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Articles

Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan

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Pages 221-236 | Received 16 Jan 2020, Accepted 17 Jan 2020, Published online: 28 Jan 2020

References

  • Chan JF, To KK, Tse H, et al. Interspecies transmission and emergence of novel viruses: lessons from bats and birds. Trends Microbiol. 2013 Oct;21(10):544–555. doi: 10.1016/j.tim.2013.05.005
  • Cheng VC, Lau SK, Woo PC, et al. Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection. Clin Microbiol Rev. 2007 Oct;20(4):660–694. doi: 10.1128/CMR.00023-07
  • Chan JF, Lau SK, To KK, et al. Middle East respiratory syndrome coronavirus: another zoonotic betacoronavirus causing SARS-like disease. Clin Microbiol Rev. 2015 Apr;28(2):465–522. doi: 10.1128/CMR.00102-14
  • Woo PC, Lau SK, Chu CM, et al. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol. 2005 Jan;79(2):884–895. doi: 10.1128/JVI.79.2.884-895.2005
  • Peiris JS, Lai ST, Poon LL, et al. Yuen KY; SARS study group. coronavirus as a possible cause of severe acute respiratory syndrome. Lancet. 2003 Apr 19;361(9366):1319–1325. doi: 10.1016/S0140-6736(03)13077-2
  • Yeung ML, Yao Y, Jia L, et al. MERS coronavirus induces apoptosis in kidney and lung by upregulating Smad7 and FGF2. Nat Microbiol. 2016 Feb 22;1:16004. doi: 10.1038/nmicrobiol.2016.4
  • World Health Organization. Novel coronavirus. [cited 2020 Jan 16]. Available from: https://www.who.int/westernpacific/emergencies/novel-coronavirus.
  • World Health Organization. Novel Coronavirus – Thailand (ex-China). [cited 2020 Jan 16]. Available from: https://www.who.int/csr/don/14-january-2020-novel-coronavirus-thailand-ex-china/en/.
  • South China Morning Post. Wuhan pneumonia: Japan confirms Chinese man had new coronavirus. [cited 2020 Jan 16]. Available from https://www.scmp.com/news/asia/east-asia/article/3046301/wuhan-pneumonia-japan-confirms-first-case-new-china-coronavirus.
  • Huang C, Wang Y, Li X, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020. DOI: https://doi.org/10.1016/S0140-6736(20)30183-5. [Epub ahead of print]
  • 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. DOI: https://doi.org/10.1016/S0140-6736(20)30154-9 [Epub ahead of print].
  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425.
  • Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985 Jul;39(4):783–791. doi: 10.1111/j.1558-5646.1985.tb00420.x
  • Zuckerkandl E, Pauling L. Evolutionary divergence and convergence in proteins. In: V Bryson, HJ Vogel, editors. Evolving genes and proteins. New York: Academic Press; 1965. p. 97–166.
  • Kumar S, Stecher G, Li M, et al. MEGA x: Molecular evolutionary Genetics analysis across computing platforms. Mol Biol Evol. 2018 Jun 1;35(6):1547–1549. doi: 10.1093/molbev/msy096
  • Buchan DWA, Jones DT. The PSIPRED protein analysis Workbench: 20 years on. Nucleic Acids Res. 2019;47(W1):W402–W407. doi: 10.1093/nar/gkz297
  • Wang Q, Qi J, Yuan Y, et al. Bat origins of MERS-CoV supported by bat coronavirus HKU4 usage of human receptor CD26. Cell Host Microbe. 2014 Sep 10;16(3):328–337. doi: 10.1016/j.chom.2014.08.009
  • Xia S, Yan L, Xu W, et al. A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike. Sci Adv. 2019 Apr 10;5(4):eaav4580. doi: 10.1126/sciadv.aav4580
  • Yount B, Roberts RS, Sims AC, et al. Severe acute respiratory syndrome coronavirus group-specific open reading frames encode nonessential functions for replication in cell cultures and mice. J Virol. 2005 Dec;79(23):14909–14922. doi: 10.1128/JVI.79.23.14909-14922.2005
  • Khan S, Fielding BC, Tan TH, et al. Over-expression of severe acute respiratory syndrome coronavirus 3b protein induces both apoptosis and necrosis in Vero E6 cells. Virus Res. 2006 Dec;122(1-2):20–27. doi: 10.1016/j.virusres.2006.06.005
  • Kopecky-Bromberg SA, Martinez-Sobrido L, Frieman M, et al. Severe acute respiratory syndrome coronavirus open reading frame (orf) 3b, orf 6, and nucleocapsid proteins function as interferon antagonists. J Virol. 2007 Jan;81(2):548–557. doi: 10.1128/JVI.01782-06
  • Zhou P, Li H, Wang H, et al. Bat severe acute respiratory syndrome-like coronavirus ORF3b homologues display different interferon antagonist activities. J Gen Virol. 2012 Feb;93(Pt 2):275–281. doi: 10.1099/vir.0.033589-0
  • Song HD, Tu CC, Zhang GW, et al. Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2430–2435. doi: 10.1073/pnas.0409608102
  • Oostra M, de Haan CA, Rottier PJ. The 29-nucleotide deletion present in human but not in animal severe acute respiratory syndrome coronaviruses disrupts the functional expression of open reading frame 8. J Virol. 2007;81:13876–13888. doi: 10.1128/JVI.01631-07
  • 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 Oct;89(20):10532–10547. doi: 10.1128/JVI.01048-15
  • 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
  • Yang D, Leibowitz JL. The structure and functions of coronavirus genomic 3’ and 5’ ends. Virus Res. 2015 Aug 3;206:120–133. doi: 10.1016/j.virusres.2015.02.025