Is The SARS-CoV2 Evolved in Human Being: A prospective Genetic Analysis
https://doi.org/10.24017/science.2020.ICHMS2020.19
Abstract views: 1087 / PDF downloads: 700Abstract
COVID-19 is the deadly respiratory disease of the century caused by new type unknown origin Coronavirus. The recent effort of the word researchers is toward finding the origin of the virus. The current study investigated the extent of molecular similarity and divergence between SARS-CoV2 and other related Coronavirus. An attempt has been made to investigate the epidemiological study of this new contagious virus using molecular biology techniques. The phylogenetic trees for all human coronaviruses with the novel Coronavirus have been built using a several complete amino acid sequences of the four known structural proteins, S (spike), E (envelope), M (membrane), and N (nucleocapsid). The result of the study revealed that the SARS-CoV2 is related to human SARS-CoV isolated from different countries very cloely, especially those strains recovered from China in recent times, 2020. The evolutionary changes observed in the inserted 23 amino acids in the RNA binding domain (RBD) of the coronvirus spike glycoprotein which cannot be detected in any other human coronavirus. Moreover, the 2019-nCoV is not closely related to other alpha, beta and gamma human Coronavirus, including MERS-CoV. The current study concluded that 2019-nCoV is more likely believed to originated from SARS-CoV. The probability is more vital to be originated from the strain isolated in China in 2020, which is coincident with the spraed of COVID-19 in the same country. The phyloepidemiologic analyses suggested that the coronaviruses are circulating in human hosts evolving gradually by times in response to the different environment stimuli facing the virus inside the host in different geographical areas. Furthermore, the analysis showed the flow of transmission, and evolutionary changes of SARS-CoV2 which may be directed from the transmission of SARS-CoV from human to Bat and Pangolin then jumped to human again in the crowded market Wuhan city in China.
Keywords:
SARS-CoV2, SARS-CoV, MERS-CoV, COVID-19 and 2019-nCoV
References
[1] J. Cui, F. Li, and Z. L. Shi, "Origin and evolution of pathogenic coronaviruses," Nat Rev Microbiol, vol. 17, pp. 181-192, Mar 2019.
https://doi.org/10.1038/s41579-018-0118-9
[2] WHO, "Coronavirus disease (COVID-2019) situation reports. https://www.who.int/emergencies/diseases/novel-coronavirus," 2019/situation-reports/ [accessed 12 February 2020]. 2020.
[3] D. S. Hui, I. A. E, T. A. Madani, F. Ntoumi, R. Kock, O. Dar, 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, vol. 91, pp. 264-266, Feb 2020.
https://doi.org/10.1016/j.ijid.2020.01.009
[4] S. Zhao, S. S. Musa, Q. Lin, J. Ran, G. Yang, W. Wang, et al., "Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak," J Clin Med, vol. 9, Feb 1 2020.
https://doi.org/10.3390/jcm9020388
[5] F. Greco, S. Dimonte, M. Babakir-Mina, T. Hama-Soor, and S. Ali, "Is It Scaly Anteater or Bat A Real Origin of The 2019-Novel CoV: A Probable Hypothesis?," Kurdistan Journal of Applied Research, vol. 5, pp. 1-12. DOI https://doi.org/10.24017/covid.1, 2020.
https://doi.org/10.24017/covid.1
[6] P. Zhou, X.-L. Yang, X.-G. Wang, B. Hu, L. Zhang, W. Zhang, et al., "A pneumonia outbreak associated with a new coronavirus of probable bat origin," Nature, vol. 579, pp. 270-273. https://doi.org/10.1038/s41586-020-2012-7, 2020.
https://doi.org/10.1038/s41586-020-2012-7
[7] T. Zhang, Q. Wu, and Z. Zhang, "Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak," Current Biology, vol. 30 pp. 1346-1351. DOI: 10.1016/j.cub.2020.03.022, Mar 19 2020.
https://doi.org/10.1016/j.cub.2020.03.022
[8] W. Ji, W. Wang, X. Zhao, J. Zai, and X. Li, "Cross-species transmission of the newly identified coronavirus 2019-nCoV," J Med Virol, vol. 92, pp. 433-440. https://doi.org/10.1002/jmv.25682, Apr 2020.
https://doi.org/10.1002/jmv.25682
[9] Q. Li, X. Guan, P. Wu, X. Wang, L. Zhou, Y. Tong, et al., "Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia," N Engl J Med, vol. 382, pp. 1199-1207. DOI: 10.1056/NEJMoa2001316, Mar 26 2020.
https://doi.org/10.1056/NEJMoa2001316
[10] M. A. Shereen, S. Khan, A. Kazmi, N. Bashir, and R. Siddique, "COVID-19 infection: Origin, transmission, and characteristics of human coronaviruses," J Adv Res, vol. 24, pp. 91-98, Jul 2020.
https://doi.org/10.1016/j.jare.2020.03.005
[11] J. F.-W. Chan, S. Yuan, K.-H. Kok, K. K.-W. To, H. Chu, J. Yang, et al., "A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster," The Lancet, vol. 395, pp. 514-523. DOI:https://doi.org/10.1016/S0140-6736(20)30154-9, 2020.
https://doi.org/10.1016/S0140-6736(20)30154-9
[12] J. Cai, W. Sun, J. Huang, M. Gamber, J. Wu, and G. He, "Indirect Virus Transmission in Cluster of COVID-19 Cases, Wenzhou, China, 2020," Emerging Infectious Diseases journal, vol. 26, p. DOI: 10.3201/eid2606.200412, 2020.
https://doi.org/10.3201/eid2606.200412
[13] P. Li, J. B. Fu, K. F. Li, Y. Chen, H. L. Wang, L. J. Liu, et al., "Transmission of COVID-19 in the terminal stage of incubation period: a familial cluster," Int J Infect Dis, Mar 16 2020.
https://doi.org/10.1016/j.ijid.2020.03.027
[14] C. Huang, Y. Wang, X. Li, L. Ren, J. Zhao, Y. Hu, et al., "Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China," The Lancet, vol. 395, pp. 497-506. DOI:https://doi.org/10.1016/S0140-6736(20)30183-5, 2020.
https://doi.org/10.1016/S0140-6736(20)30183-5
[15] N. Zhu, D. Zhang, W. Wang, X. Li, B. Yang, J. Song, et al., "A Novel Coronavirus from Patients with Pneumonia in China, 2019," N Engl J Med, vol. 382, pp. 727-733, Feb 20 2020.
https://doi.org/10.1056/NEJMoa2001017
[16] C. K.-f. Li, H. Wu, H. Yan, S. Ma, L. Wang, M. Zhang, et al., "T cell responses to whole SARS coronavirus in humans," The Journal of Immunology, vol. 181, pp. 5490-5500, 2008.
https://doi.org/10.4049/jimmunol.181.8.5490
[17] E. G. Brown and J. A. Tetro, "Comparative analysis of the SARS coronavirus genome: a good start to a long journey," The Lancet, vol. 361, pp. 1756-1757, 2003.
https://doi.org/10.1016/S0140-6736(03)13444-7
[18] J. S. Kahn and K. McIntosh, "History and recent advances in coronavirus discovery," Pediatr Infect Dis J, vol. 24, pp. S223-7, discussion S226, Nov 2005.
https://doi.org/10.1097/01.inf.0000188166.17324.60
[19] K. Kuba, Y. Imai, S. Rao, H. Gao, F. Guo, B. Guan, et al., "A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury," Nat Med, vol. 11, pp. 875-9, Aug 2005.
https://doi.org/10.1038/nm1267
[20] B. J. Bosch, R. van der Zee, C. A. de Haan, and P. J. Rottier, "The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex," J Virol, vol. 77, pp. 8801-8811. DOI: 10.1128/JVI.77.16., Aug 2003.
https://doi.org/10.1128/JVI.77.16.8801-8811.2003
[21] A. C. Walls, Y. J. Park, M. A. Tortorici, A. Wall, A. T. McGuire, and D. Veesler, "Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein," Cell, vol. https://doi.org/10.1016/j.cell.2020.02.058 Mar 6 2020.
https://doi.org/10.1016/j.cell.2020.02.058
[22] J. K. Millet and G. R. Whittaker, "Physiological and molecular triggers for SARS-CoV membrane fusion and entry into host cells," Virology, vol. 517, pp. 3-8, Apr 2018.
https://doi.org/10.1016/j.virol.2017.12.015
[23] A. Hasan, B. A. Paray, A. Hussain, F. A. Qadir, F. Attar, F. M. Aziz, et al., "A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin," J Biomol Struct Dyn, pp. 1-13. DOI: 10.1080/07391102.2020.1754293, Apr 10 2020.
https://doi.org/10.1080/07391102.2020.1754293
[24] B. Coutard, C. Valle, X. de Lamballerie, B. Canard, N. G. Seidah, and E. Decroly, "The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade," Antiviral Res, vol. 176, p. 104742. DOI: 10.1016/j.antiviral.2020.104742, Apr 2020.
https://doi.org/10.1016/j.antiviral.2020.104742
[25] D. Schoeman and B. C. Fielding, "Coronavirus envelope protein: current knowledge," Virol J, vol. 16, p. 69, May 27 2019.
https://doi.org/10.1186/s12985-019-1182-0
[26] Y. Chen, Q. Liu, and D. Guo, "Emerging coronaviruses: Genome structure, replication, and pathogenesis," J Med Virol, vol. 92, pp. 418-423, Apr 2020.
https://doi.org/10.1002/jmv.25681
[27] L. Mousavizadeh and S. Ghasemi, "Genotype and phenotype of COVID-19: Their roles in pathogenesis," J Microbiol Immunol Infect, vol. S1684?1182:30082?30087, p. http://doi.org/10.1016/j.jmii.2020.3.022, Mar 31 2020.
[28] F. Corpet, "Multiple sequence alignment with hierarchical clustering," Nucleic Acids Research, vol. 16, p. DOI: 10.1093/nar/16.22.10881, 1988.
https://doi.org/10.1093/nar/16.22.10881
[29] P. Zhou, X.-L. Yang, X.-G. Wang, B. Hu, L. Zhang, W. Zhang, et al., "Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin," BioRxiv. https://doi.org/10.1101/2020.01.22.914952, 2020.
https://doi.org/10.1101/2020.01.22.914952
[30] S. R. Weiss and S. Navas-Martin, "Coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus," Microbiol Mol Biol Rev, vol. 69, pp. 635-664. doi:10.1128/MMBR.69.4, Dec 2005.
https://doi.org/10.1128/MMBR.69.4.635-664.2005
[31] Y. Fan, K. Zhao, Z. L. Shi, and P. Zhou, "Bat Coronaviruses in China," Viruses, vol. 11, Mar 2 2019.
https://doi.org/10.3390/v11030210
[32] Z. Song, Y. Xu, L. Bao, L. Zhang, P. Yu, Y. Qu, et al., "From SARS to MERS, Thrusting Coronaviruses into the Spotlight," Viruses, vol. 11, Jan 14 2019.
https://doi.org/10.3390/v11010059
[33] N. S. Ogando, F. Ferron, E. Decroly, B. Canard, C. C. Posthuma, and E. J. Snijder, "The Curious Case of the Nidovirus Exoribonuclease: Its Role in RNA Synthesis and Replication Fidelity," Front Microbiol, vol. 10, p. 1813, 2019.
https://doi.org/10.3389/fmicb.2019.01813
[34] W. Tai, L. He, X. Zhang, J. Pu, D. Voronin, S. Jiang, et al., "Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine," Cell Mol Immunol, Mar 19 2020.
https://doi.org/10.1038/s41423-020-0400-4
[35] X. Ou, Y. Liu, X. Lei, P. Li, D. Mi, L. Ren, et al., "Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV," Nat Commun, vol. 11, pp. 1620. https://doi.org/10.1038/s41467-020-15562-9, Mar 27 2020.
https://doi.org/10.1038/s41467-020-15562-9
https://doi.org/10.1038/s41579-018-0118-9
[2] WHO, "Coronavirus disease (COVID-2019) situation reports. https://www.who.int/emergencies/diseases/novel-coronavirus," 2019/situation-reports/ [accessed 12 February 2020]. 2020.
[3] D. S. Hui, I. A. E, T. A. Madani, F. Ntoumi, R. Kock, O. Dar, 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, vol. 91, pp. 264-266, Feb 2020.
https://doi.org/10.1016/j.ijid.2020.01.009
[4] S. Zhao, S. S. Musa, Q. Lin, J. Ran, G. Yang, W. Wang, et al., "Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak," J Clin Med, vol. 9, Feb 1 2020.
https://doi.org/10.3390/jcm9020388
[5] F. Greco, S. Dimonte, M. Babakir-Mina, T. Hama-Soor, and S. Ali, "Is It Scaly Anteater or Bat A Real Origin of The 2019-Novel CoV: A Probable Hypothesis?," Kurdistan Journal of Applied Research, vol. 5, pp. 1-12. DOI https://doi.org/10.24017/covid.1, 2020.
https://doi.org/10.24017/covid.1
[6] P. Zhou, X.-L. Yang, X.-G. Wang, B. Hu, L. Zhang, W. Zhang, et al., "A pneumonia outbreak associated with a new coronavirus of probable bat origin," Nature, vol. 579, pp. 270-273. https://doi.org/10.1038/s41586-020-2012-7, 2020.
https://doi.org/10.1038/s41586-020-2012-7
[7] T. Zhang, Q. Wu, and Z. Zhang, "Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak," Current Biology, vol. 30 pp. 1346-1351. DOI: 10.1016/j.cub.2020.03.022, Mar 19 2020.
https://doi.org/10.1016/j.cub.2020.03.022
[8] W. Ji, W. Wang, X. Zhao, J. Zai, and X. Li, "Cross-species transmission of the newly identified coronavirus 2019-nCoV," J Med Virol, vol. 92, pp. 433-440. https://doi.org/10.1002/jmv.25682, Apr 2020.
https://doi.org/10.1002/jmv.25682
[9] Q. Li, X. Guan, P. Wu, X. Wang, L. Zhou, Y. Tong, et al., "Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia," N Engl J Med, vol. 382, pp. 1199-1207. DOI: 10.1056/NEJMoa2001316, Mar 26 2020.
https://doi.org/10.1056/NEJMoa2001316
[10] M. A. Shereen, S. Khan, A. Kazmi, N. Bashir, and R. Siddique, "COVID-19 infection: Origin, transmission, and characteristics of human coronaviruses," J Adv Res, vol. 24, pp. 91-98, Jul 2020.
https://doi.org/10.1016/j.jare.2020.03.005
[11] J. F.-W. Chan, S. Yuan, K.-H. Kok, K. K.-W. To, H. Chu, J. Yang, et al., "A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster," The Lancet, vol. 395, pp. 514-523. DOI:https://doi.org/10.1016/S0140-6736(20)30154-9, 2020.
https://doi.org/10.1016/S0140-6736(20)30154-9
[12] J. Cai, W. Sun, J. Huang, M. Gamber, J. Wu, and G. He, "Indirect Virus Transmission in Cluster of COVID-19 Cases, Wenzhou, China, 2020," Emerging Infectious Diseases journal, vol. 26, p. DOI: 10.3201/eid2606.200412, 2020.
https://doi.org/10.3201/eid2606.200412
[13] P. Li, J. B. Fu, K. F. Li, Y. Chen, H. L. Wang, L. J. Liu, et al., "Transmission of COVID-19 in the terminal stage of incubation period: a familial cluster," Int J Infect Dis, Mar 16 2020.
https://doi.org/10.1016/j.ijid.2020.03.027
[14] C. Huang, Y. Wang, X. Li, L. Ren, J. Zhao, Y. Hu, et al., "Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China," The Lancet, vol. 395, pp. 497-506. DOI:https://doi.org/10.1016/S0140-6736(20)30183-5, 2020.
https://doi.org/10.1016/S0140-6736(20)30183-5
[15] N. Zhu, D. Zhang, W. Wang, X. Li, B. Yang, J. Song, et al., "A Novel Coronavirus from Patients with Pneumonia in China, 2019," N Engl J Med, vol. 382, pp. 727-733, Feb 20 2020.
https://doi.org/10.1056/NEJMoa2001017
[16] C. K.-f. Li, H. Wu, H. Yan, S. Ma, L. Wang, M. Zhang, et al., "T cell responses to whole SARS coronavirus in humans," The Journal of Immunology, vol. 181, pp. 5490-5500, 2008.
https://doi.org/10.4049/jimmunol.181.8.5490
[17] E. G. Brown and J. A. Tetro, "Comparative analysis of the SARS coronavirus genome: a good start to a long journey," The Lancet, vol. 361, pp. 1756-1757, 2003.
https://doi.org/10.1016/S0140-6736(03)13444-7
[18] J. S. Kahn and K. McIntosh, "History and recent advances in coronavirus discovery," Pediatr Infect Dis J, vol. 24, pp. S223-7, discussion S226, Nov 2005.
https://doi.org/10.1097/01.inf.0000188166.17324.60
[19] K. Kuba, Y. Imai, S. Rao, H. Gao, F. Guo, B. Guan, et al., "A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury," Nat Med, vol. 11, pp. 875-9, Aug 2005.
https://doi.org/10.1038/nm1267
[20] B. J. Bosch, R. van der Zee, C. A. de Haan, and P. J. Rottier, "The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex," J Virol, vol. 77, pp. 8801-8811. DOI: 10.1128/JVI.77.16., Aug 2003.
https://doi.org/10.1128/JVI.77.16.8801-8811.2003
[21] A. C. Walls, Y. J. Park, M. A. Tortorici, A. Wall, A. T. McGuire, and D. Veesler, "Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein," Cell, vol. https://doi.org/10.1016/j.cell.2020.02.058 Mar 6 2020.
https://doi.org/10.1016/j.cell.2020.02.058
[22] J. K. Millet and G. R. Whittaker, "Physiological and molecular triggers for SARS-CoV membrane fusion and entry into host cells," Virology, vol. 517, pp. 3-8, Apr 2018.
https://doi.org/10.1016/j.virol.2017.12.015
[23] A. Hasan, B. A. Paray, A. Hussain, F. A. Qadir, F. Attar, F. M. Aziz, et al., "A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin," J Biomol Struct Dyn, pp. 1-13. DOI: 10.1080/07391102.2020.1754293, Apr 10 2020.
https://doi.org/10.1080/07391102.2020.1754293
[24] B. Coutard, C. Valle, X. de Lamballerie, B. Canard, N. G. Seidah, and E. Decroly, "The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade," Antiviral Res, vol. 176, p. 104742. DOI: 10.1016/j.antiviral.2020.104742, Apr 2020.
https://doi.org/10.1016/j.antiviral.2020.104742
[25] D. Schoeman and B. C. Fielding, "Coronavirus envelope protein: current knowledge," Virol J, vol. 16, p. 69, May 27 2019.
https://doi.org/10.1186/s12985-019-1182-0
[26] Y. Chen, Q. Liu, and D. Guo, "Emerging coronaviruses: Genome structure, replication, and pathogenesis," J Med Virol, vol. 92, pp. 418-423, Apr 2020.
https://doi.org/10.1002/jmv.25681
[27] L. Mousavizadeh and S. Ghasemi, "Genotype and phenotype of COVID-19: Their roles in pathogenesis," J Microbiol Immunol Infect, vol. S1684?1182:30082?30087, p. http://doi.org/10.1016/j.jmii.2020.3.022, Mar 31 2020.
[28] F. Corpet, "Multiple sequence alignment with hierarchical clustering," Nucleic Acids Research, vol. 16, p. DOI: 10.1093/nar/16.22.10881, 1988.
https://doi.org/10.1093/nar/16.22.10881
[29] P. Zhou, X.-L. Yang, X.-G. Wang, B. Hu, L. Zhang, W. Zhang, et al., "Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin," BioRxiv. https://doi.org/10.1101/2020.01.22.914952, 2020.
https://doi.org/10.1101/2020.01.22.914952
[30] S. R. Weiss and S. Navas-Martin, "Coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus," Microbiol Mol Biol Rev, vol. 69, pp. 635-664. doi:10.1128/MMBR.69.4, Dec 2005.
https://doi.org/10.1128/MMBR.69.4.635-664.2005
[31] Y. Fan, K. Zhao, Z. L. Shi, and P. Zhou, "Bat Coronaviruses in China," Viruses, vol. 11, Mar 2 2019.
https://doi.org/10.3390/v11030210
[32] Z. Song, Y. Xu, L. Bao, L. Zhang, P. Yu, Y. Qu, et al., "From SARS to MERS, Thrusting Coronaviruses into the Spotlight," Viruses, vol. 11, Jan 14 2019.
https://doi.org/10.3390/v11010059
[33] N. S. Ogando, F. Ferron, E. Decroly, B. Canard, C. C. Posthuma, and E. J. Snijder, "The Curious Case of the Nidovirus Exoribonuclease: Its Role in RNA Synthesis and Replication Fidelity," Front Microbiol, vol. 10, p. 1813, 2019.
https://doi.org/10.3389/fmicb.2019.01813
[34] W. Tai, L. He, X. Zhang, J. Pu, D. Voronin, S. Jiang, et al., "Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine," Cell Mol Immunol, Mar 19 2020.
https://doi.org/10.1038/s41423-020-0400-4
[35] X. Ou, Y. Liu, X. Lei, P. Li, D. Mi, L. Ren, et al., "Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV," Nat Commun, vol. 11, pp. 1620. https://doi.org/10.1038/s41467-020-15562-9, Mar 27 2020.
https://doi.org/10.1038/s41467-020-15562-9
Downloads
How to Cite
[1]
S. Dimonte, “Is The SARS-CoV2 Evolved in Human Being: A prospective Genetic Analysis”, KJAR, pp. 169–177, Dec. 2020, doi: 10.24017/science.2020.ICHMS2020.19.
Published
12-12-2020
Issue
Section
Pure and Applied Science
