THE EVOLUTION OF SARS-COV-2, A REVIEW OF GENETIC MUTATION
DOI:
https://doi.org/10.29121/granthaalayah.v12.i5.2024.5913Keywords:
COVID – 19, SARS-COV-2, Genotypes, Mutation Probability, Bats CoronavirusesAbstract [English]
SARS-CoV-2 emerged from zoonotic coronaviruses and is a novel beta-coronavirus which causes severe respiratory disease (pneumonia and lung failure), termed COVID-19. This paper describes SARS-CoV-2 genetic features (mutations and molecular epidemiology) but highlights its key differences from animal coronaviruses. We conducted a synthesis of the knowledge regarding clinical, genetic and pathological features of animal coronaviruses in comparison to SARS-CoV-2, along with recent evidence of interspecies transmission and recombination of animal coronaviruses to inform a One Health perspective of SARS-CoV-2 infection. We also take a closer look at the likely animal reservoirs and zoonotic origins of this novel virus that could help to curb disease transmission and minimize disease impact.
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Epidemiology Working Group for NCIP Epidemic Response, Chinese Center for Disease Control and Prevention. [The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) in China]. Zhonghua Liu Xing Bing Xue Za Zhi. 2020 Feb 10;41(2):145-151. Chinese. doi: 10.3760/cma.j.issn.0254-6450.2020.02.003.
Brett TS, Rohani P. Transmission dynamics reveal the impracticality of COVID-19 herd immunity strategies. Proc Natl Acad Sci U S A. 2020 Oct 13;117(41):25897-25903. doi: 10.1073/pnas.2008087117. DOI: https://doi.org/10.1073/pnas.2008087117
Guo R, Fan B, Chang X, Zhou J, Zhao Y, Shi D, Yu Z, He K, Li B. Characterization and evaluation of the pathogenicity of a natural recombinant transmissible gastroenteritis virus in China. Virology. 2020 Jun;545:24-32. doi: 10.1016/j.virol.2020.03.001. DOI: https://doi.org/10.1016/j.virol.2020.03.001
Lee PI, Hsueh PR. Emerging threats from zoonotic coronaviruses-from SARS and MERS to 2019-nCoV. J Microbiol Immunol Infect. 2020 Jun;53(3):365-367. doi: 10.1016/j.jmii.2020.02.001. DOI: https://doi.org/10.1016/j.jmii.2020.02.001
Abdelrahman Z, Li M, Wang X. Comparative Review of SARS-CoV-2, SARS-CoV, MERS-CoV, and Influenza A Respiratory Viruses. Front Immunol. 2020 Sep 11;11:552909. doi: 10.3389/fimmu.2020.552909. DOI: https://doi.org/10.3389/fimmu.2020.552909
Mohammed, G., & Abdulrahman, G. (2023). Comparative ELISA Detection of SARS-COV-2 Monoclonal Antibodies in Patients` Serum, Saliva, and Nasal Fluid in Iraq. Israa University Journal for Applied Science, 6(2), 15–41. https://doi.org/10.52865/nwgt5493. DOI: https://doi.org/10.52865/nwgt5493
Gussow AB, Auslander N, Faure G, Wolf YI, Zhang F, Koonin EV. Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. Proc Natl Acad Sci U S A. 2020 Jun 30;117(26):15193-15199. doi: 10.1073/pnas.2008176117. DOI: https://doi.org/10.1073/pnas.2008176117
Mercatelli D, Giorgi FM. Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Front Microbiol. 2020 Jul 22;11:1800. doi: 10.3389/fmicb.2020.01800. DOI: https://doi.org/10.3389/fmicb.2020.01800
Xu S, Li Y. Beware of the second wave of COVID-19. Lancet. 2020 Apr 25;395(10233):1321-1322. doi: 10.1016/S0140-6736(20)30845-X. DOI: https://doi.org/10.1016/S0140-6736(20)30845-X
Wong ACP, Li X, Lau SKP, Woo PCY. Global Epidemiology of Bat Coronaviruses. Viruses. 2019 Feb 20;11(2):174. doi: 10.3390/v11020174. DOI: https://doi.org/10.3390/v11020174
Zhang, G., Li, B., Yoo, D., Qin, T., Zhang, X., Jia, Y., & Cui, S. (2020). Animal coronaviruses and SARS‐CoV‐2. Transboundary and Emerging Diseases. doi: 10.1111/tbed.13791 . DOI: https://doi.org/10.1111/tbed.13791
Tang X, Wu C, Li X, Song Y, Yao X, Wu X, Duan Y, Zhang H, Wang Y, Qian Z, Cui J, Lu J. On the origin and continuing evolution of SARS-CoV-2. Natl Sci Rev. 2020 Jun;7(6):1012-1023. doi: 10.1093/nsr/nwaa036. DOI: https://doi.org/10.1093/nsr/nwaa036
Wen J, Cheng Y, Ling R, Dai Y, Huang B, Huang W, Zhang S, Jiang Y. Antibody-dependent enhancement of coronavirus. Int J Infect Dis. 2020 Nov;100:483-489. doi: 10.1016/j.ijid.2020.09.015. DOI: https://doi.org/10.1016/j.ijid.2020.09.015
Zhang T, Wu Q, Zhang Z. Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak. Curr Biol. 2020 Apr 6;30(7):1346-1351.e2. doi: 10.1016/j.cub.2020.03.022. Epub 2020 Mar 19. Erratum in: Curr Biol. 2020 Apr 20;30(8):1578. doi: 10.1016/j.cub.2020.03.063. DOI: https://doi.org/10.1016/j.cub.2020.03.022
Zhang X, Deng T, Lu J, Zhao P, Chen L, Qian M, Guo Y, Qiao H, Xu Y, Wang Y, Li X, Zhang G, Wang Z, Bian C. Molecular characterization of variant infectious bronchitis virus in China, 2019: Implications for control programmes. Transbound Emerg Dis. 2020 May;67(3):1349-1355. doi: 10.1111/tbed.13477. DOI: https://doi.org/10.1111/tbed.13477
Hasoksuz M, Alekseev K, Vlasova A, Zhang X, Spiro D, Halpin R, Wang S, Ghedin E, Saif LJ. Biologic, antigenic, and full-length genomic characterization of a bovine-like coronavirus isolated from a giraffe. J Virol. 2007 May;81(10):4981-90. doi: 10.1128/JVI.02361-06. DOI: https://doi.org/10.1128/JVI.02361-06
Toyoshima, Y., Nemoto, K., Matsumoto, S. et al. SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. J Hum Genet 65, 1075–1082 (2020). https://doi.org/10.1038/s10038-020-0808-9. DOI: https://doi.org/10.1038/s10038-020-0808-9
Chen Y, Liu Q, Guo D. Emerging coronaviruses: Genome structure, replication, and pathogenesis. J Med Virol. 2020 Apr;92(4):418-423. doi: 10.1002/jmv.25681. Epub 2020 Feb 7. Erratum in: J Med Virol. 2020 Oct;92(10):2249. doi: 10.1002/jmv.26234. DOI: https://doi.org/10.1002/jmv.26234
Ugurel OM, Ata O, Turgut-Balik D. An updated analysis of variations in SARS-CoV-2 genome. Turk J Biol. 2020 Jun 21;44(3):157-167. doi: 10.3906/biy-2005-111. DOI: https://doi.org/10.3906/biy-2005-111
Kang S, Yang M, Hong Z, Zhang L, Huang Z, Chen X, He S, Zhou Z, Zhou Z, Chen Q, Yan Y, Zhang C, Shan H, Chen S. Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites. Acta Pharm Sin B. 2020 Jul;10(7):1228-1238. doi: 10.1016/j.apsb.2020.04.009. DOI: https://doi.org/10.1016/j.apsb.2020.04.009
Domańska-Blicharz K, Woźniakowski G, Konopka B, Niemczuk K, Welz M, Rola J, Socha W, Orłowska A, Antas M, Śmietanka K, Cuvelier-Mizak B. Animal Coronaviruses in the Light of COVID-19. J Vet Res. 2020 Aug 2;64(3):333-345. doi: 10.2478/jvetres-2020-0050. DOI: https://doi.org/10.2478/jvetres-2020-0050
Ward JM, Munn RJ, Gribble DH, Dungworth DL. An observation of feline infectious peritonitis. Vet Rec. 1968 Oct 19;83(16):416-7. doi: 10.1136/vr.83.16.416. DOI: https://doi.org/10.1136/vr.83.16.416
Decaro N, Buonavoglia C. An update on canine coronaviruses: viral evolution and pathobiology. Vet Microbiol. 2008 Dec 10;132(3-4):221-34. doi: 10.1016/j.vetmic.2008.06.007. DOI: https://doi.org/10.1016/j.vetmic.2008.06.007
Buonavoglia C, Decaro N, Martella V, Elia G, Campolo M, Desario C, Castagnaro M, Tempesta M. Canine coronavirus highly pathogenic for dogs. Emerg Infect Dis. 2006 Mar;12(3):492-4. doi: 10.3201/eid1203.050839. DOI: https://doi.org/10.3201/eid1203.050839
Sanchez-Morgado JM, Poynter S, Morris TH. Molecular characterization of a virulent canine coronavirus BGF strain. Virus Res. 2004 Aug;104(1):27-31. doi: 10.1016/j.virusres.2004.02.038. DOI: https://doi.org/10.1016/j.virusres.2004.02.038
Alfano F, Fusco G, Mari V, Occhiogrosso L, Miletti G, Brunetti R, Galiero G, Desario C, Cirilli M, Decaro N. Circulation of pantropic canine coronavirus in autochthonous and imported dogs, Italy. Transbound Emerg Dis. 2020 Sep;67(5):1991-1999. doi: 10.1111/tbed.13542. DOI: https://doi.org/10.1111/tbed.13542
Shiba N, Maeda K, Kato H, Mochizuki M, Iwata H. Differentiation of feline coronavirus type I and II infections by virus neutralization test. Vet Microbiol. 2007 Oct 6;124(3-4):348-52. doi: 10.1016/j.vetmic.2007.04.031. DOI: https://doi.org/10.1016/j.vetmic.2007.04.031
Terada Y, Matsui N, Noguchi K, Kuwata R, Shimoda H, Soma T, Mochizuki M, Maeda K. Emergence of pathogenic coronaviruses in cats by homologous recombination between feline and canine coronaviruses. PLoS One. 2014 Sep 2;9(9):e106534. doi: 10.1371/journal.pone.0106534. DOI: https://doi.org/10.1371/journal.pone.0106534
Jaimes JA, Millet JK, Stout AE, André NM, Whittaker GR. A Tale of Two Viruses: The Distinct Spike Glycoproteins of Feline Coronaviruses. Viruses. 2020 Jan 10;12(1):83. doi: 10.3390/v12010083. DOI: https://doi.org/10.3390/v12010083
Jaimes JA, Whittaker GR. Feline coronavirus: Insights into viral pathogenesis based on the spike protein structure and function. Virology. 2018 Apr;517:108-121. doi: 10.1016/j.virol.2017.12.027. DOI: https://doi.org/10.1016/j.virol.2017.12.027
Vlasova, A. N., Wang, Q., Jung, K., Langel, S. N., Yashpal Singh Malik, & Saif, L. J. (2020). Porcine Coronaviruses. Livestock Diseases and Management, 79–110. https://doi.org/10.1007/978-981-15-0402-0_4. DOI: https://doi.org/10.1007/978-981-15-0402-0_4
Zhang X, Zhu Y, Zhu X, Chen J, Shi H, Shi D, Dong H, Feng L. ORF3a deletion in field strains of porcine-transmissible gastroenteritis virus in China: A hint of association with porcine respiratory coronavirus. Transbound Emerg Dis. 2017 Jun;64(3):698-702. doi: 10.1111/tbed.12634. DOI: https://doi.org/10.1111/tbed.12634
Chen F, Knutson TP, Rossow S, Saif LJ, Marthaler DG. Decline of transmissible gastroenteritis virus and its complex evolutionary relationship with porcine respiratory coronavirus in the United States. Sci Rep. 2019 Mar 8;9(1):3953. doi: 10.1038/s41598-019-40564-z. DOI: https://doi.org/10.1038/s41598-019-40564-z
Two consecutive proline substitutions in the fusion peptide of swine acute diarrhea syndrome coronavirus spike protein reduce cell-cell fusion. (2023). Journal of Preventive Veterinary Medicine, 47(4), 185–189. https://doi.org/10.13041/jpvm.2023.47.4.185 DOI: https://doi.org/10.13041/jpvm.2023.47.4.185
Ma T, Xu L, Ren M, Shen J, Han Z, Sun J, Zhao Y, Liu S. Novel genotype of infectious bronchitis virus isolated in China. Vet Microbiol. 2019 Mar;230:178-186. doi: 10.1016/j.vetmic.2019.01.020. DOI: https://doi.org/10.1016/j.vetmic.2019.01.020
Zhou H, Zhang M, Tian X, Shao H, Qian K, Ye J, Qin A. Identification of a novel recombinant virulent avian infectious bronchitis virus. Vet Microbiol. 2017 Feb;199:120-127. doi: 10.1016/j.vetmic.2016.12.038. DOI: https://doi.org/10.1016/j.vetmic.2016.12.038
Lam TT, Jia N, Zhang YW, Shum MH, Jiang JF, Zhu HC, Tong YG, Shi YX, Ni XB, Liao YS, Li WJ, Jiang BG, Wei W, Yuan TT, Zheng K, Cui XM, Li J, Pei GQ, Qiang X, Cheung WY, Li LF, Sun FF, Qin S, Huang JC, Leung GM, Holmes EC, Hu YL, Guan Y, Cao WC. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature. 2020 Jul;583(7815):282-285. doi: 10.1038/s41586-020-2169-0. DOI: https://doi.org/10.1038/s41586-020-2169-0
Yang YL, Yu JQ, Huang YW. Swine enteric alphacoronavirus (swine acute diarrhea syndrome coronavirus): An update three years after its discovery. Virus Res. 2020 Aug;285:198024. doi: 10.1016/j.virusres.2020.198024. DOI: https://doi.org/10.1016/j.virusres.2020.198024
Boley PA, Alhamo MA, Lossie G, Yadav KK, Vasquez-Lee M, Saif LJ, Kenney SP. Porcine Deltacoronavirus Infection and Transmission in Poultry, United States1. Emerg Infect Dis. 2020 Feb;26(2):255-265. doi: 10.3201/eid2602.190346. DOI: https://doi.org/10.3201/eid2602.190346
Puelles VG, Lütgehetmann M, Lindenmeyer MT, Sperhake JP, Wong MN, Allweiss L, Chilla S, Heinemann A, Wanner N, Liu S, Braun F, Lu S, Pfefferle S, Schröder AS, Edler C, Gross O, Glatzel M, Wichmann D, Wiech T, Kluge S, Pueschel K, Aepfelbacher M, Huber TB. Multiorgan and Renal Tropism of SARS-CoV-2. N Engl J Med. 2020 Aug 6;383(6):590-592. doi: 10.1056/NEJMc2011400. DOI: https://doi.org/10.1056/NEJMc2011400
Belser JA, Katz JM, Tumpey TM. The ferret as a model organism to study influenza A virus infection. Dis Model Mech. 2011 Sep;4(5):575-9. doi: 10.1242/dmm.007823. DOI: https://doi.org/10.1242/dmm.007823
M Najimudeen S, H Hassan MS, C Cork S, Abdul-Careem MF. Infectious Bronchitis Coronavirus Infection in Chickens: Multiple System Disease with Immune Suppression. Pathogens. 2020 Sep 24;9(10):779. doi: 10.3390/pathogens9100779. DOI: https://doi.org/10.3390/pathogens9100779
Decaro N, Martella V, Saif LJ, Buonavoglia C. COVID-19 from veterinary medicine and one health perspectives: What animal coronaviruses have taught us. Res Vet Sci. 2020 Aug;131:21-23. doi: 10.1016/j.rvsc.2020.04.009. DOI: https://doi.org/10.1016/j.rvsc.2020.04.009
Cook JK, Jackwood M, Jones RC. The long view: 40 years of infectious bronchitis research. Avian Pathol. 2012;41(3):239-50. doi: 10.1080/03079457.2012.680432. DOI: https://doi.org/10.1080/03079457.2012.680432
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