A tug-of-war between severe acute respiratory syndrome coronavirus 2 and host antiviral defence: lessons from other pathogenic viruses

References

• Woo PC, Lau SK, Lam CS, et al. Discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J Virol. 2012;86:3995–4008. doi: 10.1128/JVI.06540-11
   PubMed Web of Science ®Google Scholar
• Kendall EJ, Bynoe ML, Tyrrell DA. Virus isolations from common colds occurring in a residential school. Br Med J. 1962;2:82–86. doi: 10.1136/bmj.2.5297.82
   PubMed Web of Science ®Google Scholar
• McIntosh K, Dees JH, Becker WB, et al. Recovery in tracheal organ cultures of novel viruses from patients with respiratory disease. Proc Natl Acad Sci USA. 1967;57:933–940. doi: 10.1073/pnas.57.4.933
   PubMed Web of Science ®Google Scholar
• McIntosh K. Coronaviruses: a comparative review. Curr Top Microbiol Immunol. 1974;63:85–129.
   Google Scholar
• Pene F, Merlat A, Vabret A, et al. Coronavirus 229E-related pneumonia in immunocompromised patients. Clin Infect Dis. 2003;37:929–932. doi: 10.1086/377612
   PubMed Web of Science ®Google Scholar
• Bonavia A, Arbour N, Yong VW, et al. Infection of primary cultures of human neural cells by human coronaviruses 229E and OC43. J Virol. 1997;71:800–806. doi: 10.1128/JVI.71.1.800-806.1997
   PubMed Web of Science ®Google Scholar
• Perlman S, Netland J. Coronaviruses post-SARS: update on replication and pathogenesis. Nat Rev Microbiol. 2009;7:439–450. doi:10.1038/nrmicro2147.
   PubMed Web of Science ®Google Scholar
• Stein RA. Super-spreaders in infectious diseases. Int J Infect Dis. 2011;15:e510–e513. doi: 10.1016/j.ijid.2010.06.020
   PubMed Web of Science ®Google Scholar
• Peiris JS, Lai ST, Poon LL, et al. Coronavirus as a possible cause of severe acute respiratory syndrome. Lancet. 2003;361:1319–1325. doi: 10.1016/S0140-6736(03)13077-2
   PubMed Web of Science ®Google Scholar
• Leung WK, To KF, Chan PK, et al. Enteric involvement of severe acute respiratory syndrome-associated coronavirus infection. Gastroenterology. 2003;125:1011–1017. doi: 10.1016/j.gastro.2003.08.001
   PubMed Web of Science ®Google Scholar
• Xu J, Zhong S, Liu J, et al. Detection of severe acute respiratory syndrome coronavirus in the brain: potential role of the chemokine mig in pathogenesis. Clin Infect Dis. 2005;41:1089–1096. doi: 10.1086/444461
   PubMed Web of Science ®Google Scholar
• Desmyter J, Melnick JL, Rawls WE. Defectiveness of interferon production and of rubella virus interference in a line of African green monkey kidney cells (Vero). J Virol. 1968;2:955–961. doi: 10.1128/JVI.2.10.955-961.1968
   PubMed Web of Science ®Google Scholar
• Zornetzer GA, Frieman MB, Rosenzweig E, et al. Transcriptomic analysis reveals a mechanism for a prefibrotic phenotype in STAT1 knockout mice during severe acute respiratory syndrome coronavirus infection. J Virol. 2010;84:11297–11309. doi: 10.1128/JVI.01130-10
   PubMed Web of Science ®Google Scholar
• van der Hoek L, Pyrc K, Jebbink MF, et al. Identification of a new human coronavirus. Nat Med. 2004;10:368–373. doi: 10.1038/nm1024
   PubMed Web of Science ®Google Scholar
• Lau SK, Woo PC, Yip CC, et al. Coronavirus HKU1 and other coronavirus infections in Hong Kong. J Clin Microbiol. 2006;44:2063–2071. doi: 10.1128/JCM.02614-05
   PubMed Web of Science ®Google Scholar
• van der Hoek L, Sure K, Ihorst G, et al. Croup is associated with the novel coronavirus NL63. PLoS Med. 2005;2:e240. doi: 10.1371/journal.pmed.0020240
   PubMed Web of Science ®Google Scholar
• Wang Y, Li X, Liu W, et al. Discovery of a subgenotype of human coronavirus NL63 associated with severe lower respiratory tract infection in China, 2018. Emerg Microbes Infect. 2020;9:246–255. doi: 10.1080/22221751.2020.1717999
   PubMed Web of Science ®Google Scholar
• Zaki AM, van Boheemen S, Bestebroer TM, et al. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med. 2012;367:1814–1820. doi: 10.1056/NEJMoa1211721
   PubMed Web of Science ®Google Scholar
• Zumla A, Hui DS, Perlman S. Middle East respiratory syndrome. Lancet. 2015;386:995–1007. doi: 10.1016/S0140-6736(15)60454-8
   PubMed Web of Science ®Google Scholar
• Zhou J, Li C, Zhao G, et al. Human intestinal tract serves as an alternative infection route for Middle East respiratory syndrome coronavirus. Sci Adv. 2017;3:eaao4966. doi: 10.1126/sciadv.aao4966
   PubMed Web of Science ®Google Scholar
• Yeung ML, Yao Y, Jia L, et al. MERS coronavirus induces apoptosis in kidney and lung by upregulating Smad7 and FGF2. Nat Microbiol. 2016;1:16004. doi: 10.1038/nmicrobiol.2016.4
   PubMed Web of Science ®Google Scholar
• Ogando NS, Ferron F, Decroly E, et al. The curious case of the nidovirus exoribonuclease: its role in RNA synthesis and replication fidelity. Front Microbiol. 2019; 10:1813. doi: 10.3389/fmicb.2019.01813
   PubMed Web of Science ®Google Scholar
• Collins ND, Beck AS, Widen SG, et al. Structural and nonstructural genes contribute to the genetic diversity of RNA viruses. mBio. 2018;9:e01871–18. doi: 10.1128/mBio.01871-18
   PubMed Web of Science ®Google Scholar
• Zhao Z, Li H, Wu X, et al. Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evol Biol. 2004;4:21. doi: 10.1186/1471-2148-4-21
   PubMed Web of Science ®Google Scholar
• Jiang S, Du L, Shi Z. An emerging coronavirus causing pneumonia outbreak in Wuhan, China: calling for developing therapeutic and prophylactic strategies. Emerg Microbes Infect. 2020;9:275–277. doi: 10.1080/22221751.2020.1723441
   PubMed Web of Science ®Google Scholar
• Vijgen L, Keyaerts E, Moës E, et al. Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event. J Virol. 2005;79:1595–1604. doi: 10.1128/JVI.79.3.1595-1604.2005
   PubMed Web of Science ®Google Scholar
• Corman VM, Muth D, Niemeyer D, et al. Hosts and sources of endemic human coronaviruses. Adv Virus Res. 2018;100:163–188. doi: 10.1016/bs.aivir.2018.01.001
   PubMed Web of Science ®Google Scholar
• Guan Y, Zheng BJ, He YQ, et al. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science. 2003;302:276–278. doi: 10.1126/science.1087139
   PubMed Web of Science ®Google Scholar
• Tu C, Crameri G, Kong X, et al. Antibodies to SARS coronavirus in civets. Emerg Infect Dis. 2004;10:2244–2248. doi: 10.3201/eid1012.040520
   PubMed Web of Science ®Google Scholar
• Lau SK, Woo PC, Li KS, et al. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci USA. 2005;102:14040–14045. doi: 10.1073/pnas.0506735102
   PubMed Web of Science ®Google Scholar
• Li W, Shi Z, Yu M, et al. Bats are natural reservoirs of SARS-like coronaviruses. Science. 2005;310:676–679. doi: 10.1126/science.1118391
   PubMed Web of Science ®Google Scholar
• Ge XY, Li JL, Yang XL, et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature. 2013;503:535–538. doi: 10.1038/nature12711
   PubMed Web of Science ®Google Scholar
• Adney DR, van Doremalen N, Brown VR, et al. Replication and shedding of MERS-CoV in upper respiratory tract of inoculated dromedary camels. Emerg Infect Dis. 2014;20:1999–2005. doi: 10.3201/eid2012.141280
   PubMed Web of Science ®Google Scholar
• Kandeil A, Gomaa M, Shehata M, et al. Middle East respiratory syndrome coronavirus infection in non-camelid domestic mammals. Emerg Microbes Infect. 2019;8:103–108. doi: 10.1080/22221751.2018.1560235
   PubMed Web of Science ®Google Scholar
• Zhou P, Yang X, Wang X, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020. doi:10.1038/s41586-020-2012-7.
   Web of Science ®Google Scholar
• Huang C, Wang Y, Li X, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020;395:497–506. doi: 10.1016/S0140-6736(20)30183-5
   PubMed Web of Science ®Google Scholar
• Liu P, Chen W, Chen JP. Viral metagenomics revealed Sendai virus and coronavirus infection of Malayan pangolins (Manis javanica). Viruses. 2019;11:E979. doi: 10.3390/v11110979
   PubMed Web of Science ®Google Scholar
• Calisher CH, Childs JE, Field HE, et al. Bats: important reservoir hosts of emerging viruses. Clin Microbiol Rev. 2006;19:531–545. doi: 10.1128/CMR.00017-06
   PubMed Web of Science ®Google Scholar
• Zhang G, Cowled C, Shi Z, et al. Comparative analysis of bat genomes provides insight into the evolution of flight and immunity. Science. 2013;339:456–460. doi: 10.1126/science.1230835
   PubMed Web of Science ®Google Scholar
• Ahn M, Anderson DE, Zhang Q, et al. Dampened NLRP3-mediated inflammation in bats and implications for a special viral reservoir host. Nat Microbiol. 2019;4:789–799. doi: 10.1038/s41564-019-0371-3
   PubMed Web of Science ®Google Scholar
• Zhou P, Tachedjian M, Wynne JW, et al. Contraction of the type I IFN locus and unusual constitutive expression of IFN-α in bats. Proc Natl Acad Sci USA. 2016;113:2696–2701. doi: 10.1073/pnas.1518240113
   PubMed Web of Science ®Google Scholar
• Xie J, Li Y, Shen X, et al. Dampened STING-dependent interferon activation in bats. Cell Host Microbe. 2018;23:297–301. doi: 10.1016/j.chom.2018.01.006
   PubMed Web of Science ®Google Scholar
• Pavlovich SS, Lovett SP, Koroleva G, et al. The Egyptian rousette genome reveals unexpected features of bat antiviral immunity. Cell. 2018;173:1098–1110. doi: 10.1016/j.cell.2018.03.070
   PubMed Web of Science ®Google Scholar
• Sharp PM, Hahn BH. Origins of HIV and the AIDS pandemic. Cold Spring Harb Perspect Med. 2011;1:a006841. doi: 10.1101/cshperspect.a006841
   PubMed Web of Science ®Google Scholar
• Buffalo CZ, Stürzel CM, Heusinger E, et al. Structural basis for tetherin antagonism as a barrier to zoonotic lentiviral transmission. Cell Host Microbe. 2019;26:359–368. doi: 10.1016/j.chom.2019.08.002
   PubMed Web of Science ®Google Scholar
• Chan CP, Kok KH, Jin DY. Human T-cell leukemia virus type 1 infection and adult T-cell leukemia. Adv Exp Med Biol. 2017;1018:147–166. doi: 10.1007/978-981-10-5765-6_9
   PubMed Web of Science ®Google Scholar
• Mahieux R, Gessain A. HTLV-3/STLV-3 and HTLV-4 viruses: discovery, epidemiology, serology and molecular aspects. Viruses. 2011;3:10740–10790. doi: 10.3390/v3071074
   Web of Science ®Google Scholar
• Chan JF, Kok KH, Zhu Z, et al. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg Microbes Infect. 2020;9:221–236. doi: 10.1080/22221751.2020.1719902
   PubMed Web of Science ®Google Scholar
• Wong LY, Lui PY, Jin DY. A molecular arms race between host innate antiviral response and emerging human coronaviruses. Virol Sin. 2016;31:12–23. doi: 10.1007/s12250-015-3683-3
   PubMed Web of Science ®Google Scholar
• Shi CS, Nabar NR, Huang NN, et al. SARS-Coronavirus open reading frame-8b triggers intracellular stress pathways and activates NLRP3 inflammasomes. Cell Death Discov. 2019;5:101. doi: 10.1038/s41420-019-0181-7
   PubMed Web of Science ®Google Scholar
• Chan JF, Yuan S, Kok KH, et al. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet. 2020;395:513–524. doi: 10.1016/S0140-6736(20)30154-9
   Web of Science ®Google Scholar
• Shen Z, Ning F, Zhou W, et al. Superspreading SARS events, Beijing, 2003. Emerg Infect Dis. 2004;10:256–260. doi: 10.3201/eid1002.030732
   PubMed Web of Science ®Google Scholar
• Holshue ML, DeBolt C, Lindquist S, et al. First case of 2019 novel coronavirus in the United States. N Engl J Med. 2020. doi:10.1056/NEJMoa2001191.
   Google Scholar
• Bai Y, Yao L, Wei T, et al. Presumed asymptomatic carrier transmission of COVID-19. JAMA. 2020. doi:10.1001/jama.2020.1585.
   PubMed Web of Science ®Google Scholar
• Heimdal I, Moe N, Krokstad S, et al. Human coronavirus in hospitalized children with respiratory tract infections: a 9-year population-based study from Norway. J Infect Dis. 2019;219:1198–1206. doi: 10.1093/infdis/jiy646
   PubMed Web of Science ®Google Scholar
• Lau SK, Feng Y, Chen H, et al. Severe acute respiratory syndrome (SARS) coronavirus ORF8 protein is acquired from SARS-related coronavirus from greater horseshoe bats through recombination. J Virol. 2015;89:10532–10547. doi: 10.1128/JVI.01048-15
   PubMed Web of Science ®Google Scholar
• Huynh J, Li S, Yount B, et al. Evidence supporting a zoonotic origin of human coronavirus strain NL63. J Virol. 2012;86:12816–12825. doi: 10.1128/JVI.00906-12
   PubMed Web of Science ®Google Scholar
• Higgins PG, Phillpotts RJ, Scott GM, et al. Intranasal interferon as protection against experimental respiratory coronavirus infection in volunteers. Antimicrob Agents Chemother. 1983;24:713–715. doi: 10.1128/AAC.24.5.713
   PubMed Web of Science ®Google Scholar
• Mesel-Lemoine M, Millet J, Vidalain PO, et al. A human coronavirus responsible for the common cold massively kills dendritic cells but not monocytes. J Virol. 2012;86:7577–7587. doi: 10.1128/JVI.00269-12
   PubMed Web of Science ®Google Scholar
• Siu KL, Yeung ML, Kok KH, et al. Middle East respiratory syndrome coronavirus 4a protein is a double-stranded RNA-binding protein that suppresses PACT-induced activation of RIG-I and MDA5 in the innate antiviral response. J Virol. 2014;88:4866–4876. doi: 10.1128/JVI.03649-13
   PubMed Web of Science ®Google Scholar
• Siu KL, Kok KH, Ng MH, et al. Severe acute respiratory syndrome coronavirus M protein inhibits type I interferon production by impeding the formation of TRAF3.TANK.TBK1/IKKε complex. J Biol Chem. 2009;284:16202–16209. doi: 10.1074/jbc.M109.008227
   PubMed Web of Science ®Google Scholar
• Lui PY, Wong LY, Fung CL, et al. Middle East respiratory syndrome coronavirus M protein suppresses type I interferon expression through the inhibition of TBK1-dependent phosphorylation of IRF3. Emerg Microbes Infect. 2016;5:e39. doi: 10.1038/emi.2016.33
   PubMed Web of Science ®Google Scholar
• Shen Z, Wang G, Yang Y, et al. A conserved region of nonstructural protein 1 from alphacoronaviruses inhibits host gene expression and is critical for viral virulence. J Biol Chem. 2019;294:13606–13618. doi: 10.1074/jbc.RA119.009713
   PubMed Web of Science ®Google Scholar
• Tohya Y, Narayanan K, Kamitani W, et al. Suppression of host gene expression by nsp1 proteins of group 2 bat coronaviruses. J Virol. 2009;83:5282–5288. doi: 10.1128/JVI.02485-08
   PubMed Web of Science ®Google Scholar
• Drappier M, Michiels T. Inhibition of the OAS/RNase L pathway by viruses. Curr Opin Virol. 2015;15:19–26. doi: 10.1016/j.coviro.2015.07.002
   PubMed Web of Science ®Google Scholar
• Forni D, Cagliani R, Clerici M, et al. Molecular evolution of human coronavirus genomes. Trends Microbiol. 2017;25:35–48. doi: 10.1016/j.tim.2016.09.001
   PubMed Web of Science ®Google Scholar
• Thornbrough JM, Jha BK, Yount B, et al. Middle East respiratory syndrome coronavirus NS4b protein inhibits host RNase L activation. mBio. 2016;7:e00258. doi: 10.1128/mBio.00258-16
   PubMed Web of Science ®Google Scholar
• Danthi P. Viruses and the diversity of cell death. Annu Rev Virol. 2016;3:533–553. doi: 10.1146/annurev-virology-110615-042435
   PubMed Web of Science ®Google Scholar
• Upton JW, Chan FK. Staying alive: cell death in antiviral immunity. Mol Cell. 2014;54:273–280. doi: 10.1016/j.molcel.2014.01.027
   PubMed Web of Science ®Google Scholar
• Richard A, Tulasne D. Caspase cleavage of viral proteins, another way for viruses to make the best of apoptosis. Cell Death Dis. 2012;3:e277. doi: 10.1038/cddis.2012.18
   PubMed Web of Science ®Google Scholar
• He L, Ding Y, Zhang Q, et al. Expression of elevated levels of pro-inflammatory cytokines in SARS-CoV-infected ACE2+ cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS. J Pathol. 2006;210:288–297. doi: 10.1002/path.2067
   PubMed Web of Science ®Google Scholar
• Tang BS, Chan KH, Cheng VC, et al. Comparative host gene transcription by microarray analysis early after infection of the Huh7 cell line by severe acute respiratory syndrome coronavirus and human coronavirus 229E. J Virol. 2005;79:6180–6193. doi: 10.1128/JVI.79.10.6180-6193.2005
   PubMed Web of Science ®Google Scholar
• Siu KL, Yuen KS, Castaño-Rodriguez C, et al. Severe acute respiratory syndrome coronavirus ORF3a protein activates the NLRP3 inflammasome by promoting TRAF3-dependent ubiquitination of ASC. FASEB J. 2019;33:8865–8877. doi: 10.1096/fj.201802418R
   PubMed Web of Science ®Google Scholar
• Nieto-Torres JL, DeDiego ML, Verdiá-Báguena C, et al. Severe acute respiratory syndrome coronavirus envelope protein ion channel activity promotes virus fitness and pathogenesis. PLoS Pathog. 2014;10:e1004077. doi: 10.1371/journal.ppat.1004077
   PubMed Web of Science ®Google Scholar
• DeDiego ML, Nieto-Torres JL, Regla-Nava JA, et al. Inhibition of NF-κB-mediated inflammation in severe acute respiratory syndrome coronavirus-infected mice increases survival. J Virol. 2014;88:913–924. doi: 10.1128/JVI.02576-13
   PubMed Web of Science ®Google Scholar
• Nieto-Torres JL, Verdiá-Báguena C, Jimenez-Guardeño JM, et al. Severe acute respiratory syndrome coronavirus E protein transports calcium ions and activates the NLRP3 inflammasome. Virology. 2015;485:330–339. doi: 10.1016/j.virol.2015.08.010
   PubMed Web of Science ®Google Scholar
• Chen IY, Moriyama M, Chang MF, et al. Severe acute respiratory syndrome coronavirus viroporin 3a activates the NLRP3 inflammasome. Front Microbiol. 2019;10:50. doi: 10.3389/fmicb.2019.00050
   PubMed Web of Science ®Google Scholar
• Chau TN, Lee KC, Yao H, et al. SARS-associated viral hepatitis caused by a novel coronavirus: report of three cases. Hepatology. 2004;39:302–310. doi: 10.1002/hep.20111
   PubMed Web of Science ®Google Scholar
• Tan YX, Tan TH, Lee MJ, et al. Induction of apoptosis by the severe acute respiratory syndrome coronavirus 7a protein is dependent on its interaction with the Bcl-XL protein. J Virol. 2007;81:6346–6355. doi: 10.1128/JVI.00090-07
   PubMed Web of Science ®Google Scholar
• Yue Y, Nabar NR, Shi CS, et al. SARS-coronavirus open reading frame-3a drives multimodal necrotic cell death. Cell Death Dis. 2018;9:904. doi: 10.1038/s41419-018-0917-y
   PubMed Web of Science ®Google Scholar