Advertisement

Microbial Ecology

, Volume 75, Issue 1, pp 174–182 | Cite as

Genetic Characteristics of Coronaviruses from Korean Bats in 2016

  • Saemi Lee
  • Seong-Deok Jo
  • Kidong Son
  • Injung An
  • Jipseol Jeong
  • Seung-Jun Wang
  • Yongkwan Kim
  • Weonhwa Jheong
  • Jae-Ku Oem
Environmental Microbiology

Abstract

Bats have increasingly been recognized as the natural reservoir of severe acute respiratory syndrome (SARS), coronavirus, and other coronaviruses found in mammals. However, little research has been conducted on bat coronaviruses in South Korea. In this study, bat samples (332 oral swabs, 245 fecal samples, 38 urine samples, and 57 bat carcasses) were collected at 33 natural bat habitat sites in South Korea. RT-PCR and sequencing were performed for specific coronavirus genes to identify the bat coronaviruses in different bat samples. Coronaviruses were detected in 2.7% (18/672) of the samples: 13 oral swabs from one species of the family Rhinolophidae, and four fecal samples and one carcass (intestine) from three species of the family Vespertiliodae. To determine the genetic relationships of the 18 sequences obtained in this study and previously known coronaviruses, the nucleotide sequences of a 392-nt region of the RNA-dependent RNA polymerase (RdRp) gene were analyzed phylogenetically. Thirteen sequences belonging to SARS-like betacoronaviruses showed the highest nucleotide identity (97.1–99.7%) with Bat-CoV-JTMC15 reported in China. The other five sequences were most similar to MERS-like betacoronaviruses. Four nucleotide sequences displayed the highest identity (94.1–95.1%) with Bat-CoV-HKU5 from Hong Kong. The one sequence from a carcass showed the highest nucleotide identity (99%) with Bat-CoV-SC2013 from China. These results suggest that careful surveillance of coronaviruses from bats should be continued, because animal and human infections may result from the genetic variants present in bat coronavirus reservoirs.

Keywords

Coronavirus Bats South Korea Severe acute respiratory syndrome Middle East respiratory syndrome Phylogenetic analysis 

Notes

Acknowledgements

We thank Dr. C.W. Jeong and his colleagues for their efforts in the collection of wild bat carcasses and samples. This research was supported by grant no. 2016-01-01-033 from the NIER of the Republic of Korea. The funders had no roles in the study design, data collection and analysis, decision to publish, or the preparation of the manuscript.

References

  1. 1.
    Brian DA, Baric RS (2005) Coronavirus genome structure and replication Curr Top Microbiol Immunol 287:1–30PubMedGoogle Scholar
  2. 2.
    Gonzalez J, Gomez-Puertas P, Cavanagh D, Gorbalenya A, Enjuanes L (2003) A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae Arch Virol 148:2207–2235CrossRefPubMedGoogle Scholar
  3. 3.
    Murray PR, Rosenthal KS, Pfaller MA (2009) Medical microbiology. MOSBY Elsevier, PhiladelphiaGoogle Scholar
  4. 4.
    Saif LJ (2004) Animal coronaviruses: what can they teach us about the severe acute respiratory syndrome? Rev Sci Tech 23:643–660CrossRefPubMedGoogle Scholar
  5. 5.
    Drexler JF, Corman VM, Drosten C (2014) Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS Antivir Res 101:45CrossRefPubMedGoogle Scholar
  6. 6.
    Ge X, Li J, Yang X, Chmura AA, Zhu G, Epstein JH, Mazet JK, Hu B, Zhang W, Peng C (2013) Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor Nature 503:535–538CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Li W, Shi Z, Yu M, Ren W, Smith C, Epstein JH, Wang H, Crameri G, Hu Z, Zhang H, Zhang J, McEachern J, Field H, Daszak P, Eaton BT, Zhang S, Wang LF (2005) Bats are natural reservoirs of SARS-like coronaviruses Science 310:676–679CrossRefPubMedGoogle Scholar
  8. 8.
    Quinn PJ, Markey BK, Leonard FC, FitzPatrick ES, Fanning S, Hartigan P (2011) Veterinary microbiology and microbial disease. John Wiley & Sons, HobokenGoogle Scholar
  9. 9.
    Shi Z, Hu Z (2008) A review of studies on animal reservoirs of the SARS coronavirus Virus Res 133:74–87CrossRefPubMedGoogle Scholar
  10. 10.
    Memish ZA, Mishra N, Olival KJ, Fagbo SF, Kapoor V, Epstein JH, AlHakeem R, Al Asmari M, Islam A, Kapoor A (2013) Middle East respiratory syndrome coronavirus in bats, Saudi Arabia Emerg Infect Dis 19:1819–1823CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Ithete NL, Stoffberg S, Corman VM, Cottontail VM, Richards LR, Schoeman MC, Drosten C, Drexler JF, Preiser W (2013) Close relative of human Middle East respiratory syndrome coronavirus in bat, South Africa Emerg Infect Dis 19:1697–1699CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Moratelli R, Calisher CH (2015) Bats and zoonotic viruses: can we confidently link bats with emerging deadly viruses? Mem Inst Oswaldo Cruz 110:1–22CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Calisher CH, Childs JE, Field HE, Holmes KV, Schountz T (2006) Bats: important reservoir hosts of emerging viruses Clin Microbiol Rev 19:531–545CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Kim H, Yoon S, Kim D, Koo B, Noh J, Kim J, Choi Y, Na W, Chang K, Song D (2016) Detection of severe acute respiratory syndrome-like, Middle East respiratory syndrome-like bat coronaviruses and group H rotavirus in Faeces of Korean bats Transbound Emerg Dis 63:365–372CrossRefPubMedGoogle Scholar
  15. 15.
    Poon LL, Chu DK, Chan KH, Wong OK, Ellis TM, Leung YH, Lau SK, Woo PC, Suen KY, Yuen KY, Guan Y, Peiris JS (2005) Identification of a novel coronavirus in bats J Virol 79:2001–2009CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Yang L, Wu Z, Ren X, Yang F, Zhang J, He G, Dong J, Sun L, Zhu Y, Zhang S, Jin Q (2014) MERS-related betacoronavirus in Vespertilio superans bats, China Emerg Infect Dis 20:1260–1262CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Lau SK, Li KS, Tsang AK, Lam CS, Ahmed S, Chen H, Chan KH, Woo PC, Yuen KY (2013) Genetic characterization of betacoronavirus lineage C viruses in bats reveals marked sequence divergence in the spike protein of pipistrellus bat coronavirus HKU5 in Japanese pipistrelle: implications for the origin of the novel Middle East respiratory syndrome coronavirus J Virol 87:8638–8650CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Son SW, Choi BJ (2001) Bats. Moonji publishing, SeoulGoogle Scholar
  19. 19.
    Fleming TH, Eby P, Kunz T, Fenton M (2003) Ecology of bat migration. In: Kunz T, Fenton M (eds) Bat ecology. The University of Chicago Press, Chicago, pp. 156–208Google Scholar
  20. 20.
    Anthony S, Ojeda-Flores R, Rico-Chavez O, Navarrete-Macias I, Zambrana-Torrelio C, Rostal M, Epstein J, Tipps T, Liang E, Sanchez-Leon M (2013) Coronaviruses in bats from Mexico J Gen Virol 94:1028–1038CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Lelli D, Papetti A, Sabelli C, Rosti E, Moreno A, Boniotti MB (2013) Detection of coronaviruses in bats of various species in Italy Viruses 5:2679–2689CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Tang XC, Zhang JX, Zhang SY, Wang P, Fan XH, Li LF, Li G, Dong BQ, Liu W, Cheung CL, Xu KM, Song WJ, Vijaykrishna D, Poon LL, Peiris JS, Smith GJ, Chen H, Guan Y (2006) Prevalence and genetic diversity of coronaviruses in bats from China J Virol 80:7481–7490CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Xu L, Zhang F, Yang W, Jiang T, Lu G, He B, Li X, Hu T, Chen G, Feng Y (2016) Detection and characterization of diverse alpha-and betacoronaviruses from bats in China Virol Sin 31:69–77CrossRefPubMedGoogle Scholar
  24. 24.
    De Benedictis P, Marciano S, Scaravelli D, Priori P, Zecchin B, Capua I, Monne I, Cattoli G (2014) Alpha and lineage C betaCoV infections in Italian bats Virus Genes 48:366–371CrossRefPubMedGoogle Scholar
  25. 25.
    Chu D, Poon L, Chan K, Chen H, Guan Y, Yuen K, Peiris J (2006) Coronaviruses in bent-winged bats (Miniopterus spp.) J Gen Virol 87:2461–2466CrossRefPubMedGoogle Scholar
  26. 26.
    Falcón A, Vázquez-Morón S, Casas I, Aznar C, Ruiz G, Pozo F, Perez-Brena P, Juste J, Ibáñez C, Garin I (2011) Detection of alpha and betacoronaviruses in multiple Iberian bat species Arch Virol 156:1883–1890CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Knobler AMS, Lemon S, Mack A, Sivitz L, Oberholtzer K (2004) Microbiology, ecology, and natural history of coronaviruses. In: Knobler AMS, Lemon S, Mack A, Sivitz L, Oberholtzer K (eds) Learning from SARS: preparing for the next disease outbreak-workshop summary. National Academies Press, Washington DC, pp. 137–172Google Scholar
  28. 28.
    Eckerle I, Müller MA, Kallies S, Gotthardt DN, Drosten C (2013) In-vitro renal epithelial cell infection reveals a viral kidney tropism as a potential mechanism for acute renal failure during Middle East respiratory syndrome (MERS) coronavirus infection Virol J 10:359CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Gallagher TM, Buchmeier MJ (2001) Coronavirus spike proteins in viral entry and pathogenesis Virology 279:371CrossRefPubMedGoogle Scholar
  30. 30.
    Smith C, de Jong C, Meers J, Henning J, Wang L, Field H (2016) Coronavirus infection and diversity in bats in the Australasian region EcoHealth 13:72CrossRefPubMedGoogle Scholar
  31. 31.
    Dominguez SR, O'Shea TJ, Oko LM, Holmes KV (2007) Detection of group 1 coronaviruses in bats in North America Emerg. Infect Dis 13:1295CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2017

Authors and Affiliations

  1. 1.Environmental Health Research DepartmentNational Institute of Environmental ResearchIncheonRepublic of Korea
  2. 2.Department of Veterinary Infectious Diseases, College of Veterinary MedicineChonbuk National UniversityIksanRepublic of Korea

Personalised recommendations