Zoonotic origins of human coronaviruses

Zi-Wei Ye, Shuofeng Yuan, Kit-San Yuen, Sin-Yee Fung, Chi-Ping Chan, Dong-Yan Jin, Zi-Wei Ye, Shuofeng Yuan, Kit-San Yuen, Sin-Yee Fung, Chi-Ping Chan, Dong-Yan Jin

Abstract

Mutation and adaptation have driven the co-evolution of coronaviruses (CoVs) and their hosts, including human beings, for thousands of years. Before 2003, two human CoVs (HCoVs) were known to cause mild illness, such as common cold. The outbreaks of severe acute respiratory syndrome (SARS) and the Middle East respiratory syndrome (MERS) have flipped the coin to reveal how devastating and life-threatening an HCoV infection could be. The emergence of SARS-CoV-2 in central China at the end of 2019 has thrusted CoVs into the spotlight again and surprised us with its high transmissibility but reduced pathogenicity compared to its sister SARS-CoV. HCoV infection is a zoonosis and understanding the zoonotic origins of HCoVs would serve us well. Most HCoVs originated from bats where they are non-pathogenic. The intermediate reservoir hosts of some HCoVs are also known. Identifying the animal hosts has direct implications in the prevention of human diseases. Investigating CoV-host interactions in animals might also derive important insight on CoV pathogenesis in humans. In this review, we present an overview of the existing knowledge about the seven HCoVs, with a focus on the history of their discovery as well as their zoonotic origins and interspecies transmission. Importantly, we compare and contrast the different HCoVs from a perspective of virus evolution and genome recombination. The current CoV disease 2019 (COVID-19) epidemic is discussed in this context. In addition, the requirements for successful host switches and the implications of virus evolution on disease severity are also highlighted.

Keywords: COVID-19; MERS-CoV; SARS-CoV; SARS-CoV-2; animal reservoir; bats; coronavirus.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interest exists.

© The author(s).

Figures

Figure 1
Figure 1
Animal hosts of HCoVs. Blue, green, purple, red, orange, grey, brown arrows represent the transmission of HCoV-NL63, HCoV-229E, SARS-CoV, MERS-CoV, SARS-CoV-2, HCoV-OC43 and HCoV-HKU1 from their natural hosts (bats or rodents) to the intermediate hosts (camelids, civets, dromedary camels, pangolins or bovines), and eventually to the human population. No concrete evidence exists on the intermediated host(s) of HCoV-NL63 and HCoV-HKU1, which was shown as a question mark (?).

References

    1. Weiss SR, Navas-Martin S. Coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus. Microbiol Mol Biol Rev. 2005;69:635–64.
    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;24:490–502.
    1. Lai MM, Cavanagh D. The molecular biology of coronaviruses. Adv Virus Res. 1997;48:1–100.
    1. Wong LY, Lui PY, Jin DY. A molecular arms race between host innate antiviral response and emerging human coronaviruses. Virol Sin. 2016;31:12–23.
    1. Chan JF, Kok KH, Zhu Z, Chu H, To KK, Yuan S. et al. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg Microbes Infect. 2020;9:221–36.
    1. Chan JF, To KK, Tse H, Jin DY, Yuen KY. Interspecies transmission and emergence of novel viruses: lessons from bats and birds. Trends Microbiol. 2013;21:544–55.
    1. Hu B, Ge X, Wang LF, Shi Z. Bat origin of human coronaviruses. Virol J. 2015;12:221.
    1. Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020.
    1. Cui J, Li F, Shi ZL. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol. 2019;17:181–92.
    1. Bucknall RA, King LM, Kapikian AZ, Chanock RM. Studies with human coronaviruses. II. Some properties of strains 229E and OC43. Proc Soc Exp Biol Med. 1972;139:722–7.
    1. Woo PC, Lau SK, Tsoi HW, Huang Y, Poon RW, Chu CM. et al. Clinical and molecular epidemiological features of coronavirus HKU1-associated community-acquired pneumonia. J Infect Dis. 2005;192:1898–907.
    1. Kendall EJ, Bynoe ML, Tyrrell DA. Virus isolations from common colds occurring in a residential school. Br Med J. 1962;2:82–6.
    1. New respiratory virus. Br Med J. 1967; 3: 752.
    1. Cheng VC, Lau SK, Woo PC, Yuen KY. Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection. Clin Microbiol Rev. 2007;20:660–94.
    1. Peiris JS, Lai ST, Poon LL, Guan Y, Yam LY, Lim W. et al. Coronavirus as a possible cause of severe acute respiratory syndrome. Lancet. 2003;361:1319–25.
    1. 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;367:1814–20.
    1. Hilgenfeld R, Peiris M. From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses. Antiviral Res. 2013;100:286–95.
    1. Gao H, Yao H, Yang S, Li L. From SARS to MERS: evidence and speculation. Front Med. 2016;10:377–82.
    1. Jiang S, Shi ZL. The First Disease X is Caused by a Highly Transmissible Acute Respiratory Syndrome Coronavirus. Virol Sin. 2020.
    1. Li X, Song Y, Wong G, Cui J. Bat origin of a new human coronavirus: there and back again. Sci China Life Sci. 2020.
    1. Cunningham CH, Stuart HO. Cultivation of the virus of infectious bronchitis of chickens in embryonated chicken eggs. Am J Vet Res. 1947;8:209–12.
    1. Cheever FS, Daniels JB. et al. A murine virus (JHM) causing disseminated encephalomyelitis with extensive destruction of myelin. J Exp Med. 1949;90:181–210.
    1. Lee KM, Moro M, Baker JA. Transmissible gastroenteritis in pigs. Am J Vet Res. 1954;15:364–72.
    1. Ritchie AE, Deshmukh DR, Larsen CT, Pomeroy BS. Electron microscopy of coronavirus-like particles characteristic of turkey bluecomb disease. Avian Dis. 1973;17:546–58.
    1. Evermann JF, Baumgartener L, Ott RL, Davis EV, McKeirnan AJ. Characterization of a feline infectious peritonitis virus isolate. Vet Pathol. 1981;18:256–65.
    1. Binn LN, Lazar EC, Keenan KP, Huxsoll DL, Marchwicki RH, Strano AJ. Recovery and characterization of a coronavirus from military dogs with diarrhea. Proc Annu Meet U S Anim Health Assoc. 1974. pp. 359–66.
    1. Hamre D, Procknow JJ. A new virus isolated from the human respiratory tract. Proc Soc Exp Biol Med. 1966;121:190–3.
    1. McIntosh K, Dees JH, Becker WB, Kapikian AZ, Chanock RM. Recovery in tracheal organ cultures of novel viruses from patients with respiratory disease. Proc Natl Acad Sci U S A. 1967;57:933–40.
    1. Tyrrell DA, Cohen S, Schlarb JE. Signs and symptoms in common colds. Epidemiol Infect. 1993;111:143–56.
    1. Bradburne AF, Bynoe ML, Tyrrell DA. Effects of a "new" human respiratory virus in volunteers. Br Med J. 1967;3:767–9.
    1. To KK, Hung IF, Chan JF, Yuen KY. From SARS coronavirus to novel animal and human coronaviruses. J Thorac Dis. 2013;5(Suppl 2):S103–8.
    1. van der Hoek L, Pyrc K, Jebbink MF, Vermeulen-Oost W, Berkhout RJ, Wolthers KC. et al. Identification of a new human coronavirus. Nat Med. 2004;10:368–73.
    1. Abdul-Rasool S, Fielding BC. Understanding Human Coronavirus HCoV-NL63. Open Virol J. 2010;4:76–84.
    1. Fouchier RA, Hartwig NG, Bestebroer TM, Niemeyer B, de Jong JC, Simon JH. et al. A previously undescribed coronavirus associated with respiratory disease in humans. Proc Natl Acad Sci U S A. 2004;101:6212–6.
    1. van der Hoek L, Sure K, Ihorst G, Stang A, Pyrc K, Jebbink MF. et al. Croup is associated with the novel coronavirus NL63. PLoS Med. 2005;2:e240.
    1. Woo PC, Lau SK, Chu CM, Chan KH, Tsoi HW, Huang Y. et al. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol. 2005;79:884–95.
    1. Lau SK, Woo PC, Yip CC, Tse H, Tsoi HW, Cheng VC. et al. Coronavirus HKU1 and other coronavirus infections in Hong Kong. J Clin Microbiol. 2006;44:2063–71.
    1. Wang Y, Li X, Liu W, Gan M, Zhang L, Wang J. et al. Discovery of a subgenotype of human coronavirus NL63 associated with severe lower respiratory tract infection in China, 2018. Emerg Microbes Infect. 2020;9:246–55.
    1. Coleman CM, Frieman MB. Emergence of the Middle East respiratory syndrome coronavirus. PLoS Pathog. 2013;9:e1003595.
    1. Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020.
    1. Risku M, Lappalainen S, Rasanen S, Vesikari T. Detection of human coronaviruses in children with acute gastroenteritis. J Clin Virol. 2010;48:27–30.
    1. Centers for Disease C, Prevention. Prevalence of IgG antibody to SARS-associated coronavirus in animal traders-Guangdong Province, China, 2003. MMWR Morb Mortal Wkly Rep. 2003;52:986–7.
    1. 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;302:276–8.
    1. Poon LL, Chu DK, Chan KH, Wong OK, Ellis TM, Leung YH. et al. Identification of a novel coronavirus in bats. J Virol. 2005;79:2001–9.
    1. Tu C, Crameri G, Kong X, Chen J, Sun Y, Yu M. et al. Antibodies to SARS coronavirus in civets. Emerg Infect Dis. 2004;10:2244–8.
    1. Lau SK, Woo PC, Li KS, Huang Y, Tsoi HW, Wong BH. et al. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci U S A. 2005;102:14040–5.
    1. Li W, Shi Z, Yu M, Ren W, Smith C, Epstein JH. et al. Bats are natural reservoirs of SARS-like coronaviruses. Science. 2005;310:676–9.
    1. Ge XY, Li JL, Yang XL, Chmura AA, Zhu G, Epstein JH. et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature. 2013;503:535–8.
    1. van Boheemen S, de Graaf M, Lauber C, Bestebroer TM, Raj VS, Zaki AM, Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans. mBio. 2012. 3.
    1. Cotten M, Lam TT, Watson SJ, Palser AL, Petrova V, Grant P. et al. Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus. Emerg Infect Dis. 2013;19:736–42B.
    1. Annan A, Baldwin HJ, Corman VM, Klose SM, Owusu M, Nkrumah EE. et al. Human betacoronavirus 2c EMC/2012-related viruses in bats, Ghana and Europe. Emerg Infect Dis. 2013;19:456–9.
    1. Lau SKP, Zhang L, Luk HKH, Xiong L, Peng X, Li KSM. et al. Receptor Usage of a Novel Bat Lineage C Betacoronavirus Reveals Evolution of Middle East Respiratory Syndrome-Related Coronavirus Spike Proteins for Human Dipeptidyl Peptidase 4 Binding. J Infect Dis. 2018;218:197–207.
    1. Luo CM, Wang N, Yang XL, Liu HZ, Zhang W, Li B, Discovery of Novel Bat Coronaviruses in South China That Use the Same Receptor as Middle East Respiratory Syndrome Coronavirus. J Virol. 2018. 92.
    1. Reusken CB, Haagmans BL, Muller MA, Gutierrez C, Godeke GJ, Meyer B. et al. Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study. Lancet Infect Dis. 2013;13:859–66.
    1. Chan JF, Lau SK, To KK, Cheng VC, Woo PC, Yuen KY. Middle East respiratory syndrome coronavirus: another zoonotic betacoronavirus causing SARS-like disease. Clin Microbiol Rev. 2015;28:465–522.
    1. Raj VS, Farag EA, Reusken CB, Lamers MM, Pas SD, Voermans J. et al. Isolation of MERS coronavirus from a dromedary camel, Qatar, 2014. Emerg Infect Dis. 2014;20:1339–42.
    1. Adney DR, Letko M, Ragan IK, Scott D, van Doremalen N, Bowen RA. et al. Bactrian camels shed large quantities of Middle East respiratory syndrome coronavirus (MERS-CoV) after experimental infection() Emerg Microbes Infect. 2019;8:717–23.
    1. Samara EM, Abdoun KA. Concerns about misinterpretation of recent scientific data implicating dromedary camels in epidemiology of Middle East respiratory syndrome (MERS) mBio. 2014;5:e01430–14.
    1. Lam T, Shum M, Zhu H, Tong Y, Ni X, Liao Y. et al. Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China. BIORXIV. 2020 doi: 10.1101/2020.02.13.945485.
    1. Liu P, Chen W, Chen JP. Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica) Viruses. 2019. 11.
    1. Hon CC, Lam TY, Shi ZL, Drummond AJ, Yip CW, Zeng F. et al. Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus. J Virol. 2008;82:1819–26.
    1. Donaldson EF, Haskew AN, Gates JE, Huynh J, Moore CJ, Frieman MB. Metagenomic analysis of the viromes of three North American bat species: viral diversity among different bat species that share a common habitat. J Virol. 2010;84:13004–18.
    1. Huynh J, Li S, Yount B, Smith A, Sturges L, Olsen JC. et al. Evidence supporting a zoonotic origin of human coronavirus strain NL63. J Virol. 2012;86:12816–25.
    1. Pfefferle S, Oppong S, Drexler JF, Gloza-Rausch F, Ipsen A, Seebens A. et al. Distant relatives of severe acute respiratory syndrome coronavirus and close relatives of human coronavirus 229E in bats, Ghana. Emerg Infect Dis. 2009;15:1377–84.
    1. Corman VM, Baldwin HJ, Tateno AF, Zerbinati RM, Annan A, Owusu M. et al. Evidence for an Ancestral Association of Human Coronavirus 229E with Bats. J Virol. 2015;89:11858–70.
    1. Tao Y, Shi M, Chommanard C, Queen K, Zhang J, Markotter W, Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History. J Virol. 2017. 91.
    1. Corman VM, Eckerle I, Memish ZA, Liljander AM, Dijkman R, Jonsdottir H. et al. Link of a ubiquitous human coronavirus to dromedary camels. Proc Natl Acad Sci U S A. 2016;113:9864–9.
    1. Vijgen L, Keyaerts E, Moes E, Thoelen I, Wollants E, Lemey P. et al. Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event. J Virol. 2005;79:1595–604.
    1. Sabir JS, Lam TT, Ahmed MM, Li L, Shen Y, Abo-Aba SE. et al. Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia. Science. 2016;351:81–4.
    1. Woo PC, Lau SK, Huang Y, Yuen KY. Coronavirus diversity, phylogeny and interspecies jumping. Exp Biol Med (Maywood) 2009;234:1117–27.
    1. Duffy S. Why are RNA virus mutation rates so damn high? PLoS Biol. 2018;16:e3000003.
    1. Zhao Z, Li H, Wu X, Zhong Y, Zhang K, Zhang YP. et al. Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evol Biol. 2004;4:21.
    1. Forni D, Cagliani R, Clerici M, Sironi M. Molecular Evolution of Human Coronavirus Genomes. Trends Microbiol. 2017;25:35–48.
    1. Bolles M, Donaldson E, Baric R. SARS-CoV and emergent coronaviruses: viral determinants of interspecies transmission. Curr Opin Virol. 2011;1:624–34.
    1. Graham RL, Baric RS. Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission. J Virol. 2010;84:3134–46.
    1. Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020.
    1. Hofmann H, Pyrc K, van der Hoek L, Geier M, Berkhout B, Pohlmann S. Human coronavirus NL63 employs the severe acute respiratory syndrome coronavirus receptor for cellular entry. Proc Natl Acad Sci U S A. 2005;102:7988–93.
    1. Chinese SMEC. Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China. Science. 2004;303:1666–9.
    1. Cotten M, Watson SJ, Zumla AI, Makhdoom HQ, Palser AL, Ong SH, Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus. mBio. 2014. 5.
    1. Dijkman R, Jebbink MF, Wilbrink B, Pyrc K, Zaaijer HL, Minor PD. et al. Human coronavirus 229E encodes a single ORF4 protein between the spike and the envelope genes. Virol J. 2006;3:106.
    1. Crossley BM, Mock RE, Callison SA, Hietala SK. Identification and characterization of a novel alpaca respiratory coronavirus most closely related to the human coronavirus 229E. Viruses. 2012;4:3689–700.
    1. Calisher CH, Childs JE, Field HE, Holmes KV, Schountz T. Bats: important reservoir hosts of emerging viruses. Clin Microbiol Rev. 2006;19:531–45.
    1. Zhang G, Cowled C, Shi Z, Huang Z, Bishop-Lilly KA, Fang X. et al. Comparative analysis of bat genomes provides insight into the evolution of flight and immunity. Science. 2013;339:456–60.
    1. Pavlovich SS, Lovett SP, Koroleva G, Guito JC, Arnold CE, Nagle ER. et al. The Egyptian Rousette Genome Reveals Unexpected Features of Bat Antiviral Immunity. Cell. 2018;173:1098–110. e18.
    1. Menachery VD, Graham RL, Baric RS. Jumping species-a mechanism for coronavirus persistence and survival. Curr Opin Virol. 2017;23:1–7.
    1. Ahn M, Anderson DE, Zhang Q, Tan CW, Lim BL, Luko K. et al. Dampened NLRP3-mediated inflammation in bats and implications for a special viral reservoir host. Nat Microbiol. 2019;4:789–99.

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