1887

Abstract

The emergence and rapid worldwide spread of a novel pandemic of acute respiratory disease – eventually named coronavirus disease 2019 (COVID-19) by the World Health Organization (WHO) – across the human population has raised great concerns. It prompted a mobilization around the globe to study the underlying pathogen, a close relative of severe acute respiratory syndrome coronavirus (SARS-CoV) called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Numerous genome sequences of SARS-CoV-2 are now available and in-depth analyses are advancing. These will allow detailed characterization of sequence and protein functions, including comparative studies. Care should be taken when inferring function from sequence information alone, and reverse genetics systems can be used to unequivocally identify key features. For example, the molecular markers of virulence, host range and transmissibility of SARS-CoV-2 can be compared to those of related viruses in order to shed light on the biology of this emerging pathogen. Here, we summarize some recent insights from genomic studies and strategies for reverse genetics systems to generate recombinant viruses, which will be useful to investigate viral genome properties and evolution.

Funding
This study was supported by the:
  • , Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco
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/content/journal/jgv/10.1099/jgv.0.001458
2020-06-24
2020-10-20
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References

  1. Jin Y, Yang H, Ji W, Wu W, Chen S et al. Virology, epidemiology, pathogenesis, and control of COVID-19. Viruses 2020; 12: 372 [CrossRef]
    [Google Scholar]
  2. Zhou P, Yang X-L, Wang X-G, Hu B, Zhang L et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 2020; 579: 270 273 [CrossRef] [PubMed]
    [Google Scholar]
  3. Lu R, Zhao X, Li J, Niu P, Yang B et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet 2020; 395: 565 574 [CrossRef] [PubMed]
    [Google Scholar]
  4. Coronaviridae Study Group of the International Committee on Taxonomy of Viruses The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol 2020; 5: 536 544 [CrossRef] [PubMed]
    [Google Scholar]
  5. He F, Deng Y, Li W. Coronavirus disease 2019: what we know?. J Med Virol 2020:
    [Google Scholar]
  6. Li S-W, Lin C-W. Human coronaviruses: clinical features and phylogenetic analysis. Biomedicine 2013; 3: 43 50 [CrossRef] [PubMed]
    [Google Scholar]
  7. Corman VM, Muth D, Niemeyer D, Drosten C. Hosts and sources of endemic human coronaviruses. Adv Virus Res 2018; 100: 163 188 [CrossRef] [PubMed]
    [Google Scholar]
  8. de Wit E, van Doremalen N, Falzarano D, Munster VJ. Sars and MERS: recent insights into emerging coronaviruses. Nat Rev Microbiol 2016; 14: 523 534 [CrossRef] [PubMed]
    [Google Scholar]
  9. Song Z, Xu Y, Bao L, Zhang L, Yu P et al. From SARS to MERS, Thrusting coronaviruses into the spotlight. Viruses 2019; 11: 59 [CrossRef] [PubMed]
    [Google Scholar]
  10. Weston S, Frieman MB. COVID-19: knowns, unknowns. and Questions. mSphere 2020; 5:
    [Google Scholar]
  11. Cagliani R, Forni D, Clerici M, Sironi M. Computational inference of selection underlying the evolution of the novel coronavirus, SARS-CoV-2. J Virol 2020
    [Google Scholar]
  12. Ye Z-W, Yuan S, Yuen K-S, Fung S-Y, Chan C-P et al. Zoonotic origins of human coronaviruses. Int J Biol Sci 2020; 16: 1686 1697 [CrossRef] [PubMed]
    [Google Scholar]
  13. Cui J, Li F, Shi Z-L. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol 2019; 17: 181 192 [CrossRef] [PubMed]
    [Google Scholar]
  14. Banerjee A, Kulcsar K, Misra V, Frieman M, Mossman K. Bats and coronaviruses. Viruses 2019; 11: 41 [CrossRef]
    [Google Scholar]
  15. Khan S, Siddique R, Shereen MA, Ali A, Liu J et al. The emergence of a novel coronavirus (SARS-CoV-2), their biology and therapeutic options. J Clin Microbiol 2020; 58: e00187 20
    [Google Scholar]
  16. Zhang Y-Z, Holmes EC. A genomic perspective on the origin and emergence of SARS-CoV-2. Cell 2020; 181: 223 227 [CrossRef] [PubMed]
    [Google Scholar]
  17. Snijder EJ, Decroly E, Ziebuhr J. The nonstructural proteins directing coronavirus RNA synthesis and processing. Adv Virus Res 2016; 96: 59 126 [CrossRef] [PubMed]
    [Google Scholar]
  18. de Wilde AH, Snijder EJ, Kikkert M, van Hemert MJ. Host factors in coronavirus replication. Curr Top Microbiol Immunol 2018; 419: 1 42 [CrossRef] [PubMed]
    [Google Scholar]
  19. Forni D, Cagliani R, Clerici M, Sironi M. Molecular evolution of human coronavirus genomes. Trends Microbiol 2017; 25: 35 48 [CrossRef] [PubMed]
    [Google Scholar]
  20. Neuman BW, Buchmeier MJ. Supramolecular architecture of the coronavirus particle. Adv Virus Res 2016; 96: 1 27 [CrossRef] [PubMed]
    [Google Scholar]
  21. Liu DX, Fung TS, Chong KK-L, Shukla A, Hilgenfeld R. Accessory proteins of SARS-CoV and other coronaviruses. Antiviral Res 2014; 109: 97 109 [CrossRef] [PubMed]
    [Google Scholar]
  22. Neuman BW, Chamberlain P, Bowden F, Joseph J. Atlas of coronavirus replicase structure. Virus Res 2014; 194: 49 66 [CrossRef] [PubMed]
    [Google Scholar]
  23. Enjuanes L, Almazán F, Sola I, Zuñiga S. Biochemical aspects of coronavirus replication and virus-host interaction. Annu Rev Microbiol 2006; 60: 211 230 [CrossRef] [PubMed]
    [Google Scholar]
  24. Enjuanes L, Almazán F, Sola I, Zúñiga S, Alvarez E et al. Biochemical aspects of coronavirus replication. Adv Exp Med Biol 2006; 581: 13 24 [CrossRef] [PubMed]
    [Google Scholar]
  25. Yang D, Leibowitz JL. The structure and functions of coronavirus genomic 3' and 5' ends. Virus Res 2015; 206: 120 133 [CrossRef] [PubMed]
    [Google Scholar]
  26. Sawicki SG, Sawicki DL, Siddell SG. A contemporary view of coronavirus transcription. J Virol 2007; 81: 20 29 [CrossRef] [PubMed]
    [Google Scholar]
  27. Mahase E. Coronavirus covid-19 has killed more people than SARS and MERS combined, despite lower case fatality rate. BMJ 2020; 368: m641 [CrossRef] [PubMed]
    [Google Scholar]
  28. Coutard B, Valle C, de Lamballerie X, Canard B, Seidah NG et al. The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade. Antiviral Res 2020; 176: 104742 [CrossRef] [PubMed]
    [Google Scholar]
  29. Walls AC, Park Y-J, Tortorici MA, Wall A, McGuire AT et al. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell 2020; 181: 281 292 [CrossRef] [PubMed]
    [Google Scholar]
  30. Davidson AD, Williamson MK, Lewis S, Shoemark D, Carroll MW et al. 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
    [Google Scholar]
  31. Angeletti S, Benvenuto D, Bianchi M, Giovanetti M, Pascarella S et al. COVID-2019: the role of the Nsp2 and NSP3 in its pathogenesis. J Med Virol 2020 584 588 [CrossRef] [PubMed]
    [Google Scholar]
  32. Fahmi M, Kubota Y, Ito M. Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV. Infect Genet Evol 2020; 81: 104272 [CrossRef] [PubMed]
    [Google Scholar]
  33. Wang M, Li M, Ren R, Li L, Chen E-Q et al. International expansion of a novel SARS-CoV-2 mutant. J Virol 2020; 94: JVI.00567-20. [CrossRef] [PubMed]
    [Google Scholar]
  34. Brufsky A. Distinct viral clades of SARS-CoV-2: implications for modeling of viral spread. J Med Virol 2020 [CrossRef] [PubMed]
    [Google Scholar]
  35. Schmolke M, Manicassamy B, Pena L, Sutton T, Hai R et al. Differential contribution of PB1-F2 to the virulence of highly pathogenic H5N1 influenza A virus in mammalian and avian species. PLoS Pathog 2011; 7: e1002186 [CrossRef] [PubMed]
    [Google Scholar]
  36. Pena L, Vincent AL, Loving CL, Henningson JN, Lager KM et al. Restored PB1-F2 in the 2009 pandemic H1N1 influenza virus has minimal effects in swine. J Virol 2012; 86: 5523 5532 [CrossRef] [PubMed]
    [Google Scholar]
  37. Johnson BA, Graham RL, Menachery VD. Viral metagenomics, protein structure, and reverse genetics: key strategies for investigating coronaviruses. Virology 2018; 517: 30 37 [CrossRef] [PubMed]
    [Google Scholar]
  38. Almazán F, Sola I, Zuñiga S, Marquez-Jurado S, Morales L et al. Coronavirus reverse genetic systems: infectious clones and replicons. Virus Res 2014; 189: 262 270 [CrossRef] [PubMed]
    [Google Scholar]
  39. Scobey T, Yount BL, Sims AC, Donaldson EF, Agnihothram SS et al. Reverse genetics with a full-length infectious cDNA of the middle East respiratory syndrome coronavirus. Proc Natl Acad Sci U S A 2013; 110: 16157 16162 [CrossRef] [PubMed]
    [Google Scholar]
  40. Yount B, Curtis KM, Fritz EA, Hensley LE, Jahrling PB et al. Reverse genetics with a full-length infectious cDNA of severe acute respiratory syndrome coronavirus. Proc Natl Acad Sci U S A 2003; 100: 12995 13000 [CrossRef] [PubMed]
    [Google Scholar]
  41. Menachery VD, Yount BL, Debbink K, Agnihothram S, Gralinski LE et al. A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. Nat Med 2015; 21: 1508 1513 [CrossRef] [PubMed]
    [Google Scholar]
  42. Eriksson KK, Makia D, Thiel V. Generation of recombinant coronaviruses using vaccinia virus as the cloning vector and stable cell lines containing coronaviral replicon RNAs. Methods Mol Biol 2008; 454: 237 254 [CrossRef] [PubMed]
    [Google Scholar]
  43. Almazán F, Dediego ML, Galán C, Escors D, Alvarez E et al. Construction of a severe acute respiratory syndrome coronavirus infectious cDNA clone and a replicon to study coronavirus RNA synthesis. J Virol 2006; 80: 10900 10906 [CrossRef] [PubMed]
    [Google Scholar]
  44. Xie X, Muruato A, Lokugamage KG, Narayanan K, Zhang X et al. An infectious cDNA clone of SARS-CoV-2. Cell Host Microbe 2020; 27: 841 848 [CrossRef] [PubMed]
    [Google Scholar]
  45. Thao TTN, Labroussaa F, Ebert N, V'kovski P, Stalder H et al. Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform. Nature 2020. [CrossRef] [PubMed]
    [Google Scholar]
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