Current understanding of the origin, molecular biology and continuing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

https://doi.org/10.19106/JMedSciSI005203202005

Mohamad Saifudin Hakim(1*), Luthvia Annisa(2), Endah Supriyati(3), Edwin W. Daniwijaya(4), Rakhmat A. Wibowo(5), Eggi Arguni(6), Titik Nuryastuti(7)

(1) Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada
(2) Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
(3) Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
(4) Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
(5) Department of Physiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
(6) Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
(7) Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
(*) Corresponding Author

Abstract


Recent outbreaks of human coronaviruses, officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have put health authorities worldwide on a high alert. Firstly emerged in the city of Wuhan, China, SARS-CoV-2 infection is rapidly escalating into a global pandemic. It is first thought as the result of a zoonotic transmission event, similar to the previous epidemic of coronaviruses. However, a continuously increasing number of confirmed cases indicates that the virus gains capacity of efficient human-to-human transmission. Soon after the pandemic is arising, many efforts are focused on identifying the origin of SARS-CoV-2 infection in the human population. Current evidence suggests that the virus is probably derived from bat or pangolin coronaviruses as the natural host. Whether intermediate host(s) exist in the transmission cascade from bat or pangolin to humans is, to a great extent, elusive. This information is essential as the basis for infection prevention and control measures. In this review, we discuss our recent understanding of SARS-CoV-2 biology, highlighting its origin and molecular evolution.

Keywords


bats; evolution; origin; pangolin; SARS-CoV-2

Full Text:

PDF


References

  1. Su S, Wong G, Shi W, Liu J, Lai ACK, Zhou J, et al. Epidemiology, genetic recombination, and pathogenesis of coronaviruses. Trends Microbiol 2016; 24(6):490-502. https://doi.org/10.1016/j.tim.2016.03.003
  2. Cui J, Li F, Shi ZL. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol 2019; 17(3):181-92. https://doi.org/10.1038/s41579-018-0118-9
  3. de Wit E, van Doremalen N, Falzarano D, Munster VJ. SARS and MERS: recent insights into emerging coronaviruses. Nat Rev Microbiol 2016; 14(8):523-34. https://doi.org/10.1038/nrmicro.2016.81
  4. Hui DS, E IA, Madani TA, Ntoumi F, Kock R, Dar O, et al. The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health - The latest 2019 novel coronavirus outbreak in Wuhan, China. Int J Infect Dis 2020; 91:264-6. https://doi.org/10.1016/j.ijid.2020.01.009
  5. Zaki AM, van Boheemen S, Bestebroer TM, Osterhaus AD, Fouchier RA. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med 2012; 367(19):1814-20. https://doi.org/10.1056/NEJMoa1211721
  6. Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med 2020; 382(8):727-33. https://doi.org/10.1056/NEJMoa2001017
  7. Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhnag B, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 2020; 579(7798):270-3. https://doi.org/10.1038/s41586-020-2012-7
  8. Coronaviridae Study Group of the International Committee on Taxonomy of V. The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol 2020; 5(4):536-4 https://doi.org/10.1038/s41564-020-0695-z
  9. Wilder-Smith A, Chiew CJ, Lee VJ. Can we contain the COVID-19 outbreak with the same measures as for SARS? Lancet Infect Dis 2020; 20(5):102-7. https://doi.org/10.1016/S1473-3099(20)30129-8
  10. Liu Y, Gayle AA, Wilder-Smith A, Rocklov J. The reproductive number of COVID-19 is higher compared to SARS coronavirus. J Travel Med 2020; 27(2):021. https://doi.org/10.1093/jtm/taaa021
  11. World Health Organization. Coronavirus disease (COVID-19) sitution reports. Cite from: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports. Accessed on April 27th2020)
  12. Gorbalenya AE, Enjuanes L, Ziebuhr J, Snijder EJ. Nidovirales: evolving the largest RNA virus genome. Virus Res 2006; 117(1):17-37. https://doi.org/10.1016/j.virusres.2006.01.017
  13. Masters PS. The molecular biology of coronaviruses. Adv Virus Res 2006; 66:193-292. https://doi.org/10.1016/S0065-3527(06)66005-3
  14. Wei X, Li X, Cui J. Evolutionary perspectives on novel coronaviruses identified in pneumonia cases in China. Natl Sci Rev 2020; 7(2):239-42. https://doi.org/10.1093/nsr/nwaa009
  15. Wu A, Peng Y, Huang B, Wang X, Niu P, Jing M, et al. Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China. Cell Host Microbe 2020; 27(3):325-28. https://doi.org/10.1016/j.chom.2020.02.001
  16. Perlman S, Netland J. Coronaviruses post-SARS: update on replication and pathogenesis. Nat Rev Microbiol 2009; 7(6):439-50. https://doi.org/10.1038/nrmicro2147
  17. Wan Y, Shang J, Graham R, Baric RS, Li F. Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus. J Virol 2020; 94(7):1-9. https://doi.org/10.1128/JVI.00127-20
  18. Ou X, Liu Y, Lei X, Li P, Mi D, Ren L, et al. Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nat Commun 2020; 11(1):1620. https://doi.org/10.1038/s41467-020-15562-9
  19. Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell 2020; 181(2):281-92. https://doi.org/10.1016/j.cell.2020.02.058
  20. Hoffmann M, Kleine-Weber H, Schroeder S, Kruger N, Herrler T, Erichsen S, et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 2020; 181(2):271-80. https://doi.org/10.1016/j.cell.2020.02.052
  21. Matsuyama S, Nao N, Shirato K, Kawase M, Saito S, Takayam I, et al. Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells. Proc Natl Acad Sci U S A 2020; 117(13):7001-3. https://doi.org/10.1073/pnas.2002589117
  22. Schibli DJ, Weissenhorn W. Class I and class II viral fusion protein structures reveal similar principles in membrane fusion. Mol Membr Biol 2004; 21(6):361-71. https://doi.org/10.1080/09687860400017784
  23. Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nat Med 2020; 26(4):450-2. https://doi.org/10.1038/s41591-020-0820-9
  24. Alexander DJ, Brown IH. History of highly pathogenic avian influenza. Rev Sci Tech 2009; 28(1):19-38. https://doi.org/10.20506/rst.28.1.1856
  25. Cheng H, Wang Y, Wang GQ. Organ-protective effect of angiotensin-converting enzyme 2 and its effect on the prognosis of COVID-19. J Med Virol 2020; 27:1-5. https://doi.org/10.1002/jmv.25785
  26. Xu H, Zhong L, Deng J, et al. High expression of ACE2 receptor of 2019-nCoV on the epithelial cells of oral mucosa. Int J Oral Sci 2020; 12(1):8. https://doi.org/10.1038/s41368-020-0074-x
  27. Patel AB, Verma A. COVID-19 and Angiotensin-converting enzyme inhibitors and angiotensin receptor blockers: what is the evidence? JAMA 2020. https://doi.org/10.1001/jama.2020.4812
  28. Diaz JH. Hypothesis: angiotensin-converting enzyme inhibitors and angiotensin receptor blockers may increase the risk of severe COVID-19. J Travel Med 2020: https://doi.org/10.1093/jtm/taaa041
  29. Imai Y, Kuba K, Rao S, Huan Y, Guo F, Guan B, et al. Angiotensin-converting enzyme 2 protects from severe acute lung failure. Nature 2005; 436(7047):112-6. https://doi.org/10.1038/nature03712
  30. Zou Z, Yan Y, Shu Y, Gao R, Sun Y, Li X, et al. Angiotensin-converting enzyme 2 protects from lethal avian influenza A H5N1 infections. Nat Commun 2014; 5:3594. https://doi.org/10.1038/ncomms4594
  31. Imai Y, Kuba K, Penninger JM. The discovery of angiotensin-converting enzyme 2 and its role in acute lung injury in mice. Exp Physiol 2008; 93(5):543-8. https://doi.org/10.1113/expphysiol.2007.040048
  32. Kuba K, Imai Y, Rao S, Gao H, Guo F, Guan B, et al. A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury. Nat Med 2005; 11(8):875-9. https://doi.org/10.1038/nm1267
  33. Hanff TC, Harhay MO, Brown TS, Cohen JB, Mohareb AM. Is there an association between COVID-19 mortality and the renin-angiotensin system-a call for epidemiologic investigations. Clin Infect Dis 2020; 26:329. https://doi.org/10.1093/cid/ciaa329
  34. Fu Y, Cheng Y, Wu Y. Understanding SARS-CoV-2-mediated inflammatory responses: from mechanisms to potential therapeutic tools. Virol Sin 2020: https://doi.org/10.1007/s12250-020-00207-4
  35. Kruse RL. Therapeutic strategies in an outbreak scenario to treat the novel coronavirus originating in Wuhan, China. F1000Res 2020; 9: 72. https://doi.org/10.12688/f1000research.22211.2
  36. Batlle D, Wysocki J, Satchell K. Soluble angiotensin-converting enzyme 2: a potential approach for coronavirus infection therapy? Clin Sci (Lond) 2020; 134(5):543-5. https://doi.org/10.1042/CS20200163
  37. Meng J, Xiao G, Zhang J, Hi X, Ou M, Bi J, et al. Renin-angiotensin system inhibitors improve the clinical outcomes of COVID-19 patients with hypertension. Emerg Microbes Infect 2020; 9(1):757-60. https://doi.org/10.1080/22221751.2020.1746200
  38. Fan Y, Zhao K, Shi ZL, Zhou P. Bat coronaviruses in China. Viruses 2019; 11(3):210. https://doi.org/10.3390/v11030210
  39. Guan Y, Zheng BJ, He YQ, Liu XL, Zhuang ZX, Cheung CL, et al. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science 2003; 302(5643):276-8. https://doi.org/10.1126/science.1087139
  40. Kan B, Wang M, Jing H, Xu H, Jiang X, Yan M, et al. Molecular evolution analysis and geographic investigation of severe acute respiratory syndrome coronavirus-like virus in palm civets at an animal market and on farms. J Virol 2005; 79(18):11892-900. https://doi.org/10.1128/JVI.79.18.11892-11900.2005
  41. Tu C, Crameri G, Kong X, Che J, Sun Y, Yu M, et al. Antibodies to SARS coronavirus in civets. Emerg Infect Dis 2004; 10(12):2244-8. https://doi.org/10.3201/eid1012.040520
  42. Lau SK, Woo PC, Li KS,Tsoi HW, Wong BH, Wong SS,et al. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci USA 2005; 102(39):14040-5. https://doi.org/10.1073/pnas.0506735102
  43. Munster VJ, Koopmans M, van Doremalen N, van Riel D, de Wit E. A novel coronavirus emerging in China - key questions for impact assessment. N Engl J Med 2020; 382(8):692-4. https://doi.org/10.1056/NEJMp2000929
  44. Muller MA, Corman VM, Jores J, Younan M, Liljander A, Bosch BJ,et al. MERS coronavirus neutralizing antibodies in camels, Eastern Africa, 1983-1997. Emerg Infect Dis 2014; 20(12):2093-5. https://doi.org/10.3201/eid2012.141026
  45. Xu X, Chen P, Wang J, Feng J, Zhou H, Li X, et al. Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Sci China Life Sci 2020; 63(3):457-60. https://doi.org/10.1007/s11427-020-1637-5
  46. Benvenuto D, Giovanetti M, Salemi M, Prosperi M, De Flora C, Alcantara LCJ, et al. The global spread of 2019-nCoV: a molecular evolutionary analysis. Pathog Glob Health 2020; 114(2):64-7. https://doi.org/10.1080/20477724.2020.1725339
  47. Ji W, Wang W, Zhao X, Zai J, Li X. Cross-species transmission of the newly identified coronavirus 2019-nCoV. J Med Virol 2020; 92(4):433-40. https://doi.org/10.1002/jmv.25682
  48. Chan JF, Yuan S, Kok KH, To KKW, Chu H, Yang J, 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(10223):514-23. https://doi.org/10.1016/S0140-6736(20)30154-9
  49. Zhang T, Wu Q, Zhang Z. Probable pangolin origin of SARS-CoV-2 associated with the COVID-19 outbreak. Curr Biol 2020; 30(7):1346-51. https://doi.org/10.1016/j.cub.2020.03.022
  50. Lam TT, Shum MH, Zhu HC, Tong YG, Ni XB, Liao YS, et al. Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins. Nature 2020. https://doi.org/10.1038/s41586-020-2169-0
  51. Yuen KS, Ye ZW, Fung SY, Chan CP, Jin DY. SARS-CoV-2 and COVID-19: the most important research questions. Cell Biosci 2020; 10:40. https://doi.org/10.1186/s13578-020-00404-4
  52. Zhang C, Zheng W, Huang X, Bell EW, Zhou X, Zhang Y. Protein structure and sequence reanalysis of 2019-nCoV genome refutes snakes as its intermediate host and the unique similarity between its spike protein insertions and HIV-1. J Proteome Res 2020; 19(4):1351-60. https://doi.org/10.1021/acs.jproteome.0c00129
  53. Li X, Zai J, Zhao Q, Nie Q, Li Y, Foley BT, et al. Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2. J Med Virol 2020. https://doi.org/10.1002/jmv.25731
  54. Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y,et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet 2020; 395(10223):497-506. https://doi.org/10.1016/S0140-6736(20)30183-5
  55. Lu H, Stratton CW, Tang YW. Outbreak of pneumonia of unknown etiology in Wuhan, China: the mystery and the miracle. J Med Virol 2020; 92(4):401-2. https://doi.org/10.1002/jmv.25678
  56. Zheng J. SARS-CoV-2: an emerging coronavirus that causes a global threat. Int J Biol Sci 2020; 16(10):1678-85. https://doi.org/10.7150/ijbs.45053
  57. Xu Y. Unveiling the origin and transmission of 2019-nCoV. Trends Microbiol 2020; 28(4):239-40. https://doi.org/10.1016/j.tim.2020.02.001
  58. Bolles M, Donaldson E, Baric R. SARS-CoV and emergent coronaviruses: viral determinants of interspecies transmission. Curr Opin Virol 2011; 1(6):624-34. https://doi.org/10.1016/j.coviro.2011.10.012
  59. Denison MR, Graham RL, Donaldson EF, Eckerle LD, Baric RS. Coronaviruses: an RNA proofreading machine regulates replication fidelity and diversity. RNA Biol 2011; 8(2):270-9. https://doi.org/10.4161/rna.8.2.15013
  60. Phan T. Genetic diversity and evolution of SARS-CoV-2. Infect Genet Evol 2020; 81:104260. https://doi.org/10.1016/j.meegid.2020.104260
  61. Forster P, Forster L, Renfrew C, Forster M. Phylogenetic network analysis of SARS-CoV-2 genomes. Proc Natl Acad Sci USA 2020; 117(17):9241-3. https://doi.org/10.1073/pnas.2004999117
  62. Shen Z, Xiao Y, Kang L, Ma W, Shi L, Zhang L, et al. Genomic diversity of SARS-CoV-2 in coronavirus disease 2019 patients. Clin Infect Dis 2020; 4:203. https://doi.org/10.1093/cid/ciaa203



DOI: https://doi.org/10.19106/JMedSciSI005203202005

Article Metrics

Abstract views : 8608 | views : 5483


Bookmark and Share


Copyright (c) 2020 Mohamad Saifudin Hakim, Luthvia Annisa, Endah Supriyati, Edwin W. Daniwijaya, Rakhmat A. Wibowo, Eggi Arguni, Titik Nuryastuti

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.