1. Wu, F, Zhao, S, Yu, B, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579:265-269. doi:10.1038/s41586-020-2008-3.
Google Scholar | Crossref | Medline2. Masters, PS. The molecular biology of coronaviruses. Adv Virus Res. 2006;66:193-292. doi:10.1016/S0065-3527(06)66005-3.
Google Scholar | Crossref | Medline3. Marra, MA, Jones, SJM, Astell, CR, et al. The genome sequence of the SARS-associated coronavirus. Science. 2003;300:1399-1404. doi:10.1126/science.1085953.
Google Scholar | Crossref | Medline | ISI4. Rota, PA, Oberste, MS, Monroe, SS, et al. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science. 2003;300:1394-1399. doi:10.1126/science.1085952.
Google Scholar | Crossref | Medline | ISI5. Thiel, V, Ivanov, KA, Putics, Á, et al. Mechanisms and enzymes involved in SARS coronavirus genome expression. J Gen Virol. 2003;84:2305-2315. doi:10.1099/vir.0.19424-0.
Google Scholar | Crossref | Medline | ISI6. Liu, DX, Fung, TS, Chong, KKL, Shukla, A, Hilgenfeld, R. Accessory proteins of SARS-CoV and other coronaviruses. Antiviral Res. 2014;109:97-109. doi:10.1016/j.antiviral.2014.06.013.
Google Scholar | Crossref | Medline7. Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403-410.
Google Scholar | Crossref | Medline | ISI8. Arya, R, Kumari, S, Pandey, B, et al. Structural insights into SARS-CoV-2 proteins. J Mol Biol. 2020;433:166725. doi:10.1016/j.jmb.2020.11.024.
Google Scholar | Crossref | Medline9. Romano, M, Ruggiero, A, Squeglia, F, Maga, G, Berisio, R. A structural view of SARS-CoV-2 RNA replication machinery: RNA synthesis, proofreading and final capping. Cells. 2020;9:1267. doi:10.3390/cells9051267.
Google Scholar | Crossref10. Hussain, S, Pan, J, Chen, Y, et al. Identification of novel subgenomic RNAs and noncanonical transcription initiation signals of severe acute respiratory syndrome coronavirus. J Virol. 2005;79:5288-5295. doi:10.1128/jvi.79.9.5288-5295.2005.
Google Scholar | Crossref | Medline11. Gosert, R, Kanjanahaluethai, A, Egger, D, Bienz, K, Baker, SC. RNA replication of mouse hepatitis virus takes place at double-membrane vesicles. J Virol. 2002;76:3697-3708. doi:10.1128/jvi.76.8.3697-3708.2002.
Google Scholar | Crossref | Medline12. Prentice, E, Jerome, WG, Yoshimori, T, Mizushima, N, Denison, MR. Coronavirus replication complex formation utilizes components of cellular autophagy. J Biol Chem. 2004;279:10136-10141. doi:10.1074/jbc.M306124200.
Google Scholar | Crossref | Medline13. van der Meer, Y, Snijder, EJ, Dobbe, JC, et al. Localization of mouse hepatitis virus nonstructural proteins and RNA synthesis indicates a role for late endosomes in viral replication. J Virol. 1999;73:7641-7657. doi:10.1128/jvi.73.9.7641-7657.1999.
Google Scholar | Crossref | Medline14. Narayanan, K, Huang, C, Lokugamage, K, et al. Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells. J Virol. 2008;82:4471-4479. doi:10.1128/jvi.02472-07.
Google Scholar | Crossref | Medline15. Yang, H, Xie, W, Xue, X, et al. Design of wide-spectrum inhibitors targeting coronavirus main proteases. PLoS Biol. 2005;3:e324. doi:10.1371/journal.pbio.0030324.
Google Scholar16. Minskaia, E, Hertzig, T, Gorbalenya, AE, et al. Discovery of an RNA virus 3′→5′ exoribonuclease that is critically involved in coronavirus RNA synthesis. Proc Natl Acad Sci USA. 2006;103:5108-5113. doi:10.1073/pnas.0508200103.
Google Scholar | Crossref | Medline17. Snijder, EJ, Bredenbeek, PJ, Dobbe, JC, 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. 2003;331:991-1004. doi:10.1016/S0022-2836(03)00865-9.
Google Scholar | Crossref | Medline | ISI18. Ivanov, KA, Thiel, V, Dobbe, JC, van der Meer, Y, Snijder, EJ, Ziebuhr, J. Multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase. J Virol. 2004;78:5619-5632. doi:10.1128/jvi.78.11.5619-5632.20304.
Google Scholar | Crossref | Medline19. Decroly, E, Debarnot, C, Ferron, F, et al. Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2′-o-methyltransferase nsp10/nsp16 complex. PLoS Pathog. 2011;7:e1002059. doi:10.1371/journal.ppat.1002059.
Google Scholar | Crossref | Medline20. Chen, Y, Su, C, Ke, M, et al. Biochemical and structural insights into the mechanisms of SARS coronavirus RNA ribose 2′-O-methylation by nsp16/nsp10 protein complex. PLoS Pathog. 2011;7:e1002294. doi:10.1371/journal.ppat.1002294.
Google Scholar | Crossref21. Wathelet, MG, Orr, M, Frieman, MB, Baric, RS. Severe acute respiratory syndrome coronavirus evades antiviral signaling: role of nsp1 and rational design of an attenuated strain. J Virol. 2007;81:11620-11633. doi:10.1128/jvi.00702-07.
Google Scholar | Crossref | Medline22. Kumar, R, Verma, H, Singhvi, N, et al. Comparative genomic analysis of rapidly evolving SARS-CoV-2 reveals mosaic pattern of phylogeographical distribution. mSystems. 2020;5:e00505-20. doi:10.1128/mSystems.00505-20.
Google Scholar | Crossref23. Ziebuhr, J, Snijder, EJ, Gorbalenya, AE. Virus-encoded proteinases and proteolytic processing in the Nidovirales. J Gen Virol. 2000;81:853-879. doi:10.1099/0022-1317-81-4-853.
Google Scholar | Crossref | Medline | ISI24. Corum, J, Zimmer, C. Bad news wrapped in protein: inside the coronavirus genome A string of RNA. The New York Times. April 3, 2020. https://www.nytimes.com/interactive/2020/04/03/science/coronavirus-genome-bad-news-wrapped-in-protein.html.
Google Scholar25. Zhai, Y, Sun, F, Li, X, et al. Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer. Nat Struct Mol Biol. 2005;12:980-986. doi:10.1038/nsmb999.
Google Scholar | Crossref | Medline26. Egloff, MP, Ferron, F, Campanacci, V, et al. The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world. Proc Natl Acad Sci USA. 2004;101:3792-3796. doi:310.1073/pnas.0307877101.
Google Scholar | Crossref | Medline27. Kirchdoerfer, RN, Ward, AB. Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors. Nat Commun. 2019;10:2342. doi:10.1038/s41467-019-10280-3.
Google Scholar | Crossref | Medline28. Adedeji, AO, Marchand, B, Te Velthuis, AJ, et al. Mechanism of nucleic acid unwinding by SARS-CoV helicase. PLoS ONE. 2012;7:e36521. doi:10.1371/journal.pone.0036521.
Google Scholar | Crossref | Medline29. Ma, Y, Wu, L, Shaw, N, et al. Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex. Proc Natl Acad Sci USA. 2015;112:9436-9441. doi:10.1073/pnas.1508686112.
Google Scholar | Crossref | Medline | ISI30. Bhardwaj, K, Guarino, L, Kao, CC. The severe acute respiratory syndrome coronavirus Nsp15 protein is an endoribonuclease that prefers manganese as a cofactor. J Virol. 2004;78:12218-12224. doi:10.1128/jvi.78.22.12218-12224.2004.
Google Scholar | Crossref | Medline31. Aouadi, W, Blanjoie, A, Vasseur, J-J, Debart, F, Canard, B, Decroly, E. Binding of the methyl donor S-adenosyl-l-methionine to middle east respiratory syndrome coronavirus 2′-O-methyltransferase nsp16 promotes recruitment of the allosteric activator nsp10. J Virol. 2017;91:e02217-16. doi:10.1128/jvi.02217-16.
Google Scholar | Crossref32. Vilar, S, Isom, DG. One year of SARS-CoV-2: how much has the virus changed? Biology (Basel). 2021;10:91. doi:10.3390/biology10020091.
Google Scholar | Medline33. Connor, RF, Roper, RL. Unique SARS-CoV protein nsp1: bioinformatics, biochemistry and potential effects on virulence. Trends Microbiol. 2007;15:51-53. doi:10.1016/j.tim.2006.12.005.
Google Scholar | Crossref | Medline34. Narayanan, K, Ramirez, SI, Lokugamage, KG, Makino, S. Coronavirus nonstructural protein 1: common and distinct functions in the regulation of host and viral gene expression. Virus Res. 2015;202:89-100. doi:10.1016/j.virusres.2014.11.019.
Google Scholar | Crossref | Medline35. Clark, LK, Green, TJ, Petit, CM. Structure of nonstructural protein 1 from SARS-CoV-2. J Virol. 2021;95:e02019-20. doi:10.1128/jvi.02019-20.
Google Scholar | Crossref | Medline36. Schubert, K, Karousis, ED, Jomaa, A, et al. SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation. Nat Struct Mol Biol. 2020;27:959-966.
Google Scholar | Crossref | Medline37. Angeletti, S, Benvenuto, D, Bianchi, M, Giovanetti, M, Pascarella, S, Ciccozzi, M. COVID-2019: the role of the nsp2 and nsp3 in its pathogenesis. J Med Virol. 2020;92:584-588. doi:10.1002/jmv.25719.
Google Scholar | Crossref | Medline38. Graham, RL, Sims, AC, Brockway, SM, Baric, RS, Denison, MR. The nsp2 replicase proteins of murine hepatitis virus and severe acute respiratory syndrome coronavirus are dispensable for viral replication. J Virol. 2005;79:13399-13411. doi:10.1128/jvi.79.21.13399-13411.2005.
Google Scholar | Crossref | Medline39. Harcourt, BH, Jukneliene, D, Kanjanahaluethai, A, et al. Identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity. J Virol. 2004;78:13600-13612. doi:10.1128/jvi.78.24.13600-13612.2004.
Google Scholar | Crossref | Medline | ISI40. Schiller, JJ, Kanjanahaluethai, A, Baker, SC. Processing of the coronavirus MHV-JHM polymerase polyprotein: identification of precursors and proteolytic products spanning 400 kilodaltons of ORF1a. Virology. 1998;242:288-302. doi:10.1006/viro.1997.9010.
Google Scholar | Crossref | Medline41. Denison, MR, Zoltick, PW, Hughes, SA, et al. Intracellular processing of the N-terminal ORF 1a proteins of the coronavirus MHV-A59 requires multiple proteolytic events. Virology. 1992;189:274-284. doi:10.1016/0042-6822(92)90703-r. http://huji-primo.hosted.exlibrisgroup.com/openurl/972HUJI/972HUJI_SP?sid=EMBASE&sid=EMBASE&issn=00426822&id=doi:10.1016%2F0042-6822%2892%2990703-R&atitle=Intracellular+processing+of+the+N-terminal+ORF+1a+proteins+of+the+coronavirus+MHV-A59+requires+multiple+proteolytic+events&stitle=VIROLOGY&title=Virology&volume=189&issue=1&spage=274&epage=284&aulast=Denison&aufirst=M.R.&auinit=M.R.&aufull=Denison+M.R.&coden=VIRLA&isbn=&pages=274-284&date=1992&auinit1=M&auini.
Google Scholar42. Yang, H, Yang, M, Ding, Y, et al. The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proc Natl Acad Sci USA. 2003;100:13190-13195. doi:10.1073/pnas.1835675100.
Google Scholar | Crossref | Medline | ISI43. Tan, J, Verschueren, KHG, Anand, K, et al. pH-dependent conformational flexibility of the SARS-CoV main proteinase (M(pro)) dimer: molecular dynamics simulations and multiple X-ray structure analyses. J Mol Biol. 2005;354:25-40. doi:10.1016/j.jmb.2005.09.012.
Google Scholar | Crossref | Medline44. Shi, J, Song, J. The catalysis of the SARS 3C-like protease is under extensive regulation by its extra domain. FEBS J. 2006;273:1035-1045. doi:10.1111/j.1742-4658.2006.05130.x.
Google Scholar | Crossref | Medline45. Anand, K, Palm, GJ, Mesters, JR, Siddell, SG, Ziebuhr, J, Hilgenfeld, R. Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra α-helical domain. EMBO J. 2002;21:3213-3224. doi:10.1093/emboj/cdf327.
Google Scholar | Crossref | Medline46. Lim, L, Shi, J, Mu, Y, Song, J. Dynamically-driven enhancement of the catalytic machinery of the SARS 3C-like protease by the S284-T285-I286/A mutations on the extra domain. PLoS ONE. 2014;9:e101941. doi:10.1371/journal.pone.0101941.
Google Scholar | Crossref47. Neuman, BW. Bioinformatics and functional analyses of coronavirus nonstructural proteins involved in the formation of replicative organelles. Antiviral Res. 2016;135:97-107. doi:10.1016/j.antiviral.2016.10.005.
Google Scholar | Crossref | Medline48. Barretto, N, Jukneliene, D, Ratia, K, Chen, Z, Mesecar, AD, Baker, SC. The papain-like protease of severe acute respiratory syndrome coronavirus has deubiquitinating activity. J Virol. 2005;79:15189-15198. doi:10.1128/jvi.79.24.15189-15198.2005.
Google Scholar | Crossref |