Conclusion - We Know About the Characteristics of Viruses?

We Know About the Characteristics of Viruses?

2.7 Conclusion

The novel SARS-CoV-2 is still raging world- wide, with a corrupting impact on human health.

Specific antiviral drugs and efficient commercial

vaccines for controlling and eradicating SARS- CoV- 2 are at the preliminary stage of development. These developments require knowledge of essential viral characteristics. In the context of this chapter, we reviewed the classification of coronaviruses, compared the genome architecture of human coronaviruses, discussed the molecular features of the SARS-CoV-2 genome and proteins, and depicted SARS-CoV-2 life cycles. These are crucial for further understanding of the evolutionary and pathogenic mechanisms of SARS-CoV-2 and developing better strategies for diagnosis, prevention, and treatment of COVID-19.

References

Abdul-Rasool S, Fielding BC (2010) Understanding human coronavirus HCoV-NL63. Open Virol J 4:76–

84. https://doi.org/10.2174/1874357901004010076 Adedeji AO, Marchand B, Te Velthuis AJW, Snijder EJ,

Weiss S, Eoff RL, Singh K, Sarafianos SG (2012a) Mechanism of nucleic acid unwinding by SARS-CoV helicase. PLoS One 7(5):e36521–e36521. https://doi.

org/10.1371/journal.pone.0036521

Adedeji AO, Singh K, Sarafianos SG (2012b) Structural and biochemical basis for the difference in the helicase activity of two different constructs of SARS-CoV helicase. Cell Mol Biol (Noisy-le-Grand) 58(1):114–121 Alhammad YMO, Kashipathy MM, Roy A, Johnson

DK, McDonald P, Battaile KP, Gao P, Lovell S, Fehr AR (2020) The SARS-CoV-2 conserved macro- domain is a highly efficient ADP-ribosylhydrolase enzyme. bioRxiv:2020.2005.2011.089375. https://doi.

org/10.1101/2020.05.11.089375

Angeletti S, Benvenuto D, Bianchi M, Giovanetti M, Pascarella S, Ciccozzi M (2020) COVID-2019:

the role of the nsp2 and nsp3 in its pathogenesis. J Med Virol 92(6):584–588. https://doi.org/10.1002/

jmv.25719

Assiri A, Al-Tawfiq JA, Al-Rabeeah AA, Al-Rabiah FA, Al-Hajjar S, Al-Barrak A, Flemban H, Al-Nassir WN, Balkhy HH, Al-Hakeem RF, Makhdoom HQ, Zumla AI, Memish ZA (2013) Epidemiological, demo- graphic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study. Lancet Infect Dis 13(9):752–761. https://doi.org/10.1016/

S1473- 3099(13)70204- 4

Benvenuto D, Angeletti S, Giovanetti M, Bianchi M, Pascarella S, Cauda R, Ciccozzi M, Cassone A (2020) Evolutionary analysis of SARS-CoV-2: how muta- tion of non-structural protein 6 (NSP6) could affect viral autophagy. J Infect. https://doi.org/10.1016/j.

jinf.2020.03.058

Bhardwaj K, Sun J, Holzenburg A, Guarino LA, Kao CC (2006) RNA recognition and cleavage by the SARS coronavirus endoribonuclease. J Mol Biol 361(2):243–

256. https://doi.org/10.1016/j.jmb.2006.06.021 Bianchi M, Benvenuto D, Giovanetti M, Angeletti S,

Ciccozzi M, Pascarella S (2020) Sars-CoV-2 envelope and membrane proteins: differences from closely related proteins linked to cross-species transmission?

Preprints

Bouvet M, Debarnot C, Imbert I, Selisko B, Snijder EJ, Canard B, Decroly E (2010) In vitro reconstitution of SARS-coronavirus mRNA cap methylation. PLoS Pathog 6(4):e1000863

Bouvet M, Imbert I, Subissi L, Gluais L, Canard B, Decroly E (2012) RNA 3′-end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp10/nsp14 exoribonuclease complex. Proc Natl Acad Sci 109(24):9372–9377.

https://doi.org/10.1073/pnas.1201130109

Burrell CJ, Howard CR, Murphy FA (2017) Chapter 31 – coronaviruses. In: Burrell CJ, Howard CR, Murphy FA (eds) Fenner and White’s medical virology, 5th edn. Academic, London, pp 437–446. https://doi.

org/10.1016/B978- 0- 12- 375156- 0.00031- X

Chan JF, Lau SK, To KK, Cheng VC, Woo PC, Yuen K-Y (2015) Middle East respiratory syndrome coronavirus:

another zoonotic betacoronavirus causing SARS-like disease. Clin Microbiol Rev 28(2):465–522

Clasman JR, Everett RK, Srinivasan K, Mesecar AD (2020) Decoupling deISGylating and deubiquitinating activities of the MERS virus papain-like protease.

Antivir Res 174:104661

Claverie J-M (2020) The likely role of de-mono-ADP- ribosylation of STAT1 by the SARS-CoV-2 nsp3 protein in the cytokine storm syndrome of COVID-19 Copertino Jr DC, Lima B, Duarte R, Wilkin T, Gulick R,

de Mulder Rougvie M, Nixon D (2020) Antiretroviral drug activity and potential for pre-exposure prophy- laxis against COVID-19 and HIV infection

Davidson AD, Williamson MK, Lewis S, Shoemark D, Carroll MW, Heesom K, Zambon M, Ellis J, Lewis PA, Hiscox JA, Matthews DA (2020) Characterisation of the transcriptome and proteome of SARS-CoV-2 using direct RNA sequencing and tandem mass spectrometry reveals evidence for a cell passage induced in-frame deletion in the spike glycoprotein that removes the furin-like cleavage site. bioRxiv:2020.2003.2022.002204. https://doi.

org/10.1101/2020.03.22.002204

Decroly E, Debarnot C, Ferron F, Bouvet M, Coutard B, Imbert I, Gluais L, Papageorgiou N, Sharff A, Bricogne G, Ortiz-Lombardia M, Lescar J, Canard B (2011) Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2’-O-methyltransferase nsp10/nsp16 complex. PLoS Pathog 7(5):e1002059–

e1002059. https://doi.org/10.1371/journal.

ppat.1002059

Dinesh DC, Chalupska D, Silhan J, Veverka V, Boura E (2020) Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphopro-

tein. bioRxiv:2020.2004.2002.022194. https://doi.

org/10.1101/2020.04.02.022194

Eckerle LD, Becker MM, Halpin RA, Li K, Venter E, Lu X, Scherbakova S, Graham RL, Baric RS, Stockwell TB, Spiro DJ, Denison MR (2010) Infidelity of SARS- CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing. PLoS Pathog 6(5):e1000896. https://doi.org/10.1371/journal.ppat.1000896

Egloff M-P, Malet H, Putics A, Heinonen M, Dutartre H, Frangeul A, Gruez A, Campanacci V, Cambillau C, Ziebuhr J (2006) Structural and functional basis for ADP-ribose and poly (ADP-ribose) binding by viral macro domains. J Virol 80(17):8493–8502

Elfiky A, Ibrahim N, Elshemey W (2020) Drug repurpos- ing against MERS CoV and SARS-COV-2 PLpro in silico

Frick DN, Virdi RS, Vuksanovic N, Dahal N, Silvaggi NR (2020) Molecular basis for ADP-ribose binding to the macro-X domain of SARS-CoV-2 Nsp3.

bioRxiv:2020.2003.2031.014639. https://doi.

org/10.1101/2020.03.31.014639

Gaunt ER, Hardie A, Claas ECJ, Simmonds P, Templeton KE (2010) Epidemiology and clinical presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 3 years using a novel multiplex real-time PCR method. J Clin Microbiol 48(8):2940–

2947. https://doi.org/10.1128/jcm.00636- 10

Graham RL, Baric RS (2010) Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission. J Virol 84(7):3134–3146.

https://doi.org/10.1128/jvi.01394- 09

Graham RL, Sims AC, Brockway SM, Baric RS, Denison MR (2005) The nsp2 replicase proteins of murine hepatitis virus and severe acute respiratory syndrome coronavirus are dispensable for viral replication. J Virol 79(21):13399–13411. https://doi.org/10.1128/

jvi.79.21.13399- 13411.2005

Gui M, Song W, Zhou H, Xu J, Chen S, Xiang Y, Wang X (2017) Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding. Cell Res 27(1):119–129

Guo H, Hu B-J, Yang X-L, Zeng L-P, Li B, Ouyang S-Y, Shi Z-L (2020) Evolutionary arms race between virus and host drives genetic diversity in bat SARS related coronavirus spike genes. bioRxiv:2020.2005.2013.093658.

https://doi.org/10.1101/2020.05.13.093658

Hillen HS, Kokic G, Farnung L, Dienemann C, Tegunov D, Cramer P (2020) Structure of replicating SARS- CoV- 2 polymerase. bioRxiv:2020.2004.2027.063180.

https://doi.org/10.1101/2020.04.27.063180

Hoffmann M, Kleine-Weber H, Schroeder S, Krüger N, Herrler T, Erichsen S, Schiergens TS, Herrler G, Wu N-H, Nitsche A, Müller MA, Drosten C, Pöhlmann S (2020) SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 181(2):271–280.e278. https://doi.

org/10.1016/j.cell.2020.02.052

Irigoyen N, Firth AE, Jones JD, Chung BY-W, Siddell SG, Brierley I (2016) High-resolution analysis of coronavirus gene expression by RNA sequencing and ribo- some profiling. PLoS Pathog 12(2)

Ivanov KA, Thiel V, Dobbe JC, van der Meer Y, Snijder EJ, Ziebuhr J (2004) Multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase. J Virol 78(11):5619–5632 Jin Z, Du X, Xu Y, Deng Y, Liu M, Zhao Y, Zhang B,

Li X, Zhang L, Peng C (2020a) Structure of M pro from SARS-CoV-2 and discovery of its inhibitors.

Nature:1–5

Jin Z, Zhao Y, Sun Y, Zhang B, Wang H, Wu Y, Zhu Y, Zhu C, Hu T, Du X (2020b) Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug Carmofur. Nat Struct Mol Biol:1–4

Jockusch S, Tao C, Li X, Anderson TK, Chien M, Kumar S, Russo JJ, Kirchdoerfer RN, Ju J (2020) Triphosphates of the two components in DESCOVY and TRUVADA are inhibitors of the SARS-CoV-2 polymerase. bioRxiv:2020.2004.2003.022939. https://

doi.org/10.1101/2020.04.03.022939

Kamitani W, Huang C, Narayanan K, Lokugamage KG, Makino S (2009) A two-pronged strategy to suppress host protein synthesis by SARS coronavirus Nsp1 protein. Nat Struct Mol Biol 16(11):1134

Kang S, Yang M, Hong Z, Zhang L, Huang Z, Chen X, He S, Zhou Z, Zhou Z, Chen Q, Yan Y, Zhang C, Shan H, Chen S (2020) Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites. Acta Pharm Sin B. https://doi.org/10.1016/j.apsb.2020.04.009 Kelly JA, Dinman JD (2020) Structural and func-

tional conservation of the programmed −1 ribosomal frameshift signal of SARS-CoV-2.

bioRxiv:2020.2003.2013.991083. https://doi.

org/10.1101/2020.03.13.991083

Kim D, Lee J-Y, Yang J-S, Kim JW, Kim VN, Chang H (2020a) The architecture of SARS-CoV-2 transcriptome. Cell 181(4):914–921.e910. https://doi.

org/10.1016/j.cell.2020.04.011

Kim Y, Jedrzejczak R, Maltseva NI, Wilamowski M, Endres M, Godzik A, Michalska K, Joachimiak A (2020b) Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2. Protein Sci n/a (n/a).

https://doi.org/10.1002/pro.3873

Kneller DW, Phillips G, O’Neill HM, Jedrzejczak R, Stols L, Langan P, Joachimiak A, Coates L, Kovalevsky A (2020) Structural plasticity of the SARS-CoV-2 3CL M pro active site cavity revealed by room temperature X-ray crystallography

Krafcikova P, Silhan J, Nencka R, Boura E (2020) Structural analysis of the SARS-CoV-2 methyltransferase complex involved in coronaviral RNA cap cre- ation. bioRxiv:2020.2005.2015.097980. https://doi.

org/10.1101/2020.05.15.097980

Ku Z, Ye X, Toa Salazar G, Zhang N, An Z (2020) Antibody therapies for the treatment of COVID-19.

Antibody Ther. https://doi.org/10.1093/abt/tbaa007

Li W, Zhang C, Sui J, Kuhn JH, Moore MJ, Luo S, Wong SK, Huang IC, Xu K, Vasilieva N (2005) Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2. EMBO J 24(8):1634–1643

Li J, Guo M, Tian X, Liu C, Wang X, Yang X, Wu P, Xiao Z, Qu Y, Yin Y, Fu J, Zhu Z, Liu Z, Peng C, Zhu T, Liang Q (2020) Virus-host interactome and proteomic survey of PMBCs from COVID-19 patients reveal potential virulence factors influencing SARS-CoV-2 pathogenesis. bioRxiv:2020.2003.2031.019216.

https://doi.org/10.1101/2020.03.31.019216

Liang Q, Li J, Guo M, Tian X, Liu C, Wang X, Yang X, Wu P, Xiao Z, Qu Y (2020) Virus-host interactome and proteomic survey of PMBCs from COVID-19 patients reveal potential virulence factors influencing SARS- CoV- 2 pathogenesis. bioRxiv

Ling R, Dai Y, Huang B, Huang W, Yu J, Lu X, Jiang Y (2020) In silico design of antiviral peptides targeting the spike protein of SARS-CoV-2. Peptides 130:170328.

https://doi.org/10.1016/j.peptides.2020.170328 Littler DR, Gully BS, Colson RN, Rossjohn J (2020)

Crystal structure of the SARS-CoV-2 non-structural protein 9, Nsp9. bioRxiv:2020.2003.2028.013920.

https://doi.org/10.1101/2020.03.28.013920

Liu P, Li L, Millership JJ, Kang H, Leibowitz JL, Giedroc DP (2007) A U-turn motif-containing stem-loop in the coronavirus 5′ untranslated region plays a functional role in replication. RNA 13(5):763–780. https://doi.

org/10.1261/rna.261807

Liu DX, Fung TS, Chong KK, Shukla A, Hilgenfeld R (2014) Accessory proteins of SARS-CoV and other coronaviruses. Antivir Res 109:97–109. https://doi.

org/10.1016/j.antiviral.2014.06.013

Liu C, Yang Y, Gao Y, Shen C, Ju B, Liu C, Tang X, Wei J, Ma X, Liu W (2020a) Viral architecture of SARS- CoV- 2 with post-fusion spike revealed by Cryo-EM.

bioRxiv

Liu Y, Hu G, Wang Y, Zhao X, Ji F, Ren W, Gong M, Ju X, Li C, Hong J, Zhu Y, Cai X, Wu J, Lan X, Xie Y, Wang X, Yuan Z, Zhang R, Ding Q (2020b) Functional and genetic analysis of viral receptor ACE2 ortho- logs reveals a broad potential host range of SARS- CoV- 2. bioRxiv:2020.2004.2022.046565. https://doi.

org/10.1101/2020.04.22.046565

Masters P, Perlman S (2013) Coronaviridae, pp 825–858.

Fields virology 1

Mehta P, McAuley DF, Brown M, Sanchez E, Tattersall RS, Manson JJ (2020) COVID-19: consider cytokine storm syndromes and immunosuppression. Lancet 395(10229):1033–1034

Mielech AM, Kilianski A, Baez-Santos YM, Mesecar AD, Baker SC (2014) MERS-CoV papain-like protease has deISGylating and deubiquitinating activities.

Virology 450–451:64–70. https://doi.org/10.1016/j.

virol.2013.11.040

Minskaia E, Hertzig T, Gorbalenya AE, Campanacci V, Cambillau C, Canard B, Ziebuhr J (2006) Discovery of an RNA virus 3′→5′ exoribonuclease that is critically involved in coronavirus RNA synthesis. Proc

Natl Acad Sci U S A 103(13):5108–5113. https://doi.

org/10.1073/pnas.0508200103

Mirza MU, Froeyen M (2020) Structural elucidation of SARS-CoV-2 vital proteins: computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase. J Pharm Anal.

https://doi.org/10.1016/j.jpha.2020.04.008

Navratil V, Lionnard L, Longhi S, Hardwick JM, Combet C, Aouacheria A (2020) The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein harbors a conserved BH3-like sequence.

bioRxiv:2020.2004.2009.033522. https://doi.

org/10.1101/2020.04.09.033522

Nomburg J, Meyerson M, DeCaprio JA (2020) Noncanonical junctions in subgenomic RNAs of SARS-CoV-2 lead to variant open reading frames.

bioRxiv:2020.2004.2028.066951. https://doi.

org/10.1101/2020.04.28.066951

Ogando NS, Ferron F, Decroly E, Canard B, Posthuma CC, Snijder EJ (2019) The curious case of the Nidovirus exoribonuclease: its role in RNA synthesis and replication fidelity. Front Microbiol 10(1813).

https://doi.org/10.3389/fmicb.2019.01813

Organization WH (2004) Summary of probable SARS cases with onset of illness from 1 November 2002 to 31 July 2003 based on data as of the 31 December 2003. Computer software] http://www.who.int/csr/

sars/country/table2004_04_21/en/index.html

Peiris J, Guan Y, Yuen K (2004) Severe acute respiratory syndrome. Nat Med 10(12):S88–S97

Pene F, Merlat A, Vabret A, Rozenberg F, Buzyn A, Dreyfus F, Cariou A, Freymuth F, Lebon P (2003) Coronavirus 229E-related pneumonia in immuno- compromised patients. Clin Infect Dis 37(7):929–932.

https://doi.org/10.1086/377612

Peng Q, Peng R, Yuan B, Zhao J, Wang M, Wang X, Wang Q, Sun Y, Fan Z, Qi J, Gao GF, Shi Y (2020) Structural and biochemical characterization of nsp12- nsp7- nsp8 core polymerase complex from COVID-19 virus. bioRxiv:2020.2004.2023.057265. https://doi.

org/10.1101/2020.04.23.057265

Putics A, Filipowicz W, Hall J, Gorbalenya AE, Ziebuhr J (2005) ADP-ribose-1″-monophosphatase: a conserved coronavirus enzyme that is dispensable for viral replication in tissue culture. J Virol 79(20):12721–12731 Pyrc K, Berkhout B, van der Hoek L (2007) The novel

human coronaviruses NL63 and HKU1. J Virol 81(7):3051–3057

Rangan R, Watkins AM, Kladwang W, Das R (2020a) De novo 3D models of SARS-CoV-2 RNA elements and small-molecule-binding RNAs to guide drug discovery. bioRxiv:2020.2004.2014.041962. https://doi.

org/10.1101/2020.04.14.041962

Rangan R, Zheludev IN, Das R (2020b) RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses.

bioRxiv:2020.2003.2027.012906. https://doi.

org/10.1101/2020.03.27.012906

Ratia K, Kilianski A, Baez-Santos YM, Baker SC, Mesecar A (2014) Structural basis for the ubiquitin-linkage

specificity and deISGylating activity of SARS-CoV papain-like protease. PLoS Pathog 10(5):e1004113 Romano M, Ruggiero A, Squeglia F, Maga G, Berisio R

(2020) A structural view at SARS-CoV-2 RNA replication machinery: RNA synthesis, proofreading and final capping

Rosas-Lemus M, Minasov G, Shuvalova L, Inniss NL, Kiryukhina O, Wiersum G, Kim Y, Jedrzejczak R, Maltseva NI, Endres M, Jaroszewski L, Godzik A, Joachimiak A, Satchell KJF (2020) The crystal structure of nsp10-nsp16 heterodimer from SARS- CoV- 2 in complex with S-adenosylmethionine.

bioRxiv:2020.2004.2017.047498. https://doi.

org/10.1101/2020.04.17.047498

Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle JP, Peñaranda S, Bankamp B, Maher K, Chen M-h, Tong S, Tamin A, Lowe L, Frace M, DeRisi JL, Chen Q, Wang D, Erdman DD, Peret TCT, Burns C, Ksiazek TG, Rollin PE, Sanchez A, Liffick S, Holloway B, Limor J, McCaustland K, Olsen- Rasmussen M, Fouchier R, Günther S, Osterhaus ADME, Drosten C, Pallansch MA, Anderson LJ, Bellini WJ (2003) Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300(5624):1394–1399. https://doi.

org/10.1126/science.1085952

Rut W, Lv Z, Zmudzinski M, Patchett S, Nayak D, Snipas SJ, El Oualid F, Huang TT, Bekes M, Drag M, Olsen SK (2020a) Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design. bioRxiv:2020.2004.2029.068890. https://doi.

org/10.1101/2020.04.29.068890

Rut W, Zmudzinski M, Lyu Z, Nayak D, Snipas SJ, Bekes M, Huang TT, Olsen SK, Drag M (2020b) Activity profiling of SARS-CoV-2-PLpro protease provides structural framework for anti-COVID-19 drug design. bioRxiv:2020.2004.2029.068890. https://doi.

org/10.1101/2020.04.29.068890

Saikatendu KS, Joseph JS, Subramanian V, Clayton T, Griffith M, Moy K, Velasquez J, Neuman BW, Buchmeier MJ, Stevens RC (2005) Structural basis of severe acute respiratory syndrome coronavirus ADP- ribose- 1 ″-phosphate dephosphorylation by a conserved domain of nsP3. Structure 13(11):1665–1675 Sakai Y, Kawachi K, Terada Y, Omori H, Matsuura Y,

Kamitani W (2017) Two-amino acids change in the nsp4 of SARS coronavirus abolishes viral replication. Virology 510:165–174. https://doi.org/10.1016/j.

virol.2017.07.019

Sarkar M, Saha S (2020) Structural insight into the putative role of novel SARS CoV-2 E protein in viral infection:

a potential target for LAV development and therapeutic strategies. bioRxiv:2020.2005.2011.088781.

https://doi.org/10.1101/2020.05.11.088781

Shang J, Wan Y, Luo C, Ye G, Geng Q, Auerbach A, Li F (2020a) Cell entry mechanisms of SARS-CoV-2. Proc Natl Acad Sci:202003138. https://doi.org/10.1073/

pnas.2003138117

Shang J, Wan Y, Luo C, Ye G, Geng Q, Auerbach A, Li F (2020b) Cell entry mechanisms of SARS-CoV-2. Proc Natl Acad Sci 117(21):11727–11734

Shi Z, Hu Z (2008) A review of studies on animal reservoirs of the SARS coronavirus. Virus Res 133(1):74–

87. https://doi.org/10.1016/j.virusres.2007.03.012 Shin D, Mukherjee R, Grewe D, Bojkova D, Baek K,

Bhattacharya A, Schulz L, Widera M, Mehdipour A, Tascher G (2020) Inhibition of papain-like protease PLpro blocks SARS-CoV-2 spread and promotes antiviral immunity

Shulla A, Heald-Sargent T, Subramanya G, Zhao J, Perlman S, Gallagher T (2011) A transmembrane ser- ine protease is linked to the severe acute respiratory syndrome coronavirus receptor and activates virus entry. J Virol 85(2):873–882

Song H-D, Tu C-C, Zhang G-W, Wang S-Y, Zheng K, Lei L-C, Chen Q-X, Gao Y-W, Zhou H-Q, Xiang H (2005) Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proc Natl Acad Sci 102(7):2430–2435

Tahir Ul Qamar M, Alqahtani SM, Alamri MA, Chen L-L (2020) Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medici- nal plants. J Pharm Anal. https://doi.org/10.1016/j.

jpha.2020.03.009

Taiaroa G, Rawlinson D, Featherstone L, Pitt M, Caly L, Druce J, Purcell D, Harty L, Tran T, Roberts J (2020) Direct RNA sequencing and early evolution of SARS- CoV- 2. bioRxiv

Tang T, Bidon M, Jaimes JA, Whittaker GR, Daniel S (2020) Coronavirus membrane fusion mechanism offers a potential target for antiviral development. Antivir Res 178:104792–104792. https://doi.

org/10.1016/j.antiviral.2020.104792

Tanner JA, Watt RM, Chai Y-B, Lu L-Y, Lin MC, Peiris JM, Poon LL, Kung H-F, Huang J-D (2003) The severe acute respiratory syndrome (SARS) coronavirus NTPase/helicase belongs to a distinct class of 5′ to 3′ viral helicases. J Biol Chem 278(41):39578–39582 Thomas S (2020) The structure of the membrane pro-

tein of SARS-CoV-2 resembles the sugar transporter semiSWEET

Thoms M, Buschauer R, Ameismeier M, Koepke L, Denk T, Hirschenberger M, Kratzat H, Hayn M, Mackens-Kiani T, Cheng J, Stürzel CM, Fröhlich T, Berninghausen O, Becker T, Kirchhoff F, Sparrer KMJ, Beckmann R (2020) Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. bioRxiv:2020.2005.2018.102467.

https://doi.org/10.1101/2020.05.18.102467

Vabret A, Mourez T, Gouarin S, Petitjean J, Freymuth F (2003) An outbreak of coronavirus OC43 respiratory infection in Normandy, France. Clin Infect Dis 36(8):985–989. https://doi.org/10.1086/374222 Viehweger A, Krautwurst S, Lamkiewicz K, Madhugiri

R, Ziebuhr J, Hölzer M, Marz M (2019) Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural vari-

ants and enables modification analysis. Genome Res 29(9):1545–1554

Walls AC, Tortorici MA, Snijder J, Xiong X, Bosch B-J, Rey FA, Veesler D (2017) Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion. Proc Natl Acad Sci 114(42):11157–11162

Walls AC, Park Y-J, Tortorici MA, Wall A, McGuire AT, Veesler D (2020) Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell

Wan Y, Shang J, Graham R, Baric RS, Li F (2020) Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus. J Virol 94(7). https://doi.

org/10.1128/JVI.00127- 20

Wang S, Chen S, Lu H, Zhang X, Tan Y, Ling Y, Lu G, Liu F, Yi Z, Jia X (2020a) Viral and host factors related to the clinic outcome of the SARS-CoV-2 infection Wang T, Du Z, Zhu F, Cao Z, An Y, Gao Y, Jiang B (2020b)

Comorbidities and multi-organ injuries in the treatment of COVID-19. Lancet 395(10228):e52. https://

doi.org/10.1016/S0140- 6736(20)30558- 4

Wang W, Xu Y, Gao R, Lu R, Han K, Wu G, Tan W (2020c) Detection of SARS-CoV-2 in different types of clinical specimens. JAMA. https://doi.org/10.1001/

jama.2020.3786

Watanabe Y, Allen JD, Wrapp D, McLellan JS, Crispin M (2020) Site-specific analysis of the SARS-CoV-2 gly- can shield. bioRxiv:2020.2003.2026.010322. https://

doi.org/10.1101/2020.03.26.010322

WHO (2020a) MERS-CoV case report. https://www.who.

int/emergencies/mers- cov/en/

WHO (2020b) SARS-CoV case report. https://

w w w . w h o . i n t / c s r / d o n / a r c h i v e / d i s e a s e / severe_acute_respiratory_syndrome/en/

Wilson L, Mckinlay C, Gage P, Ewart G (2004) SARS coronavirus E protein forms cation-selective ion chan- nels. Virology 330(1):322–331

Woo PC, Lau SK, Tsoi HW, Huang Y, Poon RW, Chu CM, Lee RA, Luk WK, Wong GK, Wong BH, Cheng VC, Tang BS, Wu AK, Yung RW, Chen H, Guan Y, Chan KH, Yuen KY (2005) Clinical and molecular epidemiological features of coronavirus HKU1-associated community-acquired pneumonia. J Infect Dis 192(11):1898–1907. https://doi.org/10.1086/497151 Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL,

Abiona O, Graham BS, McLellan JS (2020) Cryo-EM structure of the 2019-nCoV spike in the prefusion con- formation. Science 367(6483):1260–1263. https://doi.

org/10.1126/science.abb2507

Wu C, Liu Y, Yang Y, Zhang P, Zhong W, Wang Y, Wang Q, Xu Y, Li M, Li X, Zheng M, Chen L, Li H (2020a)

Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharm Sin B. https://doi.org/10.1016/j.

apsb.2020.02.008

Wu Y, Li C, Xia S, Tian X, Wang Z, Kong Y, Gu C, Zhang R, Tu C, Xie Y (2020b) Fully human single-domain antibodies against SARS-CoV-2. bioRxiv

Wu Y, Wang F, Shen C, Peng W, Li D, Zhao C, Li Z, Li S, Bi Y, Yang Y, Gong Y, Xiao H, Fan Z, Tan S, Wu G, Tan W, Lu X, Fan C, Wang Q, Liu Y, Zhang C, Qi J, Gao GF, Gao F, Liu L (2020c) A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2. Science:eabc2241.

https://doi.org/10.1126/science.abc2241

Xia S, Liu M, Wang C, Xu W, Lan Q, Feng S, Qi F, Bao L, Du L, Liu S, Qin C, Sun F, Shi Z, Zhu Y, Jiang S, Lu L (2020) Inhibition of SARS-CoV-2 (previously 2019- nCoV) infection by a highly potent pan- coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion.

Cell Res 30(4):343–355. https://doi.org/10.1038/

s41422- 020- 0305- x

Yang X, Yu Y, Xu J, Shu H, Ja X, Liu H, Wu Y, Zhang L, Yu Z, Fang M, Yu T, Wang Y, Pan S, Zou X, Yuan S, Shang Y (2020) Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, obser- vational study. Lancet Respir Med 8(5):475–481.

https://doi.org/10.1016/S2213- 2600(20)30079- 5 Yuan Y, Cao D, Zhang Y, Ma J, Qi J, Wang Q, Lu G, Wu

Y, Yan J, Shi Y (2017) Cryo-EM structures of MERS- CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains. Nat Commun 8:15092

Zhang L, Lin D, Sun X, Curth U, Drosten C, Sauerhering L, Becker S, Rox K, Hilgenfeld R (2020) Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors.

Science 368(6489):409–412. https://doi.org/10.1126/

science.abb3405

Zheng Y-Y, Ma Y-T, Zhang J-Y, Xie X (2020) COVID- 19 and the cardiovascular system. Nat Rev Cardiol 17(5):259–260

Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, Si HR, Zhu Y, Li B, Huang CL, Chen HD, Chen J, Luo Y, Guo H, Jiang RD, Liu MQ, Chen Y, Shen XR, Wang X, Zheng XS, Zhao K, Chen QJ, Deng F, Liu LL, Yan B, Zhan FX, Wang YY, Xiao GF, Shi ZL (2020) A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579(7798):270–273.

https://doi.org/10.1038/s41586- 020- 2012- 7

Dalam dokumen Book Coronavirus Disease - COVID-19 (Halaman 52-58)