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 OemEmail author
Environmental Microbiology


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.


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



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.


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© 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

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