PREDICTION OF POTENTIAL MUTATION OF CHICKEN CORONAVIRUS INTO FUTURE HUMAN CORONAVIRUS BASED ON SPIKE S1 GLYCOPROTEIN GENE
Keywords:
Chicken IBV, Coronavirus, COVID-19, Mutation, Statistical prediction.
Abstract
The high mutation rates of the chicken coronavirus (IBV) cause economic threats to the poultry industry. However, the most dangerous situation is the likelihood of changing its sequences into human coronavirus (COVID-19-like virus). Therefore, in the present study we aimed to investigate the possibility of genetic mutation of IBV to COVID-19. Thus, the sequences of Spike (S1) Glycoprotein genes of both IBV and COVID-19 were aligned, analyzed and calculated to predict the possible changes that could happen in the sequences of S1. The results indicated that in the case of an independent function of probability of each cluster of S1 sequences, the potential mutation rate in the sequences of IBV to be as COVID-19 was equal to 1.87E-96. However, because the tendency for some sequence clusters of S1 gene was low or equal to zero, it is unattainable to mutate the chicken IBV into COVID-19 sequence. Furthermore, in case of the dependent function, the probability of assumed annual mutation to make IBV infectious for human may reach up to around 50% after about 260 years. As a conclusion, the mutating of chicken coronavirus into COVID-19-like virus is not impossible, but it might take a substantial period of time
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References
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Butler, N., Pewe, L., Trandem, K., and Perlman, S. (2006). Murine encephalitis caused by HCoV-OC43, a human coronavirus with broad species specificity, is partly immune-mediated. Virology. 347: 410-421.
Cavanagh, D. (2005). Coronaviruses in poultry and other birds. Av. Pathol. 34: 439-448.
Cavanagh, D. (2007). Coronavirus avian infectious bronchitis virus. Vet. Res 38: 281-297.
Cavanagh, D. and Naqi, S. (2003). Infectious bronchitis. Dis. poult. 11:101-119.
Cavanagh, D., Davis, P.J., Cook, J.K., Li, D., Kant, A., and Koch, G. (1992). Location of the amino acid differences in the S1 spike glycoprotein subunit of closely related serotypes of infectious bronchitis virus. Av. pathol. 21: 33-43.
Cavanagh, S. (1997). Content analysis: concepts, methods and applications. Nurse researcher 4: 5-16.
Chakraborty, T., and Ghosh, I. (2020). Real-time forecasts and risk assessment of novel coronavirus (COVID-19) cases: A data-driven analysis. Chaos, Solitons & Fractals 135: 109850.
Cook, J.K., Jackwood, M. and Jones, R.C. (2012). The long view: 40 years of infectious bronchitis research. Avian Pathol. 41: 239-250.
De Wit, J.J., Cook, J.K., and Van der Heijden, H.M. (2011). Infectious bronchitis virus variants: a review of the history, current situation and control measures. Avian pathol. 40: 223-235.
Ennaji, Y., Khataby, K., and Ennaji, M.M. (2020). Infectious bronchitis virus in poultry: Molecular epidemiology and factors leading to the emergence and reemergence of novel strains of infectious bronchitis virus. In Emerging and Reemerging Viral Pathogens (pp. 31-44). Academic Press.
Fan, W., Tang, N., Dong, Z., Chen, J., Zhang, W., Zhao, C., He, Y., Li, M., Wu, C., Wei, T., and Huang, T. (2019). Genetic analysis of avian coronavirus infectious bronchitis virus in yellow chickens in Southern China over the past decade: revealing the changes of genetic diversity, dominant genotypes, and selection pressure. Viruses. 11: 898.
Fischer, S., Klosterhalfen, D., Kump, F.W.S., and Casteel, M. (2020). Research Note: First evidence of infectious bronchitis virus Middle-East GI-23 lineage (Var2-like) in Germany. Poult. sci. 99: 797-800.
Howley, DMKP. (2013). Fields Virology. I. Lippincott Williams & Wilkins: 830P.
Hussen, S H. (2020). Forecasting of COVID-19 Cases in Kurdistan Region Using Some Statistical Models. Acad. J. Appl. Math. Sci. 6: 172-180.
Jackwood, M.W., Hall, D., and Handel, A. (2012). Molecular evolution and emergence of avian gammacoronaviruses. Infect. Gen. Evol. 12: 1305-1311.
Ji, W., Wang, W., Zhao, X., Zai, J., and Li, X. (2020). Cross‐species transmission of the newly identified coronavirus 2019‐nCoV. J. Med. Virol. 92: 433-440.
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., and Thierer, T. (2012). Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28: 1647-1649.
King, A.M., Lefkowitz, E., Adams, M.J., and Carstens, E.B. (2011). Virus taxonomy: ninth report of the International Committee on Taxonomy of Viruses (Vol. 9). Elsevier.
Korber, B., Fischer, W., Gnanakaran, S.G., Yoon, H., Theiler, J., Abfalterer, W., Foley, B., Giorgi, E.E., Bhattacharya, T., Parker, M.D., and Partridge, D.G. (2020). Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2. BioRxiv.
Lai, M.M., and Cavanagh, D. (1997). The molecular biology of coronaviruses. Adv. Virus Res. 48: 1-100.
Lee, C.W. (2002). Evolution of avian infectious bronchitis virus: genetic drift and recombination. Kor. J. Vet. Serv. 25: 97-103.
Lefkowitz, E.J., Dempsey, D.M., Hendrickson, R.C., Orton, R.J., Siddell, S.G., and Smith, D.B. (2018). Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucl. ac. res. 46: D708-D717.
Lin, S.Y., and Chen, H.W. (2017). Infectious bronchitis virus variants: molecular analysis and pathogenicity investigation. International journal of molecular sciences. 18: 2030.
Liu, S.W., Zhang, Q.X., Chen, J.D., Han, Z.X., Liu, X., Feng, L., Shao, Y.H., Rong, J.G., Kong, X.G., and Tong, G.Z., 2006. Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between 1995 and 2004. Arch. Virol. 151: 1133-1148.
MacLachlan N.J., and Dubovi, E.J. (2017). Fenner’s veterinary virology, 5th ed. Academic Press, New York, NY.
Matoba, Y., Abiko, C., Ikeda, T., Aoki, Y., Suzuki, Y., Yahagi, K., Matsuzaki, Y., Itagaki, T., Katsushima, F., Katsushima, Y., and Mizuta, K. (2015). Detection of the human coronavirus 229E, HKU1, NL63, and OC43 between 2010 and 2013 in Yamagata, Japan. Jap. J. Infect. Dis. 68: 138-141.
Myint, S.H. (1995). Human coronavirus infections. In The Coronaviridae (pp. 389-401). Springer, Boston, MA.
SPSS, Inc. (2019). Statistical Package for Social Sciences for Windows Graduate Pack Advanced Version. Version 26.0, SPSS Inc., IBM publications.
St-Jean, J.R., Jacomy, H., Desforges, M., Vabret, A., Freymuth, F., and Talbot, P.J. (2004). Human respiratory coronavirus OC43: genetic stability and neuroinvasion. J. Virol. 78: 8824-8834.
Umar, S., Shah, M.A.A., Munir, M.T., Ahsan, U. and Kaboudi, K. (2016). Infectious bronchitis virus: evolution and vaccination. Wor Poult. Sci. J. 72: 49-60.
Valastro, V., Holmes, E.C., Britton, P., Fusaro, A., Jackwood, M.W., Cattoli, G., and Monne, I. (2016). S1 gene-based phylogeny of infectious bronchitis virus: an attempt to harmonize virus classification. Infect. Gen. Evol. 39: 349-364.
Wang, C.H., and Huang, Y.C. (2000). Relationship between serotypes and genotypes based on the hypervariable region of the S1 gene of infectious bronchitis virus. Arch. Virol. 145: 291-300.
World Health Organization (2003). Consensus document on the epidemiology of severe acute respiratory syndrome (SARS) (No. WHO/CDS/CSR/GAR/2003.11). World Health Organization.
World Health Organization (2020). Coronavirus disease 2019 (COVID-19) strategic preparedness and response plan: Accelerating readiness in the Eastern Mediterranean Region: February 2020 (No. WHO-EM/CSR/260/E). World Health Organization. Regional Office for the Eastern Mediterranean.
Wu, A., Niu, P., Wang, L., Zhou, H., Zhao, X., Wang, W., Wang, J., Ji, C., Ding, X., Wang, X., and Lu, R. (2020). Mutations, recombination and insertion in the evolution of 2019-nCoV. BioRxiv.
Yuan, Y., Cao, D., Zhang, Y., Ma, J., Qi, J., Wang, Q., Lu, G., Wu, Y., Yan, J., Shi, Y., and Zhang, X. (2017). Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains. Nat. commun. 8: 1-9.
Published
2021-10-14
How to Cite
HUSSEN, S. H., HUSSEIN, , S. M., MUSTAFA, S. I., ISA , R. H., & BARWARY, M. S. (2021). PREDICTION OF POTENTIAL MUTATION OF CHICKEN CORONAVIRUS INTO FUTURE HUMAN CORONAVIRUS BASED ON SPIKE S1 GLYCOPROTEIN GENE. Journal of Duhok University, 24(2), 68-80. https://doi.org/10.26682/ajuod.2021.24.2.8
Section
Agriculture and Veterinary Science
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