   PubMedGoogle Scholar
• Reber AS, Baluška F. Cognition in some surprising places. Biochem Biophys L Res Commun. 2021;564:150–157.
   PubMed Web of Science ®Google Scholar
• Reber AS. The first minds: caterpillars, karyotes, and consciousness. New York: Oxford University Press; 2019.
   Google Scholar
• Shapiro JA. Evolution: a view from the 21st century. London: Pearson education; 2011.
   Google Scholar
• Shapiro JA. All living cells are cognitive. Biochem Biophys Res Commun. 2021;564:134–149.
   PubMed Web of Science ®Google Scholar
• Timsit Y, Grégoire SP. Towards the idea of molecular brains. Int J Mol Sci. 2021;22(21):11868.
   PubMed Web of Science ®Google Scholar
• Timsit Y, Sergeant-Perthuis G, Bennequin D. Evolution of ribosomal protein network architectures. Sci Rep. 2021;111:625. 12.
   PubMed Web of Science ®Google Scholar
• Annila A, Baverstock K. Genes without prominence: a reappraisal of the foundations of biology. J Royal Soc Int. 2014;11(94):20131017.
   PubMed Web of Science ®Google Scholar
• Ford BJ. Cellular intelligence: microphenomenology and the realities of being. Progr Biophys Mol Biol. 2017;131:273–287.
   PubMed Web of Science ®Google Scholar
• Ford B. Are cells ingenious? Microscope-Chicago. 2004;52(3–4):135–144.
   Google Scholar
• Marijuán PC, Del Moral R, Navarro J. On eukaryotic intelligence: signaling system’s guidance in the evolution of multicellular organization. Biosystems. 2013;114(1):8–24.
   PubMed Web of Science ®Google Scholar
• Marijuán PC, Navarro J, Del Moral R. On prokaryotic intelligence: strategies for sensing the environment. Biosystems. 2010;99(2):94–103.
   PubMed Web of Science ®Google Scholar
• Marijuán PC, Navarro J, Del Moral R. How the living is in the world: an inquiry into the informational choreographies of life. Prog Biophys Mol Biol. 2015;119(3):469–480.
   PubMed Web of Science ®Google Scholar
• Marshall P. Biology transcends the limits of computation. Progr Biophys Mol Biol. 2021.
   PubMed Web of Science ®Google Scholar
• Miller WB Jr, Baluška F, Torday JS. Cellular senomic measurements in cognition-based evolution. Progr Biophys Mol Biol. 2020;156:20–33.
   PubMed Web of Science ®Google Scholar
• Miller WB Jr. Biological information systems: evolution as cognition-based information management. Progr Biophys Mol Biol. 2018;134:1–26.
   PubMed Web of Science ®Google Scholar
• Tang S, K Y, Marshall WF. Cell learning. Curr Biol. 2018;28(20):R1180–1184.
   PubMed Web of Science ®Google Scholar
• Miller WB Jr, Torday JS, Baluška F. The N-space Episenome unifies cellular information space-time within cognition-based evolution. Progr Biophys Mol Biol. 2020;150:112–139.
   PubMed Web of Science ®Google Scholar
• Monroe JG, Srikant T, Carbonell-Bejerano P, et al. Mutation bias reflects natural selection in Arabidopsis thaliana. Nature. 2022;602(7895):101–105.
   PubMed Web of Science ®Google Scholar
• Miller WB, Enguita FJ, Leitão AL. Non-random genome editing and natural cellular engineering in cognition-based evolution. Cells. 2021;10(5):1125.
   PubMed Web of Science ®Google Scholar
• Miller WB Jr, Torday JS, Baluška F. Biological evolution as defense of’self’. Progr Biophys Mol Biol. 2019;142:54–74.
   PubMed Web of Science ®Google Scholar
• Forterre P. The origin, nature and definition of viruses (and life): new concepts and controversies. Old Herborn University, Sem Monogr. 2017;31:15–26.
   Google Scholar
• Raoult D, Forterre P. Redefining viruses: lessons from Mimivirus. Nat Rev Microbiol. 2008;6(4):315–319.
   PubMed Web of Science ®Google Scholar
• Baluška F, Miller WB Jr. Senomic view of the cell: senome versus genome. Commun Integr Biol. 2018;11(3):1–9.
   PubMedGoogle Scholar
• Krupovic M, Dolja VV, Koonin EV. Origin of viruses: primordial replicators recruiting capsids from hosts. Nat Rev Microbiol. 2019;17:449–458.
   PubMed Web of Science ®Google Scholar
• Krupovic M, Koonin EV. Multiple origins of viral capsid proteins from cellular ancestors. Proc Natl Acad Sci. 2017;114(12):E2401–2410.
   PubMed Web of Science ®Google Scholar
• Raoult D, Audic S, Robert C, et al. The 1.2-megabase genome sequence of mimivirus. Science. 2004;306:1344–1350.
   PubMed Web of Science ®Google Scholar
• Xian Y, Xiao C. Current capsid assembly models of icosahedral nucleocytoviricota viruses. Adv Virus Res. 2020;108:275.
   PubMed Web of Science ®Google Scholar
• Xiao C, Chipman PR, Battisti AJ, et al. Cryo-electron microscopy of the giant mimivirus. J Mol Biol. 2005;353(3):493–496.
   PubMed Web of Science ®Google Scholar
• Xiao Y, Rouzine IM, Bianco S, et al. RNA recombination enhances adaptability and is required for virus spread and virulence. Cell Host & Microbe. 2016;19(4):493–503.
   PubMed Web of Science ®Google Scholar
• Plemper RK. Cell entry of enveloped viruses. Curr Opin Virol. 2011;1(2):92–100.
   PubMed Web of Science ®Google Scholar
• Rey FA, Lok S-M. Common features of enveloped viruses and implications for immunogen design for next-generation vaccines. Cell. 2018;172:1319–1334.
   PubMed Web of Science ®Google Scholar
• Forterre P. To be or not to be alive: how recent discoveries challenge the traditional definitions of viruses and life. Stud Hist Phil Sci Part C Stud Biol Biomed Sci. 2016;59:100–108.
   PubMedGoogle Scholar
• Bândea CI. A new theory on the origin and the nature of viruses. J Theor Biol. 1983;105(4):591–602.
   PubMed Web of Science ®Google Scholar
• Forterre P. Defining life: the virus viewpoint origins of life and evolution of biospheres. 2010;40(2):151–160.
   Google Scholar
• Forterre P 2001. Virocell concept. eLS. https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470015902.a0023264
   Google Scholar
• Nasir A, Romero-Severson E, Claverie JM. Investigating the concept and origin of viruses. Trends Microbiol. 2020;28(12):959–967.
   PubMed Web of Science ®Google Scholar
• Schoelz JE, Leisner S. Setting up shop: the formation and function of the viral factories of cauliflower mosaic virus. Front Plant Sci. 2017;8:1832.
   PubMed Web of Science ®Google Scholar
• Mohsen MO, Gomes AC, Vogel M, et al. Interaction of viral capsid-derived virus-like particles (VLPs) with the innate immune system. Vaccines. 2018;6(3):37.
   Web of Science ®Google Scholar
• Le DT, Müller KM. In Vitro assembly of virus-like particles and their applications. Life. 2021;11(4):334.
   PubMedGoogle Scholar
• Raab-Traub N, Dittmer DP. Viral effects on the content and function of extracellular vesicles. Nat Rev Microbiol. 2017;15:559–572.
   PubMed Web of Science ®Google Scholar
• Howard-Varona C, Lindback MM, Bastien GE, et al. Phage-specific metabolic reprogramming of virocells. Isme J. 2020;14(4):881–895.
   PubMed Web of Science ®Google Scholar
• Mizuno CM, Guyomar C, Roux S, et al. Numerous cultivated and uncultivated viruses encode ribosomal proteins. Nat Commun. 2019;10(1):752.
   PubMedGoogle Scholar
• Da Cunha V, Gaia M, Ogata H, et al. Giant viruses encode actin-related proteins. Mol Biol Evol. 2022;39(2):msac022.
   PubMed Web of Science ®Google Scholar
• Rumbou A, Vainio EJ, Büttner C. Towards the forest virome: high-throughput sequencing drastically expands our understanding on virosphere in temperate forest ecosystems. Microorganisms. 2021;9(8):1730.
   PubMed Web of Science ®Google Scholar
• Moreira D, López-García P. Ten Reasons to exclude viruses from the tree of life. Nat Rev Microbiol. 2009;7(4):309.
   Web of Science ®Google Scholar
• Pavesi A. Origin and evolution of overlapping genes in the family Microviridae. J Gen Virol. 2006;87(4):1013–1017.
   PubMedGoogle Scholar
• Sabath N, Wagner A, Karlin D. Evolution of viral proteins originated de novo by overprinting. Mol Biol Evol. 2012;29(12):3767–3780.
   PubMed Web of Science ®Google Scholar
• Koonin EV, Dolja VV. Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiol Mol Biol Rev. 2014;78(2):278–303.
   PubMed Web of Science ®Google Scholar
• Witzany G. Evolution of genetic information without error replication. In: Burgin M, and Dodig-Crnković G, editors. Theoretical information studies: information in the world. Singapore: World Scientific; 2020. pp. 295–320.
   Google Scholar
• Mustafin RN. Hypothesis on the origin of viruses from transposons. Mol Genet Microbiol Virol. 2018;33(4):223–232.
   Web of Science ®Google Scholar
• Cornelis G, Vernochet C, Carradec Q, et al. Retroviral envelope gene captures and syncytin exaptation for placentation in marsupials. Proc Natl Acad Sci. 2015;112(5):E487–496.
   PubMed Web of Science ®Google Scholar
• Koonin EV, Krupovic M. The depths of virus exaptation. Curr Opin Virol. 2018;31:1–8.
   PubMed Web of Science ®Google Scholar
• Delavat F, Miyazaki R, Carraro N, et al. The hidden life of integrative and conjugative elements. FEMS Microbiol Rev. 2017;41(4):2.
   Web of Science ®Google Scholar
• Ocaña-Pallarès E, Najle SR, Scazzocchio C, et al. Reticulate evolution in eukaryotes: origin and evolution of the nitrate assimilation pathway. PLoS Genet. 2019;15(2):e1007986.
   PubMed Web of Science ®Google Scholar
• Johnson CM, Grossman AD. Integrative and conjugative elements (ICEs): what they do and how they work. Ann Rev Genet. 2015;49:577–601.
   PubMed Web of Science ®Google Scholar
• Wagner A, Whitaker RJ, Krause DJ, et al. Mechanisms of gene flow in archaea. Nat Rev Microbiol. 2017;15(8):492–501.
   PubMed Web of Science ®Google Scholar
• Demory D, Liu R, Chen Y, et al. Linking light-dependent life history traits with population dynamics for Prochlorococcus and cyanophage. mSystems. 2020; 5(2):e00586–19.
   PubMed Web of Science ®Google Scholar
• Shih HY, Goldenfeld N. Mechanisms of rapid evolution. Roadmap on biology in time varying environments. Phys Biol. 2021;18(04):041502.
   Google Scholar
• Wallau GL, Vieira C, Loreto ÉLS. Genetic exchange in eukaryotes through horizontal transfer: connected by the mobilome. Mob DNA. 2018;9(1):6.
   PubMedGoogle Scholar
• Liu H, Fu Y, Jiang D, et al. Widespread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes. J Virol. 2010;84(22):11876–11887.
   PubMed Web of Science ®Google Scholar
• Kaján GL, Doszpoly A, Tarján ZL, et al. Virus–host coevolution with a focus on animal and human DNA viruses.J. Mol Evol. 2020;88(1):41–56.
   PubMed Web of Science ®Google Scholar
• Pina M, Bize A, Forterre P, et al. The archeoviruses.Fems Microbiol. Rev. 2011;35(6):1035–1054.
   Google Scholar
• Dávila-Ramos S, Castelán-Sánchez HG, Martínez-Ávila L, et al. A review on viral metagenomics in extreme environments. Front Microbiol. 2019;10:2403.
   PubMed Web of Science ®Google Scholar
• Liu Y, Brandt D, Ishino S, et al. New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures. Env Microbiol. 2019;21(6):2002–2014.
   PubMed Web of Science ®Google Scholar
• Denner J. Function of a retroviral envelope protein in the placenta of a viviparous lizard. Proc Natl Acad Sci. 2017;114(51):13315–13317.
   PubMed Web of Science ®Google Scholar
• Fan X, Qiu H, Han W, et al. Phytoplankton pangenome reveals extensive prokaryotic horizontal gene transfer of diverse functions. Sci Adv. 2020;6(18):eaba0111.
   PubMed Web of Science ®Google Scholar
• Broecker F, Moelling K. What viruses tell us about evolution and immunity: beyond Darwin? Ann NY Acad Sci. 2019;1447(1):530.
   Web of Science ®Google Scholar
• Lima-Junior DS, Krishnamurthy SR, Bouladoux N, et al. Endogenous retroviruses promote homeostatic and inflammatory responses to the microbiota. Cell. 2021;184:3794–3811.
   PubMed Web of Science ®Google Scholar
• Sun C, Feschotte C, Wu Z, et al. DNA transposons have colonized the genome of the giant virus Pandoravirus salinus. BMC Biol. 2015;13(1):38.
   PubMedGoogle Scholar
• Zhang HH, Zhou QZ, Wang PL, et al. Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes. Mob DNA. 2018;9(1):1–12.
   PubMedGoogle Scholar
• Shapiro JA. Living organisms author their read-write genomes in evolution. Biology (Basel). 2017;6(4):42.
   PubMedGoogle Scholar
• Shapiro JA. No genome is an island: toward a 21st century agenda for evolution. Ann NY Acad Sci. 2019;1447(1):21–52.
   PubMed Web of Science ®Google Scholar
• Gilbert C, Peccoud J, Chateigner A, et al. Continuous influx of genetic material from host to virus populations. PLoS Genet. 2016;12(2).
   Web of Science ®Google Scholar
• Renner DW, Szpara ML. Impacts of genome-wide analyses on our understanding of human herpesvirus diversity and evolution. J Virol. 2018;92(1):e00908–17.
   PubMed Web of Science ®Google Scholar
• Moniruzzaman M, Martinez-Gutierrez CA, Weinheimer AR, et al. Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses. Nat Commun. 2020;11(1):1–11.
   PubMed Web of Science ®Google Scholar
• Bell SM, Bedford T, Silvestri G. Modern-day SIV viral diversity generated by extensive recombination and cross-species transmission. PLOS Pathog. 2017;13(7):e1006466.
   PubMed Web of Science ®Google Scholar
• Walzer KA, Chi JT. Trans-kingdom small RNA transfer during host-pathogen interactions: the case of P. falciparum and erythrocytes. RNA Biol. 2017;14(4):442–449.
   PubMed Web of Science ®Google Scholar
• Zhao JH, Guo HS. Trans-kingdom RNA interactions drive the evolutionary arms race between hosts and pathogens. Curr Opin Genet Dev. 2019;58:62–69.
   PubMed Web of Science ®Google Scholar
• Leitão AL, Costa MC, Gabriel AF, et al. Interspecies communication in holobionts by non-coding RNA exchange. Int J Mol Sci. 2020;21(7):2333.
   PubMed Web of Science ®Google Scholar
• Zhou K, Liu M, Cao Y. New insight into microRNA functions in cancer: oncogene–microRNA–tumor suppressor gene network. Front Mol Biosci. 2017;4:46.
   PubMed Web of Science ®Google Scholar
• Williams MR, Stedtfeld RD, Tiedje JM, et al. MicroRNAs-based inter-domain communication between the host and members of the gut microbiome. Front Microbiol. 2017;8:1896.
   PubMed Web of Science ®Google Scholar
• Teodori L, Petrignani I, Giuliani A, et al. Inflamm-aging microRnas may integrate signals from food and gut microbiota by modulating common signalling pathways. Mech Ageing Dev. 2019;182:111127.
   PubMed Web of Science ®Google Scholar
• Tsatsaronis JA, Franch-Arroyo S, Resch U, et al. Extracellular vesicle RNA: a universal mediator of microbial communication? Trends Microbiol. 2018;26(5):401–410.
   PubMed Web of Science ®Google Scholar
• Filée J. Genomic comparison of closely related giant viruses supports an accordion-like model of evolution. Front Microbiol. 2015;6:593.
   PubMed Web of Science ®Google Scholar
• Mustafin RN. Functional dualism of transposon transcripts in evolution of eukaryotic genomes. Russ J Dev Biol. 2018;49(6):339–355.
   Web of Science ®Google Scholar
• Koonin EV, Dolja VV, Krupovic M. Origins and evolution of viruses of eukaryotes: the ultimate modularity. Virology. 2015;479:2–25.
   PubMed Web of Science ®Google Scholar
• Bourque G, Burns KH, Gehring M, et al. Ten Things you should know about transposable elements. Genome Biol. 2018;19(1):1–12.
   PubMedGoogle Scholar
• Lucía-Sanz A, Manrubia S. Multipartite viruses: adaptive trick or evolutionary treat? NPJ Syst Biol Appl. 2017;3(1):1–11.
   PubMedGoogle Scholar
• Boyer M, Yutin N, Pagnier I, et al. Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms. Proc Natl Acad Sci U S A. 2009;106(51):21848–21853.
   PubMed Web of Science ®Google Scholar
• Moliner C, Fournier PE, Raoult D. Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution. FEMS Microbiol Rev. 2010;34(3):281–294.
   PubMed Web of Science ®Google Scholar
• Jeong H, Arif B, Caetano-Anollés G, et al. Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation. Sci Rep. 2019;9(1):1–18.
   PubMedGoogle Scholar
• Boto L, Pineda M, Pineda R. Potential impacts of horizontal gene transfer on human health and physiology and how anthropogenic activity can affect it. FEBS J. 2019;286(20):3959–3967.
   PubMed Web of Science ®Google Scholar
• Malik SS, Azem-E-Zahra S, Kim KM, et al. Do viruses exchange genes across superkingdoms of life? Front Microbiol. 2017;8:2110.
   PubMed Web of Science ®Google Scholar
• Botstein D. A modular theory of virus evolution. In Animal virus genetics. Academic Press; 1980. pp. 11–20.
   Google Scholar
• Spirov AV, Eremeev AV. Modularity in biological evolution and evolutionary computation. Biol Bull Rev. 2020;10(4):308–323.
   Google Scholar
• Espinosa-Soto C. On the role of sparseness in the evolution of modularity in gene regulatory networks. PLoS Comp Biol. 2018;14(5):e1006172.
   PubMed Web of Science ®Google Scholar
• Lorenz DM, Jeng A, Deem MW. The emergence of modularity in biological systems. Physics Life Rev. 2011;8(2):129–160.
   PubMed Web of Science ®Google Scholar
• Schlosser G, Wagner GP, editors. Modularity in development and evolution. Chicago: University of Chicago Press; 2004.
   Google Scholar
• Melo D, Porto A, Cheverud JM, et al. Modularity: genes, development, and evolution. Ann Rev Ecol Evol Syst. 2016;47:463–486.
   PubMed Web of Science ®Google Scholar
• Van Gestel J, Ackermann M, Wagner A. Microbial life cycles link global modularity in regulation to mosaic evolution. Nat Ecol Evol. 2019;3(8):1184–1196.
   PubMed Web of Science ®Google Scholar
• Wolf YI, Kazlauskas D, Iranzo J, et al. Origins and evolution of the global RNA virome. MBio. 2018; 9(6):e02329–18. DOI:10.1128/mBio.02329.
   PubMed Web of Science ®Google Scholar
• Gonzalez G, Koyanagi KO, Aoki K, et al. Intertypic modular exchanges of genomic segments by homologous recombination at universally conserved segments in human adenovirus species D. Gene. 2014;547(1):10–17.
   PubMed Web of Science ®Google Scholar
• Gottschling M, Bravo IG, Schulz E, et al. Modular organizations of novel cetacean papillomaviruses. Mol Phylogen Evol. 2011;59(1):34–42.
   PubMed Web of Science ®Google Scholar
• Fraser HB, Modularity and evolutionary constraint on proteins. Nature genet. 2005;37(4):351–352.
   PubMed Web of Science ®Google Scholar
• Constantino PH, Daoutidis P. A control perspective on the evolution of biological modularity. IFAC-Papersonline. 2019;52(11):172–177.
   Google Scholar
• Ding B, Qin Y, Chen M. Nucleocapsid proteins: roles beyond viral RNA packaging. Wiley Int Rev RNA. 2016;7(2):213–226.
   Google Scholar
• Aboagye JO, Yew CW, Ng OW, et al. Overexpression of the nucleocapsid protein of middle east respiratory syndrome coronavirus up-regulates CXCL10. Biosci Rep. 2018;38(5).
   PubMedGoogle Scholar
• Yamauchi Y, Greber UF. Principles of virus uncoating: cues and the snooker ball. Traffic. 2016;17(6):569–592.
   PubMed Web of Science ®Google Scholar
• Miller WB, Torday JS. A systematic approach to cancer: evolution beyond selection. Clin Transl Med. 2017;6(1):1–20.
   PubMedGoogle Scholar
• Torday JS, Miller WB Jr. The resolution of ambiguity as the basis for life: a cellular bridge between Western reductionism and Eastern holism. Progr Biophys Mol Biol. 2017;131:288–297.
   PubMed Web of Science ®Google Scholar
• Iredell J, Brown J, Tagg K. Antibiotic resistance in Enterobacteriaceae: mechanisms and clinical implications. BMJ. 2016;352.
   PubMedGoogle Scholar
• Lécuyer F, Bourassa JS, Gélinas M, et al. Biofilm formation drives transfer of the conjugative element ICEBs1 in Bacillus subtilis. mSphere. 2018; 3(5):e00473–18.
   PubMed Web of Science ®Google Scholar
• Van Gestel J, Vlamakis H, Kolter R. From cell differentiation to cell collectives: bacillus subtilis uses division of labor to migrate. PLoS Biol. 2015;13(4):e1002141.
   PubMed Web of Science ®Google Scholar
• Ben-Jacob E, Levine H. Self-engineering capabilities of bacteria. J Royal Soc Interface. 2006;3(6):197–214.
   PubMed Web of Science ®Google Scholar
• Abedon ST. Phage-phage, phage-bacteria, and phage-environment communication. In Biocommunication of Phages, and Witzany G. Phage-phage, phage-bacteria, and phage-environment communication. In:Ed. Biocommunication of Phages. Cham: Springer; 2020pp. 23–70.
   Google Scholar
• Díaz-Muñoz SL, Sanjuán R, West S. Sociovirology: conflict, cooperation, and communication among viruses. Cell Host & Microbe. 2017;22(4):437–441.
   PubMed Web of Science ®Google Scholar
• Witzany G. What does communication of phages mean? In: Witzany, G, editor. Biocommunication of Phages. Cham: Springer; 2020. p. 1–22.
   Google Scholar
• Ofir G, Sorek R. Contemporary phage biology: from classic models to new insights. Cell. 2018;172(6):1260–1270.
   PubMed Web of Science ®Google Scholar
• Erez Z, Steinberger-Levy I, Shamir M, et al. Communication between viruses guides lysis–lysogeny decisions. Nature. 2017;541(7638):488–493.
   PubMed Web of Science ®Google Scholar
• Torday JS, Miller WB. Cellular-molecular mechanisms in epigenetic evolutionary biology. Cham: Springer; 2020.
   Google Scholar
• Timsit Y, Bennequin D. Nervous-like circuits in the ribosome facts, hypotheses and perspectives. Int J Mol Sci. 2019;20(12):2911.
   PubMed Web of Science ®Google Scholar
• Poirot O, Timsit Y. Neuron-like networks between ribosomal proteins within the ribosome. Sci Rep. 2016;6:26485.
   PubMed Web of Science ®Google Scholar
• Kalra A, Sharma S. Virosomes: a viral envelope system having a promising application in vaccination and drug delivery system. Nanopharm Adv Del Syst. 2021;145–160.
   Google Scholar
• Dedrick RM, Jacobs-Sera D, Bustamante CAG, et al. Prophage-mediated defence against viral attack and viral counter-defence. Nat Microbiol. 2017;2(3):1–13.
   Web of Science ®Google Scholar
• Sanjuán R. Collective properties of viral infectivity. Curr Opin Virol. 2018;33:1–6.
   PubMed Web of Science ®Google Scholar
• Thoulouze MI, Alcover A. Can viruses form biofilms? Trends Microbiol. 2011;19(6):257–262.
   PubMed Web of Science ®Google Scholar
• Domingo-Calap P, Segredo-Otero E, Durán-Moreno M, et al. Social evolution of innate immunity evasion in a virus. Nat Microbiol. 2019;4(6):1006–1013.
   PubMed Web of Science ®Google Scholar
• Lieff J. The secret language of cells. Dallas, TX: Ben Bella Books; 2020.
   Google Scholar
• Dolgin E. The secret social lives of viruses. Nature. 2019;570(7761):290–292.
   PubMed Web of Science ®Google Scholar
• Domingo-Calap P, Mora-Quilis L, Sanjuán R. Social Bacteriophages. Microorganisms. 2020;8(4):533.
   PubMed Web of Science ®Google Scholar
• Sicard A, Pirolles E, Gallet R, et al. A multicellular way of life for a multipartite virus. Elife. 2019;8:e43599.
   PubMed Web of Science ®Google Scholar
• Domingo E, Perales C. Quasispecies and virus. Eur Biophys J. 2018;47(4):443–457.
   PubMed Web of Science ®Google Scholar
• Moelling K, Broecker F, Russo G, et al. RNase H as gene modifier, driver of evolution and antiviral defense. Front Microbiol. 2017;8:1745.
   PubMed Web of Science ®Google Scholar
• Folimonova SY. Superinfection exclusion is an active virus-controlled function that requires a specific viral protein. J Virol. 2012;86(10):5554–5561.
   PubMed Web of Science ®Google Scholar
• Ellenberg P, Linero FN, Scolaro LA. Superinfection exclusion in BHK-21 cells persistently infected with Junin virus. J Gen Virol. 2007;88(10):2730–2739.
   PubMedGoogle Scholar
• Kumar N, Sharma S, Barua S, et al. Virological and immunological outcomes of coinfections. Clin Microbiol Rev. 2018;31(4):e00111–17.
   PubMed Web of Science ®Google Scholar
• Tolmachov OE. Swarm intelligence in cell entry exclusion phenomena in viruses and plasmids: how to exploit intelligent gene vector self-scattering in therapeutic gene delivery. In: Shapshak, P, Balaji, S, Kangueane, P, Chiappelli, F, Somboonwit, C, Menezes, LJ, Sinnott, JT, editors. Global virology III: virology in the 21st century. Cham: Springer; 2019. p. 325–343.
   Google Scholar
• Reid CR, Latty T. Collective behaviour and swarm intelligence in slime moulds. FEMS Microbiol Rev. 2016;40(6):798–806.
   PubMed Web of Science ®Google Scholar
• Mirahmadizadeh A, Yaghobi R, Soleimanian S. Viral ecosystem: an epidemiological hypothesis. Rev Med Virol. 2019;29(4):e2053.
   PubMed Web of Science ®Google Scholar
• Witzany G. From molecular entities to competent agents: viral infection-derived consortia act as natural genetic engineers. In: Witzany, G editor. Viruses: essential agents of life. Dordrecht: Springer; 2012. p. 407–419.
   Google Scholar
• Baebler Š, Coll A, Gruden K. Plant molecular responses to potato virus Y: a continuum of outcomes from sensitivity and tolerance to resistance. Viruses. 2020;12(2):217.
   PubMed Web of Science ®Google Scholar
• Moreno AB, López-Moya JJ. When viruses play team sports: mixed infections in plants. Phytopathology. 2020;110(1):29–48.
   PubMed Web of Science ®Google Scholar
• Das S, Alam MM, Zhang R, et al. Proof-of-concept for the yadokari nature: a capsidless replicase-encoding but replication-dependent (+) ssRNA virus hosted by an unrelated dsRNA virus. J Virol. 2021. JVI–00467.
   Web of Science ®Google Scholar
• Ryan F. Virusphere: from common colds to Ebola epidemics–why we need the viruses that plague us. HarperCollins: UK; 2019.
   Google Scholar
• Villarreal LP, Witzany G. Social networking of quasi-species consortia drive virolution via persistence. AIMS Microbiol. 2021;7(2):138–162.
   PubMed Web of Science ®Google Scholar
• Breitbart M, Bonnain C, Malki K, et al. Phage puppet masters of the marine microbial realm. Nat Microbiol. 2018;3(7):754–766.
   PubMed Web of Science ®Google Scholar
• Agbandje-McKenna M, Kleinschmidt J. AAV capsid structure and cell interactions. In: Snyder R, and Moullier P, editors. Adeno-associated virus. methods in molecular biology (methods and protocols)Vol. 807. Humana Press; 2012.
   Google Scholar
• Leeks A, Sanjuán R, West SA. The evolution of collective infectious units in viruses. Virus Res. 2019;265:94–101.
   PubMed Web of Science ®Google Scholar
• Altan-Bonnet N, Perales C, Domingo E. Extracellular vesicles: vehicles of en bloc viral transmission. Virus Res. 2019;265:143–149.
   PubMed Web of Science ®Google Scholar
• Iranzo J, Krupovic M, Koonin EV. The double-stranded DNA virosphere as a modular hierarchical network of gene sharing. MBio. 2016; 7(4):e00978–16.
   PubMed Web of Science ®Google Scholar
• Liu K, Hu J. Secretion of empty or complete hepatitis B virions: envelopment of empty capsids versus mature nucleocapsids. Fut Virol. 2019;14(2):95–105.
   Web of Science ®Google Scholar
• Alvisi G, Palù G. Reprogramming the host: modification of cell functions upon viral infection. World J Virol. 2013;2(2):16.
   PubMedGoogle Scholar
• Noble D. Exosomes, gemmules, pangenesis and Darwin. In: Exosomes, and Edelstein L. Exosomes, gemmules, pangenesis and Darwin. In: Smythies J, Quesenberry P, and Noble D, Exosomes. Cambridge, MA: Academic Press; 2020pp. 487–501.
   Google Scholar
• Nolte E, Cremer T, Gallo RC, et al. Extracellular vesicles and viruses: are they close relatives? Proc Natl Acad Sci. 2016;113(33):9155–9161.
   PubMed Web of Science ®Google Scholar
• Margolis L, Sadovsky Y. The biology of extracellular vesicles: the known unknowns. PLoS Biol. 2019;17(7):e3000363.
   PubMed Web of Science ®Google Scholar
• Caobi A, Nair M, Raymond AD. Extracellular vesicles in the pathogenesis of viral infections in humans. Viruses. 2020;12(10):1200.
   PubMed Web of Science ®Google Scholar
• de Toledo Martins S, Alves LR. Extracellular vesicles in viral infections: two sides of the same coin? Front Cell Infect Microbiol. 2020;10:737.
   Web of Science ®Google Scholar
• Giannessi F, Aiello A, Franchi F, et al. The role of extracellular vesicles as allies of HIV, HCV and SARS viruses. Viruses. 2020;12(5):571.
   PubMed Web of Science ®Google Scholar
• Streck NT, Zhao Y, Sundstrom JM, et al. Human cytomegalovirus utilizes extracellular vesicles to enhance virus spread. J Virol. 2020;94(16):e00609–20.
   PubMed Web of Science ®Google Scholar
• Valadi H, Ekström K, Bossios A, et al. Exosome-mediated transfer of mRnas and microRnas is a novel mechanism of genetic exchange between cells. Nat Cell Biol. 2007;9(6):654–659.
   PubMed Web of Science ®Google Scholar
• York SB, Sun L, Cone AS, et al. Zika virus hijacks extracellular vesicle tetraspanin pathways for cell-to-cell transmission. mSphere. 2021;6:3.
   Web of Science ®Google Scholar
• Alqatawni A, Sharma AL, Attilus B, et al. Shedding light on the role of extracellular vesicles in HIV infection and wound healing. Viruses. 2020;12(6):584.
   PubMed Web of Science ®Google Scholar
• Baluška F, Reber AS. CBC-Clock theory of life – integration of cellular circadian clocks and cellular sentience is essential for cognitive basis of life. BioEssays. 2021;43(10):e2100121.
   PubMed Web of Science ®Google Scholar
• Lizarraga-Valderrama LR, Sheridan GK. Extracellular vesicles and intercellular communication in the central nervous system. FEBS Lett. 2021;595:1391–1410.
   PubMed Web of Science ®Google Scholar
• Luo X, Jean-Toussaint R, Sacan A, et al. Differential RNA packaging into small extracellular vesicles by neurons and astrocytes. Cell Commun Signal. 2021;19(1):1–15.
   PubMed Web of Science ®Google Scholar
• Mahjoum S, Rufino-Ramos D, Pereira de Almeida L, et al. Living proof of activity of extracellular vesicles in the central nervous system. Int J Mol Sci. 2021;22(14):7294.
   PubMed Web of Science ®Google Scholar
• Minakawa T, Matoba T, Ishidate F, et al. Extracellular vesicles synchronize cellular phenotypes of differentiating cells. J Extracell Vesicles. 2021;10:e12147.
   PubMed Web of Science ®Google Scholar
• Pinello JF, Lai AL, Millet JK, et al. Structure-function studies link class II viral fusogens with the ancestral gamete fusion protein HAP2. Curr Biol. 2017;27(5):651–660.
   PubMed Web of Science ®Google Scholar
• Shepherd JD. Arc - an endogenous neuronal retrovirus? Sem Cell Dev Biol. 2018;77:73–78.
   PubMed Web of Science ®Google Scholar
• Tao SC, Guo SC. Extracellular vesicles: potential participants in circadian rhythm synchronization. Int J Biolog Sci. 2018;14(12):1610.
   PubMed Web of Science ®Google Scholar
• Valansi C, Moi D, Leikina E, Matveev E, Graña M, Chernomordik LV … Podbilewicz B. Arabidopsis HAP2/GCS1 is a gamete fusion protein homologous to somatic and viral fusogens. J cell Biol. 2017;216(3):571–581.
   PubMed Web of Science ®Google Scholar
• Schnatz A, Müller C, Brahmer A, et al. Extracellular Vesicles in neural cell interaction and CNS homeostasis. FASE Bioadv. 3(8):577–592.
   PubMedGoogle Scholar
• Olanrewaju AA, Hakami RM. The messenger apps of the cell: extracellular vesicles as regulatory messengers of microglial function in the CNS. J Neuroimmune Pharmacol. 2020;1–14.
   Web of Science ®Google Scholar
• Roux S, Krupovic M, Daly RA, et al. Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes. Nat Microbiol. 2019;4(11):1895–1906.
   PubMed Web of Science ®Google Scholar
• White RA III, Visscher PT, Burns BP. Between a rock and a soft place: the role of viruses in lithification of modern microbial mats. Trends Microbiol. 2021;29(3):204–213.
   PubMed Web of Science ®Google Scholar
• Słowakiewicz M, Borkowski A, Syczewski MD, et al. Newly-discovered interactions between bacteriophages and the process of calcium carbonate precipitation. Geochim t Cosmochim Acta. 2021;292:482–498.
   Web of Science ®Google Scholar
• Shapiro JA. Natural genetic engineering of the bacterial genome. Curr Opin Genet Dev. 1993;3(6):845–848.
   PubMed Web of Science ®Google Scholar
• Shapiro JA. Natural genetic engineering in evolution. 1993; 325–347.
   Google Scholar
• Miller WB Jr, Torday JS. Four domains: the fundamental unicell and post-Darwinian cognition-based evolution. Progr Biophys Mol Biol. 2018;140:49–73.
   PubMed Web of Science ®Google Scholar
• Shapiro JA. Genome system architecture and natural genetic engineering in evolution. Ann NY Acad Sci. 1999;870(1):23–35.
   PubMedGoogle Scholar
• Shapiro JA. A 21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering. Gene. 2005;345(1):91–100.
   PubMed Web of Science ®Google Scholar
• Shapiro JA. Bacteria are small but not stupid: cognition, natural genetic engineering and socio-bacteriology. Stud Hist Phil Sci Part C Stud Biol Biomed Sci. 2007;38(4):807–819.
   PubMedGoogle Scholar
• Weising K, Kahl G. Natural genetic engineering of plant cells: the molecular biology of crown gall and hairy root disease. World J Microbiol Biotechnol. 1996;12(4):327–351.
   PubMed Web of Science ®Google Scholar
• Witzany G, editor. Natural genetic engineering and natural genome editing. Hoboken, NJ, USA: Wiley-Blackwell; 2009.
   Google Scholar
• Baluška F, Reber AS, Miller WB Jr. Cellular sentience as the primary source of biological order and evolution. Biosystems. 2022;218:104694.
   PubMed Web of Science ®Google Scholar
• Hein A, Carrara M, Brumley F, et al. Natural search algorithms as a bridge between organisms, evolution, and ecology. Proc Natl Acad Sci U S A. 2016;113(34):9413–9420.
   PubMed Web of Science ®Google Scholar
• Witzany G, Baluška F. Can subcellular organization be explained only by physical principles? Commun Integr Biol. 2015;8(4):e1009796.
   PubMedGoogle Scholar
• Couzigou JM, Mondy S, Sahl L, et al. To be or noot to be: evolutionary tinkering for symbiotic organ identity. Plant Signal Behav. 2013; 8(8):4498–51.
   Google Scholar
• Jacob F. Evolution and tinkering. Science. 1977;196(4295):1161–1166.
   PubMed Web of Science ®Google Scholar
• Wang J, Werner-Avidon M, Newton L, et al. Ingenuity in action: connecting tinkering to engineering design processes. J Pre-Coll Eng Edu Res (J-PEER). 2013;3(1):2.
   Google Scholar
• Shapiro JA. Mobile Genetic Elements. New York: Academic Press; 1983.
   Google Scholar
• Witzany G. Natural genome editing from a biocommunicative perspective. Biosemiotics. 2011;4(3):349–368.
   Web of Science ®Google Scholar
• Shapiro JA. DNA insertion elements and the evolution of chromosome primary structure. Trends in Biochem Sci. 1977;2:622–627.
   Web of Science ®Google Scholar
• Shapiro JA. The basic concept of the read–write genome: mini-review on cell-mediated DNA modification. Biosystems. 2016;140:35–37.
   PubMed Web of Science ®Google Scholar
• Shapiro JA. Mobile DNA and evolution in the 21st century. Mob DNA. 2010;1(1):1–4.
   PubMedGoogle Scholar
• Montaño SP, Rice PA. Moving DNA around: dNA transposition and retroviral integration. Curr Opin Struct Biol. 2011;21(3):370–378.
   PubMed Web of Science ®Google Scholar
• Aanen DK, Eggleton P. Symbiogenesis: Beyond the endosymbiosis theory?. J Theor Biol. 2017;434:99–103.
   PubMed Web of Science ®Google Scholar
• Rosenwasser S, Ziv C, Van Creveld SG, et al. Virocell metabolism: metabolic innovations during host–virus interactions in the ocean. Trends Microbiol. 2016;24(10):821–832.
   PubMed Web of Science ®Google Scholar
• Sanjuán R, Thoulouze MI. Why viruses sometimes disperse in groups. Virus Evol. 2019;5(1):vez014.
   PubMed Web of Science ®Google Scholar
• Heylighen F (2011). Stigmergy as a generic mechanism for coordination: definition, varieties and aspects. Available from:{http:/pespmc1. vub. ac. be/Papers/Stigmergy-WorkingPaper. pdf} (accessed 04.2014).
   Google Scholar
• Domínguez-Andrés J, Joosten LA, Netea MG. Induction of innate immune memory: the role of cellular metabolism. Curr Opin Immunol. 2019;56:10–16.
   PubMed Web of Science ®Google Scholar
• Pastuzyn ED, Day CE, Kearns RB, et al. The neuronal gene arc encodes a repurposed retrotransposon gag protein that mediates intercellular RNA transfer. Cell. 2018;172(1–2):275–288.
   PubMed Web of Science ®Google Scholar
• Briones C, Domingo E, Molina-Parı́s C. Memory in retroviral quasispecies: experimental evidence and theoretical model for human immunodeficiency virus. J Mol Biol. 2003;331(1):213–229.
   PubMed Web of Science ®Google Scholar
• McLeod DV, Wild G, Úbeda F, et al. Epigenetic memories and the evolution of infectious diseases. Nat. Commun.12. 2021;4273.
   PubMed Web of Science ®Google Scholar
• Wilke CO, Novella IS. Phenotypic mixing and hiding may contribute to phenotypic memory in viral quasispecies. BMC Microbiol. 2003;3(1):11.
   PubMedGoogle Scholar
• Arias A, Ruiz-Jarabo CM, Escarmı́s C, et al. Fitness increase of memory genomes in a viral quasispecies. J Royal Soc Int. 2004;339(2):405–412.
   Google Scholar
• Villarreal LP, Witzany G. Rethinking quasispecies theory: from fittest type to cooperative consortia. World J Biol Chem. 2013;4(4):79.
   PubMedGoogle Scholar
• de Castro IF, Volonté L, Risco C. Virus factories: biogenesis and structural design. Cell Microbiol. 2013;15(1):24–34.
   PubMed Web of Science ®Google Scholar
• Novoa RR, Calderita G, Arranz R, et al. Virus factories: associations of cell organelles for viral replication and morphogenesis. Biol Cell. 2005;97(2):147–1720.
   PubMed Web of Science ®Google Scholar
• Den Boon JA, Diaz A, Ahlquist P. Cytoplasmic viral replication complexes. Cell Host & Microb. 2010;8(1):77–85.
   PubMed Web of Science ®Google Scholar
• Patton JT, Silvestri LS, Tortorici MA, et al. Rotavirus genome replication and morphogenesis: role of the viroplasm. In: Roy, P, editor. Reoviruses: entry, assembly and morphogenesis. Berlin, Heidelberg: Springer; 2006. p. 169–187.
   Google Scholar
• Netherton CL, Wileman T. Virus factories, double membrane vesicles and viroplasm generated in animal cells. Curr Opin Virol. 2011;1(5):381–387.
   PubMed Web of Science ®Google Scholar
• Niehl A, Peña EJ, Amari K, et al. Microtubules in viral replication and transport. Plant J. 2013;75(2):290–308.
   PubMed Web of Science ®Google Scholar
• Claverie JM. Viruses take center stage in cellular evolution. Gen Biol. 2006;7:110.
   PubMed Web of Science ®Google Scholar
• Forterre P. The virocell concept and environmental microbiology. Isme J. 2013;7(2):233–236.
   PubMed Web of Science ®Google Scholar
• Witzany G, Baluška F. Life’s code script does not code itself: the machine metaphor for living organisms is outdated. EMBO Rep. 2012;13(12):1054–1056.
   PubMed Web of Science ®Google Scholar
• Rescan M, Grulois D, Aboud EO, et al. Predicting population genetic change in an autocorrelated random environment: insights from a large automated experiment. PLoS Genet. 2021;17(6):e1009611.
   PubMed Web of Science ®Google Scholar
• Lenormand T, Roze D, Rousset F. Stochasticity in evolution. Trends Ecol Evol. 2009;24(3):157–165.
   PubMed Web of Science ®Google Scholar
• Noble D. The role of stochasticity in biological communication processes. Progr Biophys Mol Biol. 2020;162:122–128.
   PubMed Web of Science ®Google Scholar
• Claverie JM, Abergel C. Giant viruses: the difficult breaking of multiple epistemological barriers. Stud Hist Phil Sci Part C Biol Biomed Sci. 2016;59:89–99.
   PubMedGoogle Scholar
• Sanjuán R. Collective infectious units in viruses. Trends Microbiol. 2017;25(5):402–412.
   PubMed Web of Science ®Google Scholar
• Trinh JT, Székely T, Shao Q, et al. Cell fate decisions emerge as phages cooperate or compete inside their host. Nat Commun. 2017;8(1):1–13.
   PubMedGoogle Scholar
• Agnati LF, Baluška F, Barlow PW, et al. Mosaic, self-similarity logic and biological attraction principles: three explanatory instruments in biology. Commun Integr Biol. 2009;2(6):552–563.
   PubMedGoogle Scholar
• Santiana M, Ghosh S, Ho BA, Rajasekaran V, Du WL, Mutsafi Y … Takvorian PM. Vesicle-cloaked virus clusters are optimal units for inter-organismal viral transmission. Cell Host & Microbe. 2018;24(2):208–220.
   PubMed Web of Science ®Google Scholar
• Wang Q, Guan Z, Pei K, et al. Structural basis of the arbitrium peptide–aimr communication system in the phage lysis–lysogeny decision. Nat Microbiol. 2018;3(11):1266–1273.
   PubMed Web of Science ®Google Scholar
• Stokar-Avihail A, Tal N, Erez Z, et al. Widespread utilization of peptide communication in phages infecting soil and pathogenic bacteria. Cell Host & Microbe. 2019;25(5):746–755.
   PubMed Web of Science ®Google Scholar
• Silpe JE, Bassler BL. A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Cell. 2019;176(1–2):268–280.
   PubMed Web of Science ®Google Scholar
• Erickson AK, Jesudhasan PR, Mayer MJ, et al. Bacteria facilitate enteric virus co-infection of mammalian cells and promote genetic recombination. Cell Host & Microb. 2018;23(1):77–88.
   PubMed Web of Science ®Google Scholar
• Borges AL, Zhang JY, Rollins MF, et al. Bacteriophage cooperation suppresses CRISPR-Cas3 and Cas9 immunity. Cell. 2018;174(4):917–925.
   PubMed Web of Science ®Google Scholar
• Torday JS, Rehan VK. Evolutionary biology: cell-cell communication, and complex disease. Hoboken, NJ: John Wiley & Sons; 2012.
   Google Scholar
• Witzany G. Language and communication as universal requirements for life. In: Kolb V, editor. Astrobiology: an evolutionary approach. Baca Raton: CRC Press; 2014. pp. 349–369.
   Google Scholar
• De Loof A. Organic and cultural evolution can be seamlessly integrated using the principles of communication and problem-solving: the foundations for an extended evolutionary synthesis (EES) as outlined in the mega-evolution concept. Life Exc Biol. 2015;2(4):247–269.
   Google Scholar
• Dupré J, Guttinger S. Viruses as living processes. studies in history and philosophy of science part C: stud. Hist Phil Sci Part C Stud Biol Biomed Sci. 2016;59:109–116.
   PubMedGoogle Scholar
• Koonin EV. Viruses and mobile elements as drivers of evolutionary transitions. Phil Trans Royal Soc B Biol Sci. 2016;371(1701):20150442.
   PubMed Web of Science ®Google Scholar
• Moelling K, Broecker F. Viruses and evolution–viruses first? A personal perspective. Front Microbiol. 2019;10:523.
   PubMed Web of Science ®Google Scholar
• Caldecott KW, Ward ME, Nussenzweig A. The threat of programmed DNA damage to neuronal genome integrity and plasticity. Nat Genet. 2022;54(2):115–120.
   PubMed Web of Science ®Google Scholar
• Auboeuf D. Physicochemical foundations of life that direct evolution: chance and natural selection are not evolutionary driving forces. Life. 2020;10(2):7.
   PubMedGoogle Scholar
• Wright BE. A biochemical mechanism for nonrandom mutations and evolution. J Bacteriol. 2000;182(11):2993–3001.
   PubMed Web of Science ®Google Scholar
• Zamai L. Unveiling human non-random genome editing mechanisms activated in response to chronic environmental changes: I. Where might these mechanisms come from and what might they have led to? Cells. 2020;9(11):2362.
   PubMed Web of Science ®Google Scholar
• Urquidi V, Bishop DH. Non-random reassortment between the tripartite RNA genomes of La Crosse and snowshoe hare viruses. J Gen Virol. 1992;73(9):2255–2265.
   PubMedGoogle Scholar
• Schmitz M, Driesch C, Jansen L, et al. Non-random integration of the HPV genome in cervical cancer. PLoS ONE. 2012;7(6):e39632.
   PubMed Web of Science ®Google Scholar
• Grant HE, Hodcroft EB, Ssemwanga D, et al. … Brown AJL. Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evol. 2020;6:veaa004.
   PubMed Web of Science ®Google Scholar
• Rabadan R, Levine AJ, Krasnitz M. Non-random reassortment in human influenza a viruses. Influenza Other Respir Viruses. 2008;2(1):9–22.
   PubMed Web of Science ®Google Scholar
• Ambrosi A, Cattoglio C, Di Serio C. Retroviral integration process in the human genome: is it really non-random? A new statistical approach. PLoS Comput Biol. 2008;4(8):e1000144.
   PubMed Web of Science ®Google Scholar
• Witzany G, Baluška F. Evolution: viruses are key players. Nature. 2014;515(7527):343.
   PubMed Web of Science ®Google Scholar
• Torday JS, Miller WB. Phenotype as agent for epigenetic inheritance. Biology. 2016;5(3):30.
   PubMedGoogle Scholar
• Tsai K, Cullen BR. Epigenetic and epitranscriptomic regulation of viral replication. Nat Rev Microbiol. 2020;18(10):559–570.
   PubMed Web of Science ®Google Scholar
• Eyre NS, Phillips RJ, Bowden S, et al. Hepatitis B virus and hepatitis C virus interaction in Huh-7 cells. J Hepatol. 2009;51(3):446–457.
   PubMed Web of Science ®Google Scholar
• Hall JP, Brockhurst MA, Harrison E. Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria. Phil Trans Royal Soc B Biol Sci. 2017;372(1735):20160424.
   PubMed Web of Science ®Google Scholar
• Patel MR, Emerman M, Malik HS. Paleovirology—ghosts and gifts of viruses past. Curr Opin Virol. 2011;1(4):304–309.
   PubMed Web of Science ®Google Scholar
• Nasir A, Kim KM, Caetano‐anollés G. Long‐term evolution of viruses: a Janus‐faced balance. BioEssays. 2017;39(8):1700026.
   Web of Science ®Google Scholar
• Kouvaris K, Clune J, Kounios L, et al. How evolution learns to generalise: using the principles of learning theory to understand the evolution of developmental organisation. PLoS Comput Biol. 2017;13(4):e1005358.
   PubMed Web of Science ®Google Scholar
• González R, Butković A, Elena SF. From foes to friends: viral infections expand the limits of host phenotypic plasticity. Adv Virus Res. 2020;106:85–121.
   PubMed Web of Science ®Google Scholar
• Kaján GL, Doszpoly A, Tarján ZL et al. Virus–host coevolution with a focus on animal and human DNA viruses. J Mol Evol. 2020;88(1):41–56.
   PubMed Web of Science ®Google Scholar
• de Farias ST, Jheeta S, Prosdocimi F. Viruses as a survival strategy in the armory of life. Hist Philos Life Sci. 2019;41(4):45.
   PubMed Web of Science ®Google Scholar