Structural analysis of SARS-Cov-2 nonstructural protein 1 polymorphisms found in the Brazilian Amazon

1. WHO . Weekly Operational Update on COVID-19, Emergency Situational Updates, 13 February. World Health Organization, 2021
Google Scholar2. Sabino, EC, Buss, LF, Carvalho, MPS, Prete, CA, Crispim, MAE, Fraiji, NA, Pereira, RHM, Parag, KV, Da Silva Peixoto, P, Kraemer, MUG, Oikawa, MK, Salomon, T, Cucunuba, ZM, Castro, MC, De Souza Santos, AA, Nascimento, VH, Pereira, HS, Ferguson, NM, Pybus, OG, Kucharski, A, Busch, MP, Dye, C, Faria, NR. Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence. Lancet 2021; 397:452–5
Google Scholar | Crossref | Medline3. Naveca, F, Nascimento, V, Souza, V, Corado, A, Nascimento, F, Silva, G, Costa, Á, Duarte, D, Pessoa, K, Mejía, M, Brandão, M, Gonçalves, JM, Costa, L, Sampaio, CD, Barros, V, Silva, D, Mattos, M, Pontes, T, Abdalla, G, Santos, L, Arantes, J, Dezordi, I, Siqueira, F, Wallau, M, Resende, G, Delatorre, P, Gräff, E, Bello, TG. COVID-19 epidemic in the Brazilian state of Amazonas was driven by long-term persistence of endemic SARS-CoV-2 lineages and the recent emergence of the new variant of concern P.1. Res Square 2021. DOI: 10.21203/rs.3.rs-275494/v1
Google Scholar4. FIOCRUZ/FVS-AM . Nota Técnica Conjunta N° 09. 2021
Google Scholar5. Naveca, F, da Costa, C, Nascimento, V, Souza, V, Corado, A, Nascimento, F, Costa, A, Duarte, D, Silva , G, Mejía, M, Pessoa, K, Gonçalves, L, Brandão, MJ, Jesus, M, Pinto, R, Silva, M, Mattos, T, Abdalla, L, Santos, JH, Costa-Filho, R, Wallau, GL, Siqueira, MM, Delatorre E, E, Gräf, T, Bello, G, Resende, PC. SARS-CoV-2 reinfection by the new variant of concern (VOC) P.1 in Amazonas, Brazil. 2021. https://virological.org/t/sars-cov-2-reinfection-by-the-new-variant-ofconcern-voc-p-1-in-amazonas-brazil/596 (accessed Feb 20, 2021).
Google Scholar6. Min, YQ, Mo, Q, Wang, J, Deng, F, Wang, H, Ning, YJ. SARS-CoV-2 nsp1: bioinformatics, potential structural and functional features, and implications for drug/vaccine designs. Front Microbiol 2020; 11:587317
Google Scholar | Crossref | Medline7. Schubert, K, Karousis, ED, Jomaa, A, Scaiola, A, Echeverria, B, Gurzeler, LA, Leibundgut, M, Thiel, V, Mühlemann, O, Ban, N. SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation. Nat Struct Mol Biol 2020; 27:959–66
Google Scholar | Crossref | Medline8. Xia, H, Cao, Z, Xie, X, Zhang, X, Chen, JY, Wang, H, Menachery, VD, Rajsbaum, R, Shi, PY. Evasion of type I interferon by SARS-CoV-2. Cell Rep 2020; 33:108234
Google Scholar | Crossref | Medline9. de Lima Menezes, G, da Silva, RA. Identification of potential drugs against SARS-CoV-2 non-structural protein 1 (NSP1). J Biomol Struct Dyn 2020;1–11. DOI: 10.1080/07391102.2020.1792992
Google Scholar10. Sharma, A, Tiwari, V, Sowdhamini, R. Computational search for potential COVID-19 drugs from FDA-approved drugs and small molecules of natural origin identifies several anti-virals and plant products. J Biosci 2020; 45:100. DOI: 10.1007/s12038-020-00069-8
Google Scholar | Crossref11. Shen, Z, Zhang, G, Yang, Y, Li, M, Yang, S, Peng, G. Lysine 164 is critical for SARS-CoV-2 Nsp1 inhibition of host gene expression. J Gen Virol 2021; 102:001513. DOI: 10.1099/jgv.0.001513.
Google Scholar | Crossref12. Loureiro, CL, Jaspe, RC, D´Angelo, P, Zambrano, JL, Rodriguez, L, Alarcon, V, Delgado, M, Aguilar, M, Garzaro, D, Rangel, HR, Pujol, FH. SARS-CoV-2 genetic diversity in Venezuela: predominance of D614G variants and analysis of one outbreak. PLoS One 2021; 16:e0247196
Google Scholar | Crossref | Medline13. Nascimento, VAD, Corado, ALG, Nascimento, FOD, Costa, Á, Kad Duarte, DCG, Luz, SLB, Gonçalves, LMF, Jesus, MS, Costa, CFD, Delatorre, E, Naveca, FG. Genomic and phylogenetic characterisation of an imported case of SARS-CoV-2 in Amazonas state, Brazil. Mem Inst Oswaldo Cruz 2020; 115:e200310
Google Scholar | Crossref | Medline14. Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–10
Google Scholar | Crossref | Medline | ISI15. Webb, B, Sali, A. Comparative protein structure modeling using modeller. Curr Protoc Bioinformatics 2016; 54:5.6.1–5.6.37
Google Scholar | Crossref16. Guex, N, Peitsch, MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997; 18:2714–23
Google Scholar | Crossref | Medline | ISI17. Pettersen, EF, Goddard, TD, Huang, CC, Couch, GS, Greenblatt, DM, Meng, EC, Ferrin, TE. UCSF chimera – a visualization system for exploratory research and analysis. J Comput Chem 2004; 25:1605–12
Google Scholar | Crossref | Medline | ISI18. Clark, LK, Green, TJ, Petit, CM. Structure of nonstructural protein 1 from SARS-CoV-2. J Virol 2021; 95:e02019–20
Google Scholar | Crossref | Medline19. Yuan, S, Peng, L, Park, JJ, Hu, Y, Devarkar, SC, Dong, MB, Shen, Q, Wu, S, Chen, S, Lomakin, IB, Xiong, Y. Nonstructural protein 1 of SARS-CoV-2 is a potent pathogenicity factor redirecting host protein synthesis machinery toward viral RNA. Mol Cell 2020; 80:1055–66.e6
Google Scholar | Crossref | Medline20. Anger, AM, Armache, JP, Berninghausen, O, Habeck, M, Subklewe, M, Wilson, DN, Beckmann, R. Structures of the human and drosophila 80S ribosome. Nature 2013; 497:80–5
Google Scholar | Crossref | Medline21. Laskowski, RA, MacArthur, MW, Moss, DS, Thornton, JM. PROCHECK: a program to check the stereochemical quality of protein structures. Crystallogr 1993; 26:283–91
Google Scholar | Crossref22. Semper, C, Watanabe, N, Savchenko, A. Structural characterization of nonstructural protein 1 from SARS-CoV-2. iScience 2021; 24:101903
Google Scholar | Crossref | Medline23. Gavenonis, J, Sheneman, BA, Siegert, TR, Eshelman, MR, Kritzer, JA. Comprehensive analysis of loops at protein-protein interfaces for macrocycle design. Nat Chem Biol 2014; 10:716–22
Google Scholar | Crossref | Medline24. Shi, M, Wang, L, Fontana, P, Vora, S, Zhang, Y, Fu, TM, Lieberman, J, Wu, H. SARS-CoV-2 Nsp1 suppresses host but not viral translation through a bipartite mechanism. SSRN Electron J 2020. DOI: 10.1101/2020.09.18.302901
Google Scholar | Medline25. Benedetti, F, Snyder, GA, Giovanetti, M, Angeletti, S, Gallo, RC, Ciccozzi, M, Zella, D. Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1. J Transl Med 2020; 18:329
Google Scholar | Crossref | Medline26. Thoms, M, Buschauer, R, Ameismeier, M, Koepke, L, Denk, T, Hirschenberger, M, Kratzat, H, Hayn, M, Mackens-Kiani, T, Cheng, J, Straub, JH, Stürzel, CM, Fröhlich, T, Berninghausen, O, Becker, T, Kirchhoff, F, Sparrer, KMJ, Beckmann, R. Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science 2020; 369:1249–55
Google Scholar | Crossref | Medline27. Almeida, MS, Johnson, MA, Herrmann, T, Geralt, M, Wüthrich, K. Novel beta-barrel fold in the nuclear magnetic resonance structure of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus. J Virol 2007; 81:3151–61
Google Scholar | Crossref | Medline28. Kucirka, LM, Lauer, SA, Laeyendecker, O, Boon, D, Lessler, J. Variation in False-Negative rate of reverse transcriptase polymerase chain Reaction-Based SARS-CoV-2 tests by time since exposure. Ann Intern Med 2020; 173:262–7
Google Scholar | Crossref | Medline29. 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
Google Scholar | Crossref | Medline

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