Abstract
SARS-CoV-2 was originated from zoonotic coronaviruses and confirmed as a novel beta-coronavirus, which causes serious respiratory illness such as pneumonia and lung failure, COVID-19. In this review, we describe the genetic characteristics of SARS-CoV-2, including types of mutation, and molecular epidemiology, highlighting its key difference from animal coronaviruses. We further summarized the current knowledge on clinical, genetic, and pathological features of several animal coronaviruses and compared them with SARS-CoV-2, as well as recent evidences of interspecies transmission and recombination of animal coronaviruses to provide a better understanding of SARS-CoV-2 infection in One Health perspectives. We also discuss the potential wildlife hosts and zoonotic origin of this emerging virus in detail, that may help mitigate the spread and damages caused by the disease.
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Abdelrahman, Z., Li, M., and Wang, X. 2020. Comparative review of SARS-CoV-2, SARS-CoV, MERS-CoV, and influenza A respiratory viruses. Front. Immunol. 11, 552909.
Alfano, F., Fusco, G., Mari, V., Occhiogrosso, L., Miletti, G., Brunetti, R., Galiero, G., Desario, C., Cirilli, M., and Decaro, N. 2020. Circulation of pantropic canine coronavirus in autochthonous and imported dogs, Italy. Transbound. Emerg. Dis. 67, 1991–1999.
Belser, J.A., Katz, J.M., and Tumpey, T.M. 2011. The ferret as a model organism to study influenza A virus infection. Dis. Model. Mech. 4, 575–579.
Belsham, G.J., Rasmussen, T.B., Normann, P., Vaclavek, P., Strandbygaard, B., and Bøtner, A. 2016. Characterization of a novel chimeric swine enteric coronavirus from diseased pigs in central eastern Europe in 2016. Transbound. Emerg. Dis. 63, 595–601.
Binn, L.N., Lazar, E.C., Keenan, K.P., Huxsoll, D.L., Marchwicki, R.H., and Strano, A.J. 1974. Recovery and characterization of a coronavirus from military dogs with diarrhea. Proc. Annu. Meet. US Anim. Health Assoc. 78, 359–366.
Boley, P.A., Alhamo, M.A., Lossie, G., Yadav, K.K., Vasquez-Lee, M., Saif, L.J., and Kenney, S.P. 2020. Porcine deltacoronavirus infection and transmission in poultry, United States. Emerg. Infect. Dis. 26, 255–265.
Boniotti, M.B., Papetti, A., Lavazza, A., Alborali, G., Sozzi, E., Chiapponi, C., Faccini, S., Bonilauri, P., Cordioli, P., and Marthaler, D. 2016. Porcine epidemic diarrhea virus and discovery of a recombinant swine enteric coronavirus, Italy. Emerg. Infect. Dis. 22, 83–87.
Brett, T.S. and Rohani, P. 2020. Transmission dynamics reveal the impracticality of COVID-19 herd immunity strategies. Proc. Natl. Acad. Sci. USA 117, 25897–25903.
Buonavoglia, C., Decaro, N., Martella, V., Elia, G., Campolo, M., Desario, C., Castagnaro, M., and Tempesta, M. 2006. Canine coronavirus highly pathogenic for dogs. Emerg. Infect. Dis. 12, 492–494.
Cha, R.H., Yang, S.H., Moon, K.C., Joh, J.S., Lee, J.Y., Shin, H.S., Kim, D.K., and Kim, Y.S. 2016. A case report of a middle east respiratory syndrome survivor with kidney biopsy results. J. Korean Med. Sci. 31, 635–640.
Chen, F., Knutson, T.P., Rossow, S., Saif, L.J., and Marthaler, D.G. 2019. Decline of transmissible gastroenteritis virus and its complex evolutionary relationship with porcine respiratory coronavirus in the United States. Sci. Rep. 9, 3953.
Chen, Y., Liu, Q., and Guo, D. 2020. Emerging coronaviruses: Genome structure, replication, and pathogenesis. J. Med. Virol. 92, 418–423.
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 Nova, P.J.G., Cortey, M., Díaz, I., Puente, H., Rubio, P., Martín, M., and Carvajal, A. 2020. A retrospective study of porcine epidemic diarrhoea virus (PEDV) reveals the presence of swine enteric coronavirus (SeCoV) since 1993 and the recent introduction of a recombinant PEDV-SeCoV in Spain. Transbound. Emerg. Dis. 67, 2911–2922.
Decaro, N. and Buonavoglia, C. 2008. An update on canine coronaviruses: viral evolution and pathobiology. Vet. Microbiol. 132, 221–234.
Decaro, N., Mari, V., Elia, G., Addie, D.D., Camero, M., Lucente, M.S., Martella, V., and Buonavoglia, C. 2010. Recombinant canine coronaviruses in dogs, Europe. Emerg. Infect. Dis. 16, 41–47.
Decaro, N., Martella, V., Saif, L.J., and Buonavoglia, C. 2020. COVID-19 from veterinary medicine and one health perspectives: What animal coronaviruses have taught us. Res. Vet. Sci. 131, 21–23.
Domańska-Blicharz, K., Woźniakowski, G., Konopka, B., Niemczuk, K., Welz, M., Rola, J., Socha, W., Orłowska, A., Antas, M., Śmietanka, K., et al. 2020. Animal coronaviruses in the light of COVID-19. J. Vet. Res. 64, 333–345.
Dye, C., Temperton, N., and Siddell, S.G. 2007. Type I feline coronavirus spike glycoprotein fails to recognize aminopeptidase N as a functional receptor on feline cell lines. J. Gen. Virol. 88, 1753–1760.
Edwards, C.E., Yount, B.L., Graham, R.L., Leist, S.R., Hou, Y.J., Dinnon, K.H. 3rd, Sims, A.C., Swanstrom, J., Gully, K., Scobey, T.D., et al. 2020. Swine acute diarrhea syndrome coronavirus replication in primary human cells reveals potential susceptibility to infection. Proc. Natl. Acad. Sci. USA 117, 26915–26925.
Epidemiology Working Group for NCIP Epidemic Response and Chinese Center for Disease Control and Prevention. 2020. The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) in China. Chin. J. Epidemiol. 41, 145–151.
Fiscus, S.A. and Teramoto, Y.A. 1987. Antigenic comparison of feline coronavirus isolates: evidence for markedly different peplomer glycoproteins. J. Virol. 61, 2607–2613.
Gu, J., Gong, E., Zhang, B., Zheng, J., Gao, Z., Zhong, Y., Zou, W., Zhan, J., Wang, S., Xie, Z., et al. 2005. Multiple organ infection and the pathogenesis of SARS. J. Exp. Med. 202, 415–424.
Guo, R., Fan, B., Chang, X., Zhou, J., Zhao, Y., Shi, D., Yu, Z., He, K., and Li, B. 2020. Characterization and evaluation of the pathogenicity of a natural recombinant transmissible gastroenteritis virus in China. Virology 545, 24–32.
Gussow, A.B., Auslander, N., Faure, G., Wolf, Y.I., Zhang, F., and Koonin, E.V. 2020. Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. Proc. Natl. Acad. Sci. USA 117, 15193–15199.
Hasoksuz, M., Alekseev, K., Vlasova, A., Zhang, X., Spiro, D., Halpin, R., Wang, S., Ghedin, E., and Saif, L.J. 2007. Biologic, antigenic, and full-length genomic characterization of a bovine-like coronavirus isolated from a giraffe. J. Virol. 81, 4981–4990.
Herrewegh, A.A., Smeenk, I., Horzinek, M.C., Rottier, P.J., and de Groot, R.J. 1998. Feline coronavirus type II strains 79–1683 and 79–1146 originate from a double recombination between feline coronavirus type I and canine coronavirus. J. Virol. 72, 4508–4514.
Jaimes, J.A., Millet, J.K., Stout, A.E., André, N.M., and Whittaker, G.R. 2020. A tale of two viruses: the distinct spike glycoproteins of feline coronaviruses. Viruses 12, 83.
Jaimes, J.A. and Whittaker, G.R. 2018. Feline coronavirus: Insights into viral pathogenesis based on the spike protein structure and function. Virology 517, 108–121.
Kang, S., Yang, M., Hong, Z., Zhang, L., Huang, Z., Chen, X., He, S., Zhou, Z., Zhou, Z., Chen, Q., et al. 2020. Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites. Acta Pharm. Sin. B 10, 1228–1238.
Krishnamoorthy, S., Swain, B., Verma, R.S., and Gunthe, S.S. 2020. SARS-CoV, MERS-CoV, and 2019-nCoV viruses: an overview of origin, evolution, and genetic variations. VirusDisease 31, 411–423.
Lam, T.T., Jia, N., Zhang, Y.W., Shum, M.H., Jiang, J.F., Zhu, H.C., Tong, Y.G., Shi, Y.X., Ni, X.B., Liao, Y.S., et al. 2020. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 583, 282–285.
Lee, P.I. and Hsueh, P.R. 2020. Emerging threats from zoonotic coronaviruses-from SARS and MERS to 2019-nCoV. J. Microbiol. Immunol. Infect. 53, 365–367.
Ma, T., Xu, L., Ren, M., Shen, J., Han, Z., Sun, J., Zhao, Y., and Liu, S. 2019. Novel genotype of infectious bronchitis virus isolated in China. Vet. Microbiol. 230, 178–186.
Meli, M., Kipar, A., Müller, C., Jenal, K., Gönczi, E., Borel, N., Gunn-Moore, D., Chalmers, S., Lin, F., Reinacher, M., et al. 2004. High viral loads despite absence of clinical and pathological findings in cats experimentally infected with feline coronavirus (FCoV) type i and in naturally FCoV-infected cats. J. Feline Med. Surg. 6, 69–81.
Mercatelli, D. and Giorgi, F.M. 2020. Geographic and genomic distribution of SARS-CoV-2 mutations. Front. Microbiol. 11, 1800.
Najimudeen, S.M., Hassan, M.S.H., Cork, S.C., and Abdul-Careem, M.F. 2020. Infectious bronchitis coronavirus infection in chickens: multiple system disease with immune suppression. Pathogens 9, 779.
Pedersen, N.C., Liu, H., Scarlett, J., Leutenegger, C.M., Golovko, L., Kennedy, H., and Kamal, F.M. 2012. Feline infectious peritonitis: Role of the feline coronavirus 3c gene in intestinal tropism and pathogenicity based upon isolates from resident and adopted shelter cats. Virus Res. 165, 17–28.
Plans-Rubió, P. 2012. The vaccination coverage required to establish herd immunity against influenza viruses. Prev. Med. 55, 72–77.
Pratelli, A., Martella, V., Decaro, N., Tinelli, A., Camero, M., Cirone, F., Elia, G., Cavalli, A., Corrente, M., Greco, G., et al. 2003. Genetic diversity of a canine coronavirus detected in pups with diarrhoea in Italy. J. Virol. Methods 110, 9–17.
Puelles, V.G., Lütgehetmann, M., Lindenmeyer, M.T., Sperhake, J.P., Wong, M.N., Allweiss, L., Chilla, S., Heinemann, A., Wanner, N., Liu, S., et al. 2020. Multiorgan and renal tropism of SARS-CoV-2. N Engl. J. Med. 383, 590–592.
Regan, A.D. and Whittaker, G.R. 2008. Utilization of DC-SIGN for entry of feline coronaviruses into host cells. J. Virol. 82, 11992–11996.
Sanchez-Morgado, J.M., Poynter, S., and Morris, T.H. 2004. Molecular characterization of a virulent canine coronavirus BGF strain. Virus Res. 104, 27–31.
Shiba, N., Maeda, K., Kato, H., Mochizuki, M., and Iwata, H. 2007. Differentiation of feline coronavirus type I and II infections by virus neutralization test. Vet. Microbiol. 124, 348–352.
Song, H.D., Tu, C.C., Zhang, G.W., Wang, S.Y., Zheng, K., Lei, L.C., Chen, Q.X., Gao, Y.W., Zhou, H.Q., Xiang, H., et al. 2005. Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proc. Natl. Acad. Sci. USA 102, 2430–2435.
Sun, W., Wang, L., Huang, H., Wang, W., Cao, L., Zhang, J., Zheng, M., and Lu, H. 2020. Genetic characterization and phylogenetic analysis of porcine deltacoronavirus (PDCoV) in Shandong province, China. Virus Res. 278, 197869.
Tang, X., Wu, C., Li, X., Song, Y., Yao, X., Wu, X., Duan, Y., Zhang, H., Wang, Y., and Qian, Z. 2020. On the origin and continuing evolution of SARS-CoV-2. Natl. Sci. Rev. 7, 1012–1023.
Tekes, G. and Thiel, H.J. 2016. Feline coronaviruses: pathogenesis of feline infectious peritonitis. Adv. Virus Res. 96, 193–218.
Tennant, B.J., Gaskell, R.M., Kelly, D.F., Carter, S.D., and Gaskell, C.J. 1991. Canine coronavirus infection in the dog following oronasal inoculation. Res. Vet. Sci. 51, 11–18.
Terada, Y., Matsui, N., Noguchi, K., Kuwata, R., Shimoda, H., Soma, T., Mochizuki, M., and Maeda, K. 2014. Emergence of pathogenic coronaviruses in cats by homologous recombination between feline and canine coronaviruses. PLoS ONE 9, e106534.
Toyoshima, Y., Nemoto, K., Matsumoto, S., Nakamura, Y., and Kiyotani, K. 2020. SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. J. Hum. Genet. 65, 1075–1082.
Ugurel, O.M., Ata, O., and Turgut-Balik, D. 2020. An updated analysis of variations in SARS-CoV-2 genome. Turk. J. Biol. 44, 157–167.
Vlasova, A., Wang, Q., Jung, K., Langel, S., Malik, Y.S., and Saif, L. 2020. Porcine coronaviruses. In Malik, Y., Singh, R., and Yadav, M. (eds.), Emerging and transboundary animal viruses, pp. 79–110. Springer, Singapore.
Ward, J.M., Munn, R.J., Gribble, D.H., and Dungworth, D.L. 1968. An observation of feline infectious peritonitis. Vet. Rec. 83, 416–417.
Wen, J., Cheng, Y., Ling, R., Dai, Y., Huang, B., Huang, W., Zhang, S., and Jiang, Y. 2020. Antibody-dependent enhancement of coronavirus. Int. J. Infect. Dis. 100, 483–489.
Wille, M. and Holmes, E.C. 2020. Wild birds as reservoirs for diverse and abundant gamma- and deltacoronaviruses. FEMS Microbiol. Rev. 44, 631–644.
Wong, A.C.P., Li, X., Lau, S.K.P., and Woo, P.C.Y. 2019. Global epidemiology of bat coronaviruses. Viruses 11, 174.
Xu, S. and Li, Y. 2020. Beware of the second wave of COVID-19. Lancet 395, 1321–1322.
Xu, Z., Zhong, H., Zhou, Q., Du, Y., Chen, L., Zhang, Y., Xue, C., and Cao, Y. 2018. A highly pathogenic strain of porcine deltacoronavirus caused watery diarrhea in newborn piglets. Virol. Sin. 33, 131–141.
Yang, Y.L., Yu, J.Q., and Huang, Y.W. 2020. Swine enteric alphacoronavirus (swine acute diarrhea syndrome coronavirus): an update three years after its discovery. Virus Res. 285, 198024.
Zhang, X., Deng, T., Lu, J., Zhao, P., Chen, L., Qian, M., Guo, Y., Qiao, H., Xu, Y., Wang, Y., et al. 2020a. Molecular characterization of variant infectious bronchitis virus in china, 2019: implications for control programmes. Transbound. Emerg. Dis. 67, 1349–1355.
Zhang, G., Li, B., Yoo, D., Qin, T., Zhang, X., Jia, Y., and Cui, S., 2020b. Animal coronaviruses and SARS-CoV-2. Transbound. Emerg. Dis. 1–14, Early View. doi: https://doi.org/10.1111/tbed.13791.
Zhang, Z., Shen, L., and Gu, X. 2016. Evolutionary dynamics of MERS-CoV: Potential recombination, positive selection and transmission. Sci. Rep. 6, 25049.
Zhang, T., Wu, Q., and Zhang, Z. 2020c. Probable pangolin origin of SARS-CoV-2 associated with the COVID-19 outbreak. Curr. Biol. 30, 1346–1351.
Zhang, X., Zhu, Y., Zhu, X., Chen, J., Shi, H., Shi, D., Dong, H., and Feng, L. 2017. ORF3a deletion in field strains of porcine-transmissible gastroenteritis virus in China: a hint of association with porcine respiratory coronavirus. Transbound. Emerg. Dis. 64, 698–702.
Zhou, P., Fan, H., Lan, T., Yang, X.L., Shi, W.F., Zhang, W., Zhu, Y., Zhang, Y.W., Xie, Q.M., Mani, S., et al. 2018. Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin. Nature 556, 255–258.
Zhou, H., Zhang, M., Tian, X., Shao, H., Qian, K., Ye, J., and Qin, A. 2017. Identification of a novel recombinant virulent avian infectious bronchitis virus. Vet. Microbiol. 199, 120–127.
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This research was supported by Korea Mouse Phenotyping Project (NRF-2019M3A9D5A01102797) of the Ministry of Science and ICT through the National Research Foundation, and supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. 2020R1C1C1008347).
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Na, W., Moon, H. & Song, D. A comprehensive review of SARS-CoV-2 genetic mutations and lessons from animal coronavirus recombination in one health perspective. J Microbiol. 59, 332–340 (2021). https://doi.org/10.1007/s12275-021-0660-4
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DOI: https://doi.org/10.1007/s12275-021-0660-4