D. Ivanovski, Über die Mosaikkrankheit der Tabakspflanze, Izv. Imp. Akad. Nauk

J. Claverie and C. Abergel, Giant viruses: The difficult breaking of multiple epistemological barriers, Stud. Hist. Philos. Biol. Biomed. Sci, vol.59, pp.89-99, 2016.

G. P. Salmond and P. C. Fineran, A century of the phage: Past, present and future, Nat. Rev. Genet, vol.13, pp.777-786, 2015.

B. L. Scola, A Giant Virus in Amoebae, Science, vol.299, 2003.

D. Raoult, S. Audic, C. Robert, C. Abergel, P. Renesto et al., The 1.2-Megabase Genome Sequence of Mimivirus, Science, vol.306, pp.1344-1350, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00651656

J. Claverie and C. Abergel, Mimiviridae: An Expanding Family of Highly Diverse Large dsDNA Viruses Infecting a Wide Phylogenetic Range of Aquatic Eukaryotes, Viruses, vol.10, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01887346

M. G. Fischer, M. J. Allen, W. H. Wilson, and C. A. Suttle, Giant virus with a remarkable complement of genes infects marine zooplankton, Proc. Natl. Acad. Sci, vol.107, pp.19508-19513, 2010.

M. Moniruzzaman, G. R. Lecleir, C. M. Brown, C. J. Gobler, K. D. Bidle et al., Genome of brown tide virus (AaV), the little giant of the Megaviridae, elucidates NCLDV genome expansion and host-virus coevolution, Virology, vol.467, pp.1130-1141, 2014.

C. M. Deeg, C. T. Chow, and C. A. Suttle, The kinetoplastid-infecting Bodo saltans virus (BsV), a window into the most abundant giant viruses in the sea, vol.7, 2018.

L. Gallot-lavallée, G. Blanc, and J. Claverie, Comparative Genomics of Chrysochromulina Ericina Virus and Other Microalga-Infecting Large DNA Viruses Highlights Their Intricate Evolutionary Relationship with the Established Mimiviridae Family, J. Virol, vol.91, pp.230-247, 2017.

C. R. Schvarcz and G. F. Steward, A giant virus infecting green algae encodes key fermentation genes, Virology, vol.518, pp.423-433, 2018.

C. Abergel, M. Legendre, and J. Claverie, The rapidly expanding universe of giant viruses: Mimivirus, Pandoravirus, Pithovirus and Mollivirus, FEMS Microbiol. Rev, vol.39, pp.779-796, 2015.

S. Aherfi, B. La-scola, I. Pagnier, D. Raoult, and P. Colson, The expanding family Marseilleviridae, Virology, vol.466, pp.27-37, 2014.

J. Andreani, S. Aherfi, J. Y. Khalil, F. Di-pinto, I. Bitam et al., Cedratvirus, a Double-Cork Structured Giant Virus, is a Distant Relative of Pithoviruses, Viruses, vol.8, p.300, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01453281

D. G. Reteno, S. Benamar, J. B. Khalil, J. Andreani, N. Armstrong et al., La Scola, B. Faustovirus, an Asfarvirus-Related New Lineage of Giant Viruses Infecting Amoebae, J. Virol, vol.89, pp.6585-6594, 2015.

G. Yoshikawa, R. Blanc-mathieu, C. Song, Y. Kayama, T. Mochizuki et al., Medusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water, J. Virol, vol.93, 2019.

P. Hingamp, N. Grimsley, S. G. Acinas, C. Clerissi, L. Subirana et al., Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes, ISME J, vol.7, pp.1678-1695, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01258223

F. Schulz, L. Alteio, D. Goudeau, E. M. Ryan, F. B. Yu et al., Hidden diversity of soil giant viruses, Nat. Commun, vol.9, p.4881, 2018.

D. M. Needham, S. Yoshizawa, T. Hosaka, C. Poirier, C. J. Choi et al., A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators, Proc. Natl. Acad. Sci, vol.116, pp.20574-20583, 2019.

J. Claverie, C. Abergel, . Mimivirus, and . Virophage, Annu. Rev. Genet, vol.43, pp.49-66, 2009.

M. G. Fischer and T. Hackl, Host genome integration and giant virus-induced reactivation of the virophage mavirus, Nat. Cell Biol, vol.540, pp.288-291, 2016.

J. R. Schrad, J. S. Abrahão, J. R. Cortines, and K. N. Parent, Structural and Proteomic Characterization of the Initiation of Giant Virus Infection, Cell, vol.181, pp.1046-1061, 2020.

E. Fabre, S. Jeudy, S. Santini, M. Legendre, M. Trauchessec et al., Noumeavirus replication relies on a transient remote control of the host nucleus, Nat. Commun, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01534406

D. C. Gajdusek, Unconventional viruses and the origin and disappearance of kuru, Science, vol.197, pp.943-960, 1977.

A. Igel-egalon, J. Bohl, M. Moudjou, L. Herzog, F. Reine et al., Heterogeneity and Architecture of Pathological Prion Protein Assemblies: Time to Revisit the Molecular Basis of the Prion Replication Process? Viruses, vol.11, p.429, 2019.

J. Claverie and C. Abergel, Open Questions About Giant Viruses, Adv. Virus Res, vol.85, pp.25-56, 2013.

A. Nasir, F. Sun, K. M. Kim, and G. Caetano-anollés, Untangling the origin of viruses and their impact on cellular evolution, Ann. N. Y. Acad. Sci, pp.61-74, 1341.

E. V. Koonin, M. Krupovic, and N. Yutin, Evolution of double-stranded DNA viruses of eukaryotes: From bacteriophages to transposons to giant viruses, Ann. N. Y. Acad. Sci, pp.10-24, 1341.
URL : https://hal.archives-ouvertes.fr/pasteur-01977390

P. Forterre and M. Gaïa, Giant viruses and the origin of modern eukaryotes, Curr. Opin. Microbiol, vol.31, pp.44-49, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01443846

E. V. Koonin and N. Yutin, Multiple evolutionary origins of giant viruses, 1840.

P. Colson, A. Levasseur, B. La-scola, V. Sharma, A. Nasir et al., Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes, Front. Microbiol, vol.9, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01948086

E. V. Koonin and N. Yutin, Evolution of the Large Nucleocytoplasmic DNA Viruses of Eukaryotes and Convergent Origins of Viral Gigantism, Adv. Virus Res, vol.103, pp.167-202, 2018.

J. Guglielmini, A. C. Woo, M. Krupovic, P. Forterre, and M. Gaia, Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes, Proc. Natl. Acad. Sci, vol.116, pp.19585-19592, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02294232

F. Mughal, A. Nasir, and G. Caetano-anollés, The origin and evolution of viruses inferred from fold family structure, Arch. Virol, vol.2020, pp.2177-2191

A. Nasir, E. Romero-severson, and J. M. Claverie, Investigating the concept and origin of viruses, Trends Microbiol, 2020.

J. Monod and F. Jacob, General Conclusions: Teleonomic Mechanisms in Cellular Metabolism, Growth, and Differentiation, Cold Spring Harb. Symp. Quant. Biol, vol.26, pp.389-401, 1961.

I. Pagnier, N. Yutin, O. Croce, K. S. Makarova, Y. I. Wolf et al., Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae, Boil. Direct, vol.10, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01217089

T. Driscoll, V. I. Verhoeve, M. L. Guillotte, S. S. Lehman, S. A. Rennoll et al., Wholly Rickettsia! Reconstructed Metabolic Profile of the Quintessential Bacterial Parasite of Eukaryotic Cells, vol.8, pp.859-876, 2017.

A. Omsland, B. S. Sixt, M. Horn, and T. Hackstadt, Chlamydial metabolism revisited: Interspecies metabolic variability and developmental stage-specific physiologic activities, FEMS Microbiol. Rev, vol.38, pp.779-801, 2014.

S. López-madrigal, A. Latorre, M. Porcar, A. Moya, and R. Gil-benso, Mealybugs nested endosymbiosis: Going into the 'matryoshka' system in Planococcus citri in depth, BMC Microbiol, vol.13, 2013.

, International Committee on Taxonomy of Viruses Executive Committee; Gorbalenya, A.E. The new scope of virus taxonomy: Partitioning the virosphere into 15 hierarchical ranks, Nat. Microbiol, vol.5, pp.668-674, 2020.

P. Hidalgo, L. Anzures, A. Hernandez-mendoza, A. Guerrero, C. Wood et al., Morphological, Biochemical, and Functional Study of Viral Replication Compartments Isolated from Adenovirus-Infected Cells, J. Virol, vol.90, pp.3411-3427, 2016.

J. Dupré and S. Guttinger, Viruses as living processes, Stud. Hist. Philos. Biol. Biomed. Sci, vol.59, pp.109-116, 2016.

A. Lwoff and D. J. Nicholas, The Concept of Virus, Microbiology, vol.17, pp.239-253, 1957.

P. Renesto, N. Crapoulet, H. Ogata, B. La-scola, G. Vestris et al., Genome-based design of a cell-free culture medium for Tropheryma whipplei, Lancet, vol.362, pp.447-449, 2003.

A. Rector and M. Van-ranst, Animal papillomaviruses, Virology, vol.445, pp.213-223, 2013.

S. Calvignac-spencer, Polyomaviridae Study Group of the International Committee on Taxonomy of Viruses

M. C. Feltkamp, M. D. Daugherty, U. Moens, T. Ramqvist, R. Johne et al., A taxonomy update for the family Polyomaviridae, Arch. Virol, vol.161, pp.1739-1750, 2016.

J. Abrahao, L. Silva, L. S. Silva, J. Y. Khalil, R. A. Rodrigues et al., Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere, Nat. Commun, vol.9, pp.1-12, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01780642

S. Petrovski, Z. A. Dyson, R. J. Seviour, and D. Tillett, Small but Sufficient: The Rhodococcus Phage RRH1 Has the Smallest Known Siphoviridae Genome at 14.2 Kilobases, J. Virol, vol.86, pp.358-363, 2011.

B. Al-shayeb, R. Sachdeva, L. Chen, F. Ward, P. Munk et al., Clades of huge phages from across Earth's ecosystems, Nat. Cell Biol, vol.578, pp.425-431, 2020.

N. Yutin, Y. I. Wolf, D. Raoult, and E. V. Koonin, Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution, Virol. J, vol.6, 2009.

E. V. Koonin and N. Yutin, Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses, Intervirology, vol.53, pp.284-292, 2010.

M. J. Allen, J. Howard, K. S. Lilley, and W. Wilson, Proteomic analysis of the EhV-86 virion, Proteome Sci, vol.6, 2008.

J. Drezen, M. Leobold, A. Bézier, E. Huguet, A. Volkoff et al., Endogenous viruses of parasitic wasps: Variations on a common theme, Curr. Opin. Virol, vol.25, pp.41-48, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01605633

N. A. Moran, H. J. Mclaughlin, and R. Sorek, The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria, Science, vol.323, pp.379-382, 2009.

G. Blanc, H. Ogata, C. Robert, S. Audic, K. Suhre et al., Reductive Genome Evolution from the Mother of Rickettsia, PLoS Genet, vol.3, 2007.

M. Lescot, S. Audic, C. Robert, T. T. Nguyen, G. Blanc et al., The Genome of Borrelia recurrentis, the Agent of Deadly Louse-Borne Relapsing Fever, Is a Degraded Subset of Tick-Borne Borrelia duttonii, PLoS Genet, 2008.

D. G. Gibson, J. I. Glass, C. Lartigue, V. N. Noskov, R. Chuang et al., Science, vol.329, pp.52-56, 2010.

N. Yutin, Y. I. Wolf, and E. V. Koonin, Origin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life, Virology, vol.467, pp.38-52, 2014.

Y. I. Wolf and E. V. Koonin, Genome reduction as the dominant mode of evolution, BioEssays, vol.35, pp.829-837, 2013.

G. Mahmoudabadi, R. Milo, and R. Phillips, Energetic cost of building a virus, Proc. Natl. Acad. Sci, vol.114, pp.4324-4333, 2017.

S. Rosenwasser, C. Ziv, S. G. Van-creveld, and A. Vardi, Virocell Metabolism: Metabolic Innovations During Host-Virus Interactions in the Ocean, Trends Microbiol, vol.24, pp.821-832, 2016.

C. Howard-varona, M. M. Lindback, G. E. Bastien, N. Solonenko, A. A. Zayed et al., Phage-specific metabolic reprogramming of virocells, ISME J, vol.2020, pp.881-895

S. Jeudy, S. Rigou, J. Alempic, J. Claverie, C. Abergel et al., The DNA methylation landscape of giant viruses, Nat. Commun, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02634342

J. L. Van-etten, I. Agarkova, D. D. Dunigan, and . Chloroviruses, , vol.12, 2019.

M. Legendre, A. Lartigue, L. Bertaux, S. Jeudy, J. Bartoli et al., In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba, Proc. Natl. Acad. Sci, vol.112, pp.5327-5335, 2015.
URL : https://hal.archives-ouvertes.fr/cea-01825900

N. Philippe, M. Legendre, G. Doutre, Y. Couté, O. Poirot et al., Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes, Science, vol.341, pp.281-286, 2013.
URL : https://hal.archives-ouvertes.fr/cea-00862677

J. Iranzo, M. Krupovic, and E. V. Koonin, The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing, vol.7, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01977375

N. Yutin and E. V. Koonin, Pandoraviruses are highly derived phycodnaviruses, Biol. Direct, vol.8, 2013.

N. Yutin and E. V. Koonin, Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes, Virol. J, vol.9, p.161, 2012.

J. Iranzo, M. Krupovic, and E. V. Koonin, A network perspective on the virus world, Commun. Integr. Biol, vol.10, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01977360

M. Krupovic, N. Yutin, and E. V. Koonin, Evolution of a major virion protein of the giant pandoraviruses from an inactivated bacterial glycoside hydrolase

M. Krupovic and E. V. Koonin, Multiple origins of viral capsid proteins from cellular ancestors, Proc. Natl. Acad. Sci, vol.114, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01977364

M. Legendre, E. Fabre, O. Poirot, S. Jeudy, A. Lartigue et al., Diversity and evolution of the emerging Pandoraviridae family, Nat. Commun, vol.9, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01830344