References
- Balderhaar, H. J., & Ungermann, C. (2013). CORVET and HOPS tethering complexes - Coordinators of endosome and lysosome fusion. Journal of Cell Science, 126(Pt 6), 1307–1316. https://doi.org/https://doi.org/10.1242/jcs.107805
- Binette, J., Dubé, M., Mercier, J., Halawani, D., Latterich, M., & Cohen, E. A. (2007). Requirements for the selective degradation of CD4 receptor molecules by the human immunodeficiency virus type 1 Vpu protein in the endoplasmic reticulum. Retrovirology, 4, 75. https://doi.org/https://doi.org/10.1186/1742-4690-4-75
- Blanchard, E., Belouzard, S., Goueslain, L., Wakita, T., Dubuisson, J., Wychowski, C., & Rouillé, Y. (2006). Hepatitis C virus entry depends on clathrin-mediated endocytosis. Journal of Virology, 80(14), 6964–6972. https://doi.org/https://doi.org/10.1128/JVI.00024-06
- Bordi, L., Castilletti, C., Falasca, L., Ciccosanti, F., Calcaterra, S., Rozera, G., Di Caro, A., Zaniratti, S., Rinaldi, A., Ippolito, G., Piacentini, M., & Capobianchi, M. R. (2006). Bcl-2 inhibits the caspase-dependent apoptosis induced by SARS-CoV without affecting virus replication kinetics. Archives of Virology, 151(2), 369–377. https://doi.org/https://doi.org/10.1007/s00705-005-0632-8
- Burkard, C., Verheije, M. H., Wicht, O., van Kasteren, S. I., van Kuppeveld, F. J., Haagmans, B. L., Pelkmans, L., Rottier, P. J. M., Bosch, B. J., & de Haan, C. A. M. (2014). Coronavirus cell entry occurs through the endo-/lysosomal pathway in a proteolysis-dependent manner. PLoS Pathogens, 10(11), e1004502. https://doi.org/https://doi.org/10.1371/journal.ppat.1004502
- Cali, T., Galli, C., Olivari, S., & Molinari, M. (2008). Segregation and rapid turnover of EDEM1 by an autophagy-like mechanism modulates standard ERAD and folding activities. Biochemical and Biophysical Research Communications, 371(3), 405–410. https://doi.org/https://doi.org/10.1016/j.bbrc.2008.04.098
- Chatr-Aryamontri, A., Ceol, A., Palazzi, L. M., Nardelli, G., Schneider, M. V., Castagnoli, L., & Cesareni, G. (2007). MINT: The molecular interaction database. Nucleic Acids Research, 35(Database issue), D572–D574. https://doi.org/https://doi.org/10.1093/nar/gkl950
- de Wilde, A. H., Wannee, K. F., Scholte, F. E. M., Goeman, J. J., Ten Dijke, P., Snijder, E. J., Kikkert, M., & van Hemert, M. J. (2015). A kinome-wide small interfering RNA screen identifies proviral and antiviral host factors in severe acute respiratory syndrome coronavirus replication, including double-stranded RNA-activated protein kinase and early secretory pathway proteins. Journal of Virology, 89(16), 8318–8333. https://doi.org/https://doi.org/10.1128/JVI.01029-15
- Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A. (2003). DAVID: Database for annotation, visualization, and integrated discovery. Genome Biology, 4(5), P3. https://doi.org/https://doi.org/10.1186/gb-2003-4-5-p3
- Doolittle, J. M., & Gomez, S. M. (2010). Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens. Virology Journal, 7, 82. https://doi.org/https://doi.org/10.1186/1743-422X-7-82
- Doolittle, J. M., & Gomez, S. M. (2011). Mapping protein interactions between Dengue virus and its human and insect hosts. PLoS Neglected Tropical Diseases, 5(2), e954. https://doi.org/https://doi.org/10.1371/journal.pntd.0000954
- Eifart, P., Ludwig, K., Böttcher, C., de Haan, C. A. M., Rottier, P. J. M., Korte, T., & Herrmann, A. (2007). Role of endocytosis and low pH in murine hepatitis virus strain A59 cell entry. Journal of Virology, 81(19), 10758–10768. https://doi.org/https://doi.org/10.1128/JVI.00725-07
- Elmore, S. (2007). Apoptosis: A review of programmed cell death. Toxicologic Pathology, 35(4), 495–516. https://doi.org/https://doi.org/10.1080/01926230701320337
- Fabregat, A., Sidiropoulos, K., Viteri, G., Forner, O., Marin-Garcia, P., Arnau, V., D'Eustachio, P., Stein, L., & Hermjakob, H. (2017). Reactome pathway analysis: A high-performance in-memory approach. BMC Bioinformatics, 18(1), 142. https://doi.org/https://doi.org/10.1186/s12859-017-1559-2
- Fujiwara, T., Oda, K., Yokota, S., Takatsuki, A., & Ikehara, Y. (1988). Brefeldin A causes disassembly of the golgi complex and accumulation of secretory proteins in the endoplasmic reticulum. The Journal of Biological Chemistry, 263(34), 18545–18552. https://doi.org/https://doi.org/10.1016/S0021-9258(19)81393-5
- Gadotti, A. C., de Castro Deus, M., Telles, J. P., Wind, R., Goes, M., Garcia Charello Ossoski, R., de Padua, A. M., de Noronha, L., Moreno-Amaral, A., Baena, C. P., & Tuon, F. F. (2020). IFN-γ is an independent risk factor associated with mortality in patients with moderate and severe COVID-19 infection. Virus Research, 289, 198171. https://doi.org/https://doi.org/10.1016/j.virusres.2020.198171
- Galluzzi, L., Vitale, I., Aaronson, S. A., Abrams, J. M., Adam, D., Agostinis, P., Alnemri, E. S., Altucci, L., Amelio, I., Andrews, D. W., Annicchiarico-Petruzzelli, M., Antonov, A. V., Arama, E., Baehrecke, E. H., Barlev, N. A., Bazan, N. G., Bernassola, F., Bertrand, M. J. M., Bianchi, K., … Kroemer, G. (2018). Molecular mechanisms of cell death: Recommendations of the Nomenclature Committee on Cell Death 2018. Cell Death and Differentiation, 25(3), 486–541. https://doi.org/https://doi.org/10.1038/s41418-017-0012-4
- Goel, R., Harsha, H. C., Pandey, A., & Prasad, T. S. (2012). Human protein reference database and human proteinpedia as resources for phosphoproteome analysis. Molecular Biosystems, 8(2), 453–463. https://doi.org/https://doi.org/10.1039/c1mb05340j
- Gordon, D. E., Jang, G. M., Bouhaddou, M., Xu, J., Obernier, K., White, K. M., O’Meara, M. J., Rezelj, V. V., Guo, J. Z., Swaney, D. L., Tummino, T. A., Hüttenhain, R., Kaake, R. M., Richards, A. L., Tutuncuoglu, B., Foussard, H., Batra, J., Haas, K., Modak, M., … Krogan, N. J. (2020). A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature, 583(7816), 459–468. https://doi.org/https://doi.org/10.1038/s41586-020-2286-9
- Graham, R. L., Donaldson, E. F., & Baric, R. S. (2013). A decade after SARS: Strategies for controlling emerging coronaviruses. Nature Reviews. Microbiology, 11(12), 836–848. https://doi.org/https://doi.org/10.1038/nrmicro3143
- Hagemeijer, M. C., Monastyrska, I., Griffith, J., van der Sluijs, P., Voortman, J., van Bergen En Henegouwen, P. M., Vonk, A. M., Rottier, P. J. M., Reggiori, F., & de Haan, C. A. M. (2014). Membrane rearrangements mediated by coronavirus nonstructural proteins 3 and 4. Virology, 458–459, 125–135. https://doi.org/https://doi.org/10.1016/j.virol.2014.04.027
- Holm, L. (2019). Benchmarking fold detection by DaliLite v.5. Bioinformatics (Oxford, England), 35(24), 5326–5327. https://doi.org/https://doi.org/10.1093/bioinformatics/btz536
- Huang, I.C., Bosch, B. J., Li, F., Li, W., Lee, K. H., Ghiran, S., Vasilieva, N., Dermody, T. S., Harrison, S. C., Dormitzer, P. R., Farzan, M., Rottier, P. J. M., & Choe, H. (2006). SARS coronavirus, but not human coronavirus NL63, utilizes cathepsin L to infect ACE2-expressing cells. The Journal of Biological Chemistry, 281(6), 3198–3203. https://doi.org/https://doi.org/10.1074/jbc.M508381200
- Huang, Q., & Figueiredo-Pereira, M. E. (2010). Ubiquitin/proteasome pathway impairment in neurodegeneration: Therapeutic implications. Apoptosis: An International Journal on Programmed Cell Death, 15(11), 1292–1311. https://doi.org/https://doi.org/10.1007/s10495-010-0466-z
- Inoue, Y., Tanaka, N., Tanaka, Y., Inoue, S., Morita, K., Zhuang, M., Hattori, T., & Sugamura, K. (2007). Clathrin-dependent entry of severe acute respiratory syndrome coronavirus into target cells expressing ACE2 with the cytoplasmic tail deleted. Journal of Virology, 81(16), 8722–8729. https://doi.org/https://doi.org/10.1128/JVI.00253-07
- Jackson, R. J., Hellen, C. U., & Pestova, T. V. (2010). The mechanism of eukaryotic translation initiation and principles of its regulation. Nature Reviews. Molecular Cell Biology, 11(2), 113–127. https://doi.org/https://doi.org/10.1038/nrm2838
- Klumperman, J., Locker, J. K., Meijer, A., Horzinek, M. C., Geuze, H. J., & Rottier, P. J. (1994). Coronavirus M proteins accumulate in the Golgi complex beyond the site of virion budding. Journal of Virology, 68(10), 6523–6534. https://doi.org/https://doi.org/10.1128/JVI.68.10.6523-6534.1994
- Knoops, K., Kikkert, M., Worm, S. H. E. v. d., Zevenhoven-Dobbe, J. C., van der Meer, Y., Koster, A. J., Mommaas, A. M., & Snijder, E. J. (2008). SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum. PLoS Biology, 6(9), e226. https://doi.org/https://doi.org/10.1371/journal.pbio.0060226
- Ksiazek, T. G., Erdman, D., Goldsmith, C. S., Zaki, S. R., Peret, T., Emery, S., Tong, S., Urbani, C., Comer, J. A., Lim, W., Rollin, P. E., Dowell, S. F., Ling, A. E., Humphrey, C. D., Shieh, W.J., Guarner, J., Paddock, C. D., Rota, P., Fields, B., … Anderson, L. J. (2003). A novel coronavirus associated with severe acute respiratory syndrome. The New England Journal of Medicine, 348(20), 1953–1966. https://doi.org/https://doi.org/10.1056/NEJMoa030781
- Lamason, R. L., & Welch, M. D. (2017). Actin-based motility and cell-to-cell spread of bacterial pathogens. Current Opinion in Microbiology, 35, 48–57. https://doi.org/https://doi.org/10.1016/j.mib.2016.11.007
- Li, W., & Ye, Y. (2008). Polyubiquitin chains: Functions, structures, and mechanisms. Cellular and Molecular Life Sciences, 65(15), 2397–2406. https://doi.org/https://doi.org/10.1007/s00018-008-8090-6
- Liu, J., Liao, X., Qian, S., Yuan, J., Wang, F., Liu, Y., Wang, Z., Wang, F.S., Liu, L., & Zhang, Z. (2020). Community transmission of severe acute respiratory syndrome coronavirus 2, Shenzhen, China, 2020. Emerging Infectious Diseases, 26(6), 1320–1323. https://doi.org/https://doi.org/10.3201/eid2606.200239
- Masters, P. S. (2006). The molecular biology of coronaviruses. Advances in Virus Research, 66, 193–292. https://doi.org/https://doi.org/10.1016/S0065-3527(06)66005-3
- Mire, C. E., White, J. M., & Whitt, M. A. (2010). A spatio-temporal analysis of matrix protein and nucleocapsid trafficking during vesicular stomatitis virus uncoating. PLoS Pathogens, 6(7), e1000994. https://doi.org/https://doi.org/10.1371/journal.ppat.1000994
- Misumi, Y., Misumi, Y., Miki, K., Takatsuki, A., Tamura, G., & Ikehara, Y. (1986). Novel blockade by brefeldin A of intracellular transport of secretory proteins in cultured rat hepatocytes. The Journal of Biological Chemistry, 261(24), 11398–11403.
- Neveu, G., Barouch-Bentov, R., Ziv-Av, A., Gerber, D., Jacob, Y., & Einav, S. (2012). Identification and targeting of an interaction between a tyrosine motif within hepatitis C virus core protein and AP2M1 essential for viral assembly. PLoS Pathogens, 8(8), e1002845. https://doi.org/https://doi.org/10.1371/journal.ppat.1002845
- Otasek, D., Morris, J. H., Boucas, J., Pico, A. R., & Demchak, B. (2019). Cytoscape automation: Empowering workflow-based network analysis. Genome Biology, 20(1), 185. https://doi.org/https://doi.org/10.1186/s13059-019-1758-4
- Oughtred, R., Stark, C., Breitkreutz, B.-J., Rust, J., Boucher, L., Chang, C., Kolas, N., O'Donnell, L., Leung, G., McAdam, R., Zhang, F., Dolma, S., Willems, A., Coulombe-Huntington, J., Chatr-Aryamontri, A., Dolinski, K., & Tyers, M. (2019). The BioGRID interaction database: 2019 update. Nucleic Acids Research, 47(D1), D529–D541. https://doi.org/https://doi.org/10.1093/nar/gky1079
- Pal, R., Mumbauer, S., Hoke, G. M., Takatsuki, A., & Sarngadharan, M. G. (1991). Brefeldin A inhibits the processing and secretion of envelope glycoproteins of human immunodeficiency virus type 1. AIDS Research and Human Retroviruses, 7(8), 707–712. https://doi.org/https://doi.org/10.1089/aid.1991.7.707
- Pfefferle, S., Schöpf, J., Kögl, M., Friedel, C. C., Müller, M. A., Carbajo-Lozoya, J., Stellberger, T., von Dall'Armi, E., Herzog, P., Kallies, S., Niemeyer, D., Ditt, V., Kuri, T., Züst, R., Pumpor, K., Hilgenfeld, R., Schwarz, F., Zimmer, R., Steffen, I., … von Brunn, A. (2011). The SARS-coronavirus-host interactome: Identification of cyclophilins as target for pan-coronavirus inhibitors. PLoS Pathogens, 7(10), e1002331. https://doi.org/https://doi.org/10.1371/journal.ppat.1002331
- Rajasekharan, S., Rana, J., Gulati, S., Sharma, S. K., Gupta, V., & Gupta, S. (2013). Predicting the host protein interactors of Chandipura virus using a structural similarity -based approach. Pathogens and Disease, 69(1), 29–35. https://doi.org/https://doi.org/10.1111/2049-632X.12064
- Rana, J., Sreejith, R., Gulati, S., Bharti, I., Jain, S., & Gupta, S. (2013). Deciphering the host-pathogen protein interface in chikungunya virus-mediated sickness. Archives of Virology, 158(6), 1159–1172. https://doi.org/https://doi.org/10.1007/s00705-013-1602-1
- Romero-Brey, I., & Bartenschlager, R. (2016). Endoplasmic Reticulum: The favorite intracellular niche for viral replication and assembly. Viruses, 8(6), 160. https://doi.org/https://doi.org/10.3390/v8060160
- Schubert, U., Antón, L. C., Bacík, I., Cox, J. H., Bour, S., Bennink, J. R., Orlowski, M., Strebel, K., & Yewdell, J. W. (1998). CD4 glycoprotein degradation induced by human immunodeficiency virus type 1 Vpu protein requires the function of proteasomes and the ubiquitin-conjugating pathway. Journal of Virology, 72(3), 2280–2288. https://doi.org/https://doi.org/10.1128/JVI.72.3.2280-2288.1998
- Sun, X., Yau, V. K., Briggs, B. J., & Whittaker, G. R. (2005). Role of clathrin-mediated endocytosis during vesicular stomatitis virus entry into host cells. Virology, 338(1), 53–60. https://doi.org/https://doi.org/10.1016/j.virol.2005.05.006
- Tavakolpour, S., Rakhshandehroo, T., Wei, E. X., & Rashidian, M. (2020). Lymphopenia during the COVID-19 infection: What it shows and what can be learned. Immunology Letters, 225, 31–32. https://doi.org/https://doi.org/10.1016/j.imlet.2020.06.013
- Tay, M. Z., Poh, C. M., Rénia, L., MacAry, P. A., & Ng, L. F. P. (2020). The trinity of COVID-19: Immunity, inflammation and intervention. Nature Reviews. Immunology, 20(6), 363–374. https://doi.org/https://doi.org/10.1038/s41577-020-0311-8
- The Uniport Consortium. (2019). UniProt: A worldwide hub of protein knowledge. Nucleic Acids Research, 47, D506–D5015.
- Tiwari, R., de la Torre, J. C., McGavern, D. B., & Nayak, D. (2019). Beyond tethering the viral particles: Immunomodulatory functions of tetherin (BST-2). DNA and Cell Biology, 38(11), 1170–1177. https://doi.org/https://doi.org/10.1089/dna.2019.4777
- Tiwari, R., Mishra, A. R., Mikaeloff, F., Gupta, S., Mirazimi, A., Byrareddy, S. N., Neogi, U., & Nayak, D. (2020). In silico and in vitro studies reveal complement system drives coagulation cascade in SARS-CoV-2 pathogenesis. Computational and Structural Biotechnology Journal, 18, 3734–3744. https://doi.org/https://doi.org/10.1016/j.csbj.2020.11.005
- Urbe, S., Huber, L. A., Zerial, M., Tooze, S. A., & Parton, R. G. (1993). Rab11, a small GTPase associated with both constitutive and regulated secretory pathways in PC12 cells. FEBS Letters, 334(2), 175–182. https://doi.org/https://doi.org/10.1016/0014-5793(93)81707-7
- Uruno, T., Liu, J., Zhang, P., Fan, Y., Egile, C., & Li, R. (2001). Activation of Arp2/3 complex-mediated actin polymerization by cortactin. Nature Cell Biology, 3, 259–266. https://doi.org/https://doi.org/10.1038/35060051
- V’kovski, P., Gerber, M., Kelly, J., Pfaender, S., Ebert, N., Braga Lagache, S., Simillion, C., Portmann, J., Stalder, H., Gaschen, V., Bruggmann, R., Stoffel, M. H., Heller, M., Dijkman, R., & Thiel, V. (2019). Determination of host proteins composing the microenvironment of coronavirus replicase complexes by proximity-labeling. eLife, 8, e42037. https://doi.org/https://doi.org/10.7554/eLife.42037
- V’kovski, P., Kratzel, A., Steiner, S., Stalder, H., & Thiel, V. (2020). Coronavirus biology and replication: Implications for SARS-CoV-2. Nature Reviews Microbiology, 1–16.
- van der Hoek, L. (2007). Human coronaviruses: What do they cause? Antiviral Therapy, 12(4 Pt B), 651–658.
- von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P., & Snel, B. (2003). STRING: A database of predicted functional associations between proteins. Nucleic Acids Research, 31(1), 258–261.
- Wang, Y., Zhang, D., Du, G., Du, R., Zhao, J., Jin, Y., Fu, S., Gao, L., Cheng, Z., Lu, Q., Hu, Y., Luo, G., Wang, K., Lu, Y., Li, H., Wang, S., Ruan, S., Yang, C., Mei, C., … Wang, C. (2020). Remdesivir in adults with severe COVID-19: A randomised, double-blind, placebo-controlled, multicentre trial. Lancet (London, England), 395(10236), 1569–1578. https://doi.org/https://doi.org/10.1016/S0140-6736(20)31022-9
- Wilkinson, K. D. (1995). Roles of ubiquitinylation in proteolysis and cellular regulation. Annual Review of Nutrition, 15, 161–189. https://doi.org/https://doi.org/10.1146/annurev.nu.15.070195.001113
- Wolff, G., Melia, C. E., Snijder, E. J., & Bárcena, M. (2020). Double-membrane vesicles as platforms for viral replication. Trends in Microbiology, 28(12), 1022–1033. https://doi.org/https://doi.org/10.1016/j.tim.2020.05.009
- Wong, C. K., Lam, C. W. K., Wu, A. K. L., Ip, W. K., Lee, N. L. S., Chan, I. H. S., Lit, L. C. W., Hui, D. S. C., Chan, M. H. M., Chung, S. S. C., & Sung, J. J. Y. (2004). Plasma inflammatory cytokines and chemokines in severe acute respiratory syndrome. Clinical & Experimental Immunology, 136(1), 95–103. https://doi.org/https://doi.org/10.1111/j.1365-2249.2004.02415.x
- Xiong, Y., Liu, Y., Cao, L., Wang, D., Guo, M., Jiang, A., Guo, D., Hu, W., Yang, J., Tang, Z., Wu, H., Lin, Y., Zhang, M., Zhang, Q., Shi, M., Liu, Y., Zhou, Y., Lan, K., & Chen, Y. (2020). Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients. Emerging Microbes & Infections, 9(1), 761–770. https://doi.org/https://doi.org/10.1080/22221751.2020.1747363
- Yao, Z., Zheng, Z., Wu, K., & Junhua, Z. (2020). Immune environment modulation in pneumonia patients caused by coronavirus: SARS-CoV, MERS-CoV and SARS-CoV-2. Aging, 12(9), 7639–7651. https://doi.org/https://doi.org/10.18632/aging.103101
- Zhang, C., Zheng, W., Huang, X., Bell, E. W., Zhou, X., & Zhang, Y. (2020). Protein structure and sequence reanalysis of 2019-nCoV genome refutes snakes as its intermediate host and the unique similarity between its spike protein insertions and HIV-1. Journal of Proteome Research, 19(4), 1351–1360. https://doi.org/https://doi.org/10.1021/acs.jproteome.0c00129
- Zhao, Q., Meng, M., Kumar, R., Wu, Y., Huang, J., Deng, Y., Weng, Z., & Yang, L. (2020). Lymphopenia is associated with severe coronavirus disease 2019 (COVID-19) infections: A systemic review and meta-analysis. International Journal of Infectious Diseases, 96, 131–135. https://doi.org/https://doi.org/10.1016/j.ijid.2020.04.086