A. Acevedo, L. Brodsky, A. , and R. , Mutational and fitness landscapes of an RNA virus revealed through population sequencing, Nature, vol.505, pp.686-690, 2014.

M. L. Agostini, E. L. Andres, A. C. Sims, R. L. Graham, T. P. Sheahan et al., Coronavirus susceptibility to the antiviral remdesivir (GS-5734) is mediated by the viral polymerase and the proofreading exoribonuclease, vol.9, pp.221-239, 2018.

D. G. Ahn, J. K. Choi, D. R. Taylor, and J. W. Oh, Biochemical characterization of a recombinant SARS coronavirus nsp12 RNA-dependent RNA polymerase capable of copying viral RNA templates, Arch. Virol, vol.157, pp.2095-2104, 2012.

W. Aouadi, C. Eydoux, B. Coutard, B. Martin, F. Debart et al., Toward the identification of viral cap-methyltransferase inhibitors by fluorescence screening assay, Antiviral Res, vol.144, pp.330-339, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01802844

M. H. Barnes, P. Spacciapoli, D. H. Li, and N. C. Brown, The 3'-5' exonuclease site of DNA polymerase III from gram-positive bacteria: definition of a novel motif structure, Gene, vol.165, pp.45-50, 1995.

M. Becares, A. Pascual-iglesias, A. Nogales, I. Sola, L. Enjuanes et al., Mutagenesis of coronavirus nsp14 reveals its potential role in modulation of the innate immune response, J. Virol, vol.90, pp.5399-5414, 2016.

L. S. Beese and T. A. Steitz, Structural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism, EMBO J, vol.10, pp.25-33, 1991.

A. Bernad, L. Blanco, J. M. Lazaro, G. Martin, and M. Salas, A conserved 3'--5' exonuclease active site in prokaryotic and eukaryotic DNA polymerases, Cell, vol.59, pp.219-228, 1989.

M. Bouvet, C. Debarnot, I. Imbert, B. Selisko, E. J. Snijder et al., In vitro reconstitution of SARS-coronavirus mRNA cap methylation, PLoS Pathog, vol.6, p.1000863, 2010.

M. Bouvet, I. Imbert, L. Subissi, L. Gluais, B. Canard et al., RNA 3'-end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp10/nsp14 exoribonuclease complex, Proc. Natl. Acad. Sci. U.S.A, vol.109, pp.9372-9377, 2012.

M. Bouvet, A. Lugari, C. C. Posthuma, J. C. Zevenhoven, S. Bernard et al., Coronavirus Nsp10, a critical co-factor for activation of multiple replicative enzymes, J. Biol. Chem, vol.289, pp.25783-25796, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01910944

K. Bukhari, G. Mulley, A. A. Gulyaeva, L. Zhao, G. Shu et al., Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus Alphaletovirus, Virology, vol.524, pp.160-171, 2018.

M. Byszewska, M. Smietanski, E. Purta, and J. M. Bujnicki, RNA methyltransferases involved in 5' cap biosynthesis, RNA Biol, vol.11, pp.1597-1607, 2014.

J. B. Case, A. W. Ashbrook, T. S. Dermody, and M. R. Denison, Mutagenesis of S-Adenosyl-l-Methionine-Binding residues in coronavirus nsp14 N7-Methyltransferase demonstrates differing requirements for genome translation and resistance to innate immunity, J. Virol, vol.90, pp.7248-7256, 2016.

J. B. Case, Y. Li, R. Elliott, X. Lu, K. W. Graepel et al., Murine hepatitis virus nsp14 exoribonuclease activity is required for resistance to innate immunity, J. Virol, vol.92, pp.1531-1548, 2018.

P. Chen, M. Jiang, T. Hu, Q. Liu, X. S. Chen et al., Biochemical characterization of exoribonuclease encoded by SARS coronavirus, J. Biochem. Mol. Biol, vol.40, pp.649-655, 2007.

Y. Chen, H. Cai, J. Pan, N. Xiang, P. Tien et al., Functional screen reveals SARS coronavirus nonstructural protein nsp14 as a novel cap N7 methyltransferase, Proc. Natl. Acad. Sci. U.S.A, vol.106, pp.3484-3489, 2009.

Y. Chen, J. Tao, Y. Sun, A. Wu, C. Su et al., Structurefunction analysis of severe acute respiratory syndrome coronavirus RNA cap guanine-N7-methyltransferase, J. Virol, vol.87, pp.6296-6305, 2013.

B. P. Chouhan, S. Maimaiti, M. Gade, and P. Laurino, , 2019.

, Rossmann-Fold methyltransferases: taking a "beta-Turn" around their cofactor, S-adenosylmethionine, Biochemistry, vol.58, pp.166-170

S. Crotty, C. E. Cameron, A. , and R. , RNA virus error catastrophe: direct molecular test by using ribavirin, Proc. Natl. Acad. Sci. U.S.A, vol.98, pp.6895-6900, 2001.

S. Crotty, D. Maag, J. J. Arnold, W. Zhong, J. Y. Lau et al., The broad-spectrum antiviral ribonucleoside ribavirin is an RNA virus mutagen, Nat. Med, vol.6, pp.1375-1379, 2000.

E. Decroly, C. Debarnot, F. Ferron, M. Bouvet, B. Coutard et al., Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2'-O-methyltransferase nsp10/nsp16 complex, PLoS Pathog, vol.7, p.1002059, 2011.

E. Decroly, F. Ferron, J. Lescar, and B. Canard, Conventional and unconventional mechanisms for capping viral mRNA, Nat. Rev. Microbiol, vol.10, pp.51-65, 2011.

E. Decroly, I. Imbert, B. Coutard, M. Bouvet, B. Selisko et al., Coronavirus nonstructural protein 16 is a cap-0 binding enzyme possessing (nucleoside-2'O)-methyltransferase activity, J. Virol, vol.82, pp.8071-8084, 2008.

J. A. Den-boon, E. J. Snijder, E. D. Chirnside, A. A. De-vries, M. C. Horzinek et al., Equine arteritis virus is not a togavirus but belongs to the coronaviruslike superfamily, J. Virol, vol.65, pp.2910-2920, 1991.

M. R. Denison, R. L. Graham, E. F. Donaldson, L. D. Eckerle, and R. S. Baric, Coronaviruses: an RNA proofreading machine regulates replication fidelity and diversity, RNA Biol, vol.8, pp.270-279, 2011.

V. Derbyshire, N. D. Grindley, J. , and C. M. , The 3'-5' exonuclease of DNA polymerase I of Escherichia coli: contribution of each amino acid at the active site to the reaction, EMBO J, vol.10, pp.17-24, 1991.

M. P. Deutscher and C. W. Marlor, Purification and characterization of Escherichia coli RNase T, J. Biol. Chem, vol.260, pp.7067-7071, 1985.

J. W. Drake and J. J. Holland, Mutation rates among RNA viruses, Proc. Natl. Acad. Sci. U.S.A, vol.96, pp.13910-13913, 1999.

I. Durzynska, M. Sauerwald, N. Karl, R. Madhugiri, and J. Ziebuhr, Characterization of a bafinivirus exoribonuclease activity, J. Gen. Virol, vol.99, pp.1253-1260, 2018.

L. D. Eckerle, M. M. Becker, R. A. Halpin, K. Li, E. Venter et al., Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing, PLoS Pathog, vol.6, p.1000896, 2010.

L. D. Eckerle, X. Lu, S. M. Sperry, L. Choi, and M. R. Denison, High fidelity of murine hepatitis virus replication is decreased in nsp14 exoribonuclease mutants, J. Virol, vol.81, pp.12135-12144, 2007.

M. Eigen, Error catastrophe and antiviral strategy, Proc. Natl. Acad. Sci. U.S.A, vol.99, pp.13374-13376, 2002.

F. Ferron, L. Subissi, A. T. Silveira-de-morais, N. T. Le, and M. Sevajol, Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA, Proc. Natl. Acad. Sci. U.S.A, vol.115, pp.162-171, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02094607

A. E. Gorbalenya, L. Enjuanes, J. Ziebuhr, and E. J. Snijder, Nidovirales: evolving the largest RNA virus genome, Virus Res, vol.117, pp.17-37, 2006.

A. E. Gorbalenya, E. V. Koonin, A. P. Donchenko, and V. M. Blinov, Coronavirus genome: prediction of putative functional domains in the nonstructural polyprotein by comparative amino acid sequence analysis, Nucleic Acids Res, vol.17, pp.4847-4861, 1989.

R. Gosert, A. Kanjanahaluethai, D. Egger, K. Bienz, and S. C. Baker, RNA replication of mouse hepatitis virus takes place at double-membrane vesicles, J. Virol, vol.76, pp.3697-3708, 2002.

K. W. Graepel, X. Lu, J. B. Case, N. R. Sexton, E. C. Smith et al., Proofreading-Deficient coronaviruses adapt for increased fitness over long-term passage without reversion of exoribonucleaseinactivating mutations, mBio, vol.8, pp.1503-1520, 2017.

R. L. Graham, M. M. Becker, L. D. Eckerle, M. Bolles, M. R. Denison et al., A live, impaired-fidelity coronavirus vaccine protects in an aged, immunocompromised mouse model of lethal disease, Nat. Med, vol.18, pp.1820-1826, 2012.

M. Habjan, N. Penski, M. Spiegel, and F. Weber, T7 RNA polymerasedependent and -independent systems for cDNA-based rescue of Rift Valley fever virus, J. Gen. Virol, vol.89, pp.2157-2166, 2008.

K. M. Hastie, C. R. Kimberlin, M. A. Zandonatti, I. J. Macrae, and E. O. Saphire, Structure of the Lassa virus nucleoprotein reveals a dsRNA-specific 3' to 5' exonuclease activity essential for immune suppression, Proc. Natl. Acad. Sci. U.S.A, vol.108, pp.2396-2401, 2011.

I. Imbert, J. C. Guillemot, J. M. Bourhis, C. Bussetta, B. Coutard et al., A second, non-canonical RNA-dependent RNA polymerase in SARS coronavirus, EMBO J, vol.25, pp.4933-4942, 2006.

X. Jin, Y. Chen, Y. Sun, C. Zeng, Y. Wang et al., Characterization of the guanine-N7 methyltransferase activity of coronavirus nsp14 on nucleotide GTP, Virus Res, vol.176, pp.45-52, 2013.

E. Kindler and V. Thiel, To sense or not to sense viral RNA-essentials of coronavirus innate immune evasion, Curr. Opin. Microbiol, vol.20, pp.69-75, 2014.

R. N. Kirchdoerfer and A. B. Ward, Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors, Nat. Commun, vol.10, p.2342, 2019.

K. Knoops, M. Kikkert, S. H. Worm, J. C. Zevenhoven-dobbe, Y. Van-der-meer et al., SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum, PLoS Biol, vol.6, p.226, 2008.

V. Lam, K. A. Duca, Y. , and J. , Arrested spread of vesicular stomatitis virus infections in vitro depends on interferon-mediated antiviral activity, Biotechnol. Bioeng, vol.90, pp.793-804, 2005.

C. Lauber, J. J. Goeman, M. Del-carmen-parquet, P. T. Nga, E. J. Snijder et al., The footprint of genome architecture in the largest genome expansion in RNA viruses, PLoS Pathog, vol.9, p.1003500, 2013.

K. C. Lehmann, A. Gulyaeva, J. C. Zevenhoven-dobbe, G. M. Janssen, M. Ruben et al., Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerasecontaining protein of all nidoviruses, Nucleic Acids Res, vol.43, pp.8416-8434, 2015.

Y. Ma, L. Wu, N. Shaw, Y. Gao, J. Wang et al., Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex, Proc. Natl. Acad. Sci. U.S.A, vol.112, pp.9436-9441, 2015.

S. C. Manrubia, E. Domingo, L. , and E. , Pathways to extinction: beyond the error threshold, Philos. Trans. R. Soc. Lond. B Biol. Sci, vol.365, pp.1943-1952, 2010.

J. L. Martin and F. M. Mcmillan, SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold, Curr. Opin. Struct. Biol, vol.12, pp.783-793, 2002.

E. Minskaia, T. Hertzig, A. E. Gorbalenya, V. Campanacci, C. Cambillau et al., Discovery of an RNA virus 3'->5' exoribonuclease that is critically involved in coronavirus RNA synthesis, Proc. Natl. Acad. Sci. U.S.A, vol.103, pp.5108-5113, 2006.

B. W. Neuman, How the double spherules of infectious bronchitis virus impact our understanding of RNA virus replicative organelles, vol.4, pp.987-1000, 2013.

B. W. Neuman, P. Chamberlain, F. Bowden, J. , and J. , Atlas of coronavirus replicase structure, Virus Res, vol.194, pp.49-66, 2014.

P. T. Nga, C. Parquet-mdel, C. Lauber, M. Parida, T. Nabeshima et al., Discovery of the first insect nidovirus, a missing evolutionary link in the emergence of the largest RNA virus genomes, PLoS Pathog, vol.7, p.1002215, 2011.

A. O. Pasternak, W. J. Spaan, and E. J. Snijder, Nidovirus transcription: how to make sense, J. Gen. Virol, vol.87, pp.1403-1421, 2006.

J. K. Pfeiffer and K. Kirkegaard, Increased fidelity reduces poliovirus fitness and virulence under selective pressure in mice, PLoS Pathog, vol.1, p.11, 2005.

C. C. Posthuma, A. J. Velthuis, and E. J. Snijder, Nidovirus RNA polymerases: complex enzymes handling exceptional RNA genomes, Virus Res, vol.234, pp.58-73, 2017.

S. T. Rao and M. G. Rossmann, Comparison of super-secondary structures in proteins, J. Mol. Biol, vol.76, pp.241-256, 1973.

M. Russier, S. Reynard, X. Carnec, and S. Baize, The exonuclease domain of Lassa virus nucleoprotein is involved in antigen-presenting-cell-mediated NK cell responses, J. Virol, vol.88, pp.13811-13820, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01911067

A. Saberi, A. A. Gulyaeva, J. L. Brubacher, P. A. Newmark, and A. E. Gorbalenya, A planarian nidovirus expands the limits of RNA genome size, PLoS Pathog, vol.14, p.1007314, 2018.

S. G. Sawicki, D. L. Sawicki, and S. G. Siddell, A contemporary view of coronavirus transcription, J. Virol, vol.81, pp.20-29, 2007.

H. L. Schubert, R. M. Blumenthal, and X. Cheng, Many paths to methyltransfer: a chronicle of convergence, Trends Biochem. Sci, vol.28, pp.329-335, 2003.

M. Sevajol, L. Subissi, E. Decroly, B. Canard, and I. Imbert, Insights into RNA synthesis, capping, and proofreading mechanisms of SARS-coronavirus, Virus Res, vol.194, pp.90-99, 2014.

N. R. Sexton, E. C. Smith, H. Blanc, M. Vignuzzi, O. B. Peersen et al., Homology-Based identification of a mutation in the coronavirus RNA-Dependent RNA polymerase that confers resistance to multiple mutagens, J. Virol, vol.90, pp.7415-7428, 2016.

T. P. Sheahan, A. C. Sims, R. L. Graham, V. D. Menachery, L. E. Gralinski et al., Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses, Sci. Transl. Med, vol.9, p.3653, 2017.

M. Shi, X. D. Lin, X. Chen, J. H. Tian, L. J. Chen et al., Author correction: the evolutionary history of vertebrate RNA viruses, Nature, vol.561, p.6, 2018.

M. Shi, X. D. Lin, X. Chen, J. H. Tian, L. J. Chen et al., The evolutionary history of vertebrate RNA viruses, Nature, vol.556, pp.197-202, 2018.

M. Shi, X. D. Lin, J. H. Tian, L. J. Chen, X. Chen et al., Redefining the invertebrate RNA virosphere, Nature, vol.540, pp.539-543, 2016.

S. G. Siddell, P. J. Walker, E. J. Lefkowitz, A. R. Mushegian, M. J. Adams et al., Additional changes to taxonomy ratified in a special vote by the international committee on taxonomy of viruses, Arch. Virol, vol.164, pp.943-946, 2018.

E. C. Smith, H. Blanc, M. C. Surdel, M. Vignuzzi, and M. R. Denison, Coronaviruses lacking exoribonuclease activity are susceptible to lethal mutagenesis: evidence for proofreading and potential therapeutics, PLoS Pathog, vol.9, p.1003565, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-00918207

E. C. Smith, J. B. Case, H. Blanc, O. Isakov, N. Shomron et al., Mutations in coronavirus nonstructural protein 10 decrease virus replication fidelity, J. Virol, vol.89, pp.6418-6426, 2015.

E. C. Smith and M. R. Denison, Implications of altered replication fidelity on the evolution and pathogenesis of coronaviruses, Curr. Opin. Virol, vol.2, pp.519-524, 2012.

E. J. Snijder, P. J. Bredenbeek, J. C. Dobbe, V. Thiel, J. Ziebuhr et al., Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage, J. Mol. Biol, vol.331, pp.991-1004, 2003.

E. J. Snijder, E. Decroly, and J. Ziebuhr, The nonstructural proteins directing coronavirus RNA synthesis and processing, Adv. Virus Res, vol.96, pp.59-126, 2016.

J. Soding, Protein homology detection by HMM-HMM comparison, Bioinformatics, vol.21, pp.951-960, 2005.

I. Sola, F. Almazan, S. Zuniga, and L. Enjuanes, Continuous and discontinuous RNA synthesis in coronaviruses, Annu. Rev. Virol, vol.2, pp.265-288, 2015.

D. A. Steinhauer, E. Domingo, and J. J. Holland, Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase, Gene, vol.122, pp.281-288, 1992.

T. A. Steitz and J. A. Steitz, A general two-metal-ion mechanism for catalytic RNA, Proc. Natl. Acad. Sci. U.S.A, vol.90, pp.6498-6502, 1993.

L. Subissi, I. Imbert, F. Ferron, A. Collet, B. Coutard et al., , 2014.

. Sars-cov, ORF1b-encoded nonstructural proteins 12-16: replicative enzymes as antiviral targets, Antiviral Res, vol.101, pp.122-130

L. Subissi, C. C. Posthuma, A. Collet, J. C. Zevenhoven-dobbe, A. E. Gorbalenya et al., One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities, Proc. Natl. Acad. Sci. U.S.A, vol.111, pp.3900-3909, 2014.

Y. Sun, Z. Wang, J. Tao, Y. Wang, A. Wu et al., Yeast-based assays for the high-throughput screening of inhibitors of coronavirus RNA cap guanine-N7-methyltransferase, Antiviral Res, vol.104, pp.156-164, 2014.

A. J. Te-velthuis, J. J. Arnold, C. E. Cameron, S. H. Van-den-worm, and E. J. Snijder, The RNA polymerase activity of SARS-coronavirus nsp12 is primer dependent, Nucleic Acids Res, vol.38, pp.203-214, 2010.

J. Tvarogova, R. Madhugiri, G. Bylapudi, L. J. Ferguson, N. Karl et al., Identification and characterization of a human coronavirus 229E nonstructural protein 8-associated RNA 3'-terminal adenylyltransferase activity, J. Virol, vol.93, pp.291-310, 2019.

R. Ulferts, T. C. Mettenleiter, and J. Ziebuhr, Characterization of Bafinivirus main protease autoprocessing activities, J. Virol, vol.85, pp.1348-1359, 2011.

M. Vignuzzi, J. K. Stone, J. J. Arnold, C. E. Cameron, A. et al., Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population, Nature, vol.439, pp.344-348, 2006.

T. K. Warren, R. Jordan, M. K. Lo, A. S. Ray, R. L. Mackman et al., Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys, Nature, vol.531, pp.381-385, 2016.

Y. Xiao, Q. Ma, T. Restle, W. Shang, D. I. Svergun et al., Nonstructural proteins 7 and 8 of feline coronavirus form a 2:1 heterotrimer that exhibits primer-independent RNA polymerase activity, J. Virol, vol.86, pp.4444-4454, 2012.

X. Xu, Y. Liu, S. Weiss, E. Arnold, S. G. Sarafianos et al., Molecular model of SARS coronavirus polymerase: implications for biochemical functions and drug design, Nucleic Acids Res, vol.31, 2003.

E. Yekwa, C. Aphibanthammakit, X. Carnec, C. Picard, B. Canard et al., Arenaviridae exoribonuclease presents genomic RNA edition capacity. bioRxiv 541698, 2019.

Y. Zhai, F. Sun, X. Li, H. Pang, X. Xu et al., Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer, Nat. Struct. Mol. Biol, vol.12, pp.980-986, 2005.

J. Ziebuhr, E. J. Snijder, and A. E. Gorbalenya, Virus-encoded proteinases and proteolytic processing in the Nidovirales, J. Gen. Virol, vol.81, pp.853-879, 2000.

L. Zimmermann, A. Stephens, S. Z. Nam, D. Rau, J. Kubler et al., A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core, J. Mol. Biol, vol.430, pp.2237-2243, 2018.

A. Zumla, J. F. Chan, E. I. Azhar, D. S. Hui, and K. Y. Yuen, Coronaviruses -drug discovery and therapeutic options, Nat. Rev. Drug Discov, vol.15, pp.327-347, 2016.

Y. Zuo and M. P. Deutscher, Exoribonuclease superfamilies: structural analysis and phylogenetic distribution, Nucleic Acids Res, vol.29, pp.1017-1026, 2001.

R. Zust, L. Cervantes-barragan, M. Habjan, R. Maier, B. W. Neuman et al., Ribose 2'-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5, Nat. Immunol, vol.12, pp.137-143, 2011.