F. Wu, A new coronavirus associated with human respiratory disease in China, Nature, vol.579, pp.265-269, 2020.

D. Kim, The Architecture of SARS-CoV-2 Transcriptome, Cell, vol.181, pp.914-921, 2020.

J. F. Chan, Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan, Emerg Microbes Infect, vol.9, pp.221-236, 2020.

G. A. Belov and F. J. Van-kuppeveld, +)RNA viruses rewire cellular pathways to build replication organelles

E. Blanchard and P. Roingeard, Virus-induced double-membrane vesicles, Cellular microbiology, vol.17, pp.45-50, 2015.
URL : https://hal.archives-ouvertes.fr/inserm-01575078

D. E. Gordon, A SARS-CoV-2 protein interaction map reveals targets for drug repurposing, Nature, vol.583, pp.459-468, 2020.

A. Stukalov, Multi-level proteomics reveals host-perturbation strategies of SARS-CoV-2 and SARS-CoV. bioRxiv, 2006.

J. Li, Virus-host interactome and proteomic survey of PMBCs from COVID-19 patients reveal potential virulence factors influencing SARS-CoV-2 pathogenesis. bioRxiv, 2003.

A. C. Gingras, K. T. Abe, and B. Raught, Getting to know the neighborhood: using proximitydependent biotinylation to characterize protein complexes and map organelles, Curr Opin Chem Biol, vol.48, pp.44-54, 2019.

K. J. Roux, D. I. Kim, M. Raida, and B. Burke, A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells, J Cell Biol, vol.196, pp.801-810, 2012.

A. L. Couzens, Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions, Sci Signal, vol.6, p.15, 2013.

N. St-denis, Phenotypic and Interaction Profiling of the Human Phosphatases Identifies Diverse Mitotic Regulators, Cell Rep, vol.17, pp.2488-2501, 2016.

J. Y. Youn, High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies, Mol Cell, vol.69, p.511, 2018.

G. D. Gupta, A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface, Cell, vol.163, pp.1484-1499, 2015.

E. Coyaud, Global Interactomics Uncovers Extensive Organellar Targeting by Zika Virus, Mol Cell Proteomics, vol.17, pp.2242-2255, 2018.

P. Samavarchi-tehrani, R. Samson, and A. C. Gingras, Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches, Mol Cell Proteomics, vol.19, pp.757-773, 2020.

T. C. Branon, Efficient proximity labeling in living cells and organisms with TurboID, Nat Biotechnol, vol.36, pp.880-887, 2018.

P. Samavarchi-tehrani, H. Abdouni, R. Samson, and A. C. Gingras, A Versatile Lentiviral Delivery Toolkit for Proximity-dependent Biotinylation in Diverse Cell Types, Mol Cell Proteomics, vol.17, pp.2256-2269, 2018.

D. K. Kim, Flexible Collection of SARS-CoV-2 Coding Regions. G3 (Bethesda), 2020.

C. D. Go, A proximity biotinylation map of a human cell, bioRxiv, p.796391, 2019.

W. Kamitani, C. Huang, K. Narayanan, K. G. Lokugamage, and S. Makino, A two-pronged strategy to suppress host protein synthesis by SARS coronavirus Nsp1 protein, Nat Struct Mol Biol, vol.16, pp.1134-1140, 2009.

, International license (which was not certified by peer review) is the author/funder

K. Narayanan, Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells, J Virol, vol.82, pp.4471-4479, 2008.

G. Teo, SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software, J Proteomics, vol.100, pp.37-43, 2014.

R. Oughtred, The BioGRID interaction database: 2019 update, Nucleic Acids Res, vol.47, pp.529-541, 2019.

A. Dominguez-andres, SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells. bioRxiv, 2020, 2008.

Y. Zhang, The ORF8 Protein of SARS-CoV-2 Mediates Immune Evasion through Potently Downregulating MHC-I. bioRxiv, 2005.

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.

I. Imbert, A second, non-canonical RNA-dependent RNA polymerase in SARS coronavirus, EMBO J, vol.25, pp.4933-4942, 2006.

M. M. Angelini, M. Akhlaghpour, B. W. Neuman, and M. J. Buchmeier, Severe acute respiratory syndrome coronavirus nonstructural proteins 3, 4, and 6 induce double-membrane vesicles, vol.4, 2013.

M. A. Clementz, A. Kanjanahaluethai, T. E. O'brien, and S. C. Baker, Mutation in murine coronavirus replication protein nsp4 alters assembly of double membrane vesicles, Virology, vol.375, pp.118-129, 2008.

T. Di-mattia, Identification of MOSPD2, a novel scaffold for endoplasmic reticulum membrane contact sites, EMBO Rep, vol.19, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02177612

H. W. Jiang, SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70, Cell Mol Immunol, 2020.

Z. Ren, Regulation of MAVS Expression and Signaling Function in the Antiviral Innate Immune Response, Frontiers in immunology, vol.11, p.1030, 2020.

H. Antonicka, A High-Density Human Mitochondrial Proximity Interaction Network, Cell Metabolism, vol.32, pp.479-497, 2020.

L. Han, SARS-CoV-2 ORF9b Antagonizes Type I and III Interferons by Targeting Multiple Components of RIG-I/MDA-5-MAVS, TLR3-TRIF, and cGAS-STING Signaling Pathways. bioRxiv, 2008.

Z. A. Jaafar and J. S. Kieft, Viral RNA structure-based strategies to manipulate translation, Nature reviews. Microbiology, vol.17, pp.110-123, 2019.

M. Thoms, Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2, Science, p.8665, 2020.

W. L. Chiu, The C-terminal region of eukaryotic translation initiation factor 3a (eIF3a) promotes mRNA recruitment, scanning, and, together with eIF3j and the eIF3b RNA recognition motif, selection of AUG start codons, Mol Cell Biol, vol.30, pp.4415-4434, 2010.

C. E. Aitken, Eukaryotic translation initiation factor 3 plays distinct roles at the mRNA entry and exit channels of the ribosomal preinitiation complex, Elife, vol.5, 2016.

A. Chaudhuri, Comparative analysis of non structural protein 1 of SARS-COV2 with SARS-COV1 and MERS-COV: An i<em>n silico</em> study. bioRxiv, 2006.

M. Egloff, The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world, Proceedings of the National Academy of Sciences of the United States of America, vol.101, pp.3792-3796, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02459257

Y. Li, LSm14A is a processing body-associated sensor of viral nucleic acids that initiates cellular antiviral response in the early phase of viral infection, Proceedings of the National Academy of Sciences, vol.109, pp.11770-11775, 2012.

T. Brandmann, Molecular architecture of LSM14 interactions involved in the assembly of mRNA silencing complexes, EMBO J, vol.37, 2018.

T. Nishimura, The eIF4E-Binding Protein 4E-T Is a Component of the mRNA Decay Machinery that Bridges the 5? and 3? Termini of Target mRNAs, Cell Reports, vol.11, pp.1425-1436, 2015.

M. Y. Hein, A human interactome in three quantitative dimensions organized by stoichiometries and abundances

E. L. Huttlin, Architecture of the human interactome defines protein communities and disease networks

D. Jain, ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2, vol.7, p.30919, 2018.

P. Gosselin, Tracking a refined eIF4E-binding motif reveals Angel1 as a new partner of eIF4E
URL : https://hal.archives-ouvertes.fr/hal-01002440

J. Y. Youn, Properties of Stress Granule and P-Body Proteomes, Mol Cell, vol.76, pp.286-294, 2019.

Y. T. Yen, Modeling the early events of severe acute respiratory syndrome coronavirus infection in vitro

V. A. Corman and -. , Link of a ubiquitous human coronavirus to dromedary camels

J. F. Chan, Differential cell line susceptibility to the emerging novel human betacoronavirus 2c EMC/2012: implications for disease pathogenesis and clinical manifestation

C. L. Miller, Stress Granules and Virus Replication

T. M. Perdikari, SARS-CoV-2 nucleocapsid protein undergoes liquid-liquid phase separation stimulated by RNA and partitions into phases of human ribonucleoproteins

S. M. Cascarina and E. D. Ross, A proposed role for the SARS-CoV-2 nucleocapsid protein in the formation and regulation of biomolecular condensates

A. Savastano, A. I. De-opakua, M. Rankovic, and M. Zweckstetter, Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates. bioRxiv, 2020, 2006.

C. Iserman, Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate. bioRxiv, 2006.

K. F. Cho, Split-TurboID enables contact-dependent proximity labeling in cells, Proc Natl Acad Sci U S A, vol.117, pp.12143-12154, 2020.

M. Hoffmann, SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor, Cell, vol.181, pp.271-280, 2020.

F. Hikmet, The protein expression profile of ACE2 in human tissues, Molecular systems biology 16, e9610, 2020.

A. Werion, SARS-CoV-2 Causes a Specific Dysfunction of the Kidney Proximal Tubule, Kidney international, 2020.

Z. Li, Caution on Kidney Dysfunctions of COVID-19 Patients. medRxiv, 2002.

Y. Cheng, Kidney impairment is associated with in-hospital death of COVID-19 patients. medRxiv, 2002.

Y. Y. Zheng, Y. T. Ma, J. Y. Zhang, and X. Xie, COVID-19 and the cardiovascular system, Nature reviews. Cardiology, vol.17, pp.259-260, 2020.

Y. Wang, SARS-CoV-2 infection of the liver directly contributes to hepatic impairment in patients with COVID-19, Journal of hepatology, 2020.

X. Yang, Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study. The Lancet, Respiratory medicine, vol.8, pp.475-481, 2020.

P. Song, W. Li, J. Xie, Y. Hou, and C. You, Cytokine storm induced by SARS-CoV-2. Clinica chimica acta, international journal of clinical chemistry, vol.509, pp.280-287, 2020.

V. G. Puelles, Multiorgan and Renal Tropism of SARS-CoV-2, The New England journal of medicine, vol.383, pp.590-592, 2020.

G. Liu, ProHits: integrated software for mass spectrometry-based interaction proteomics, Nat Biotechnol, vol.28, pp.1015-1017, 2010.

J. K. Eng, T. A. Jahan, and M. R. Hoopmann, Comet: an open-source MS/MS sequence database search tool, Proteomics, vol.13, pp.22-24, 2013.

A. Keller, A. I. Nesvizhskii, E. Kolker, and R. Aebersold, Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search, Analytical chemistry, vol.74, pp.5383-5392, 2002.

D. Shteynberg, iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates, Mol Cell Proteomics, vol.10, 2011.

D. Mellacheruvu, The CRAPome: a contaminant repository for affinity purification-mass spectrometry data, Nat Methods, vol.10, pp.730-736, 2013.

U. Raudvere, Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update), Nucleic Acids Res, vol.47, pp.191-198, 2019.

P. Samaras, ProteomicsDB: a multi-omics and multi-organism resource for life science research, Nucleic Acids Res, vol.48, pp.1153-1163, 2020.

S. El-gebali, The Pfam protein families database in 2019, Nucleic Acids Res, vol.47, pp.427-432, 2019.

C. Stark, BioGRID: a general repository for interaction datasets, Nucleic Acids Res, vol.34, pp.535-539, 2006.

J. D. Knight, ProHits-viz: a suite of web tools for visualizing interaction proteomics data, Nat Methods, vol.14, pp.645-646, 2017.

P. Shannon, Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome research, vol.13, pp.2498-2504, 2003.