Genetic Characteristics of Coronaviruses from Korean Bats in 2016

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

Fig. 1

Location of South Korea and geographical location of coronavirus-positive bat samples. Black circle Bat-CoV from oral swabsm. Black up-pointing triangle Bat-CoV from fecal samples. White up-pointing triangle Bat-CoV from a bat carcass

Fig. 2

Phylogenetic tree constructed from 392-nt RdRp sequences of Korean bat coronaviruses detected in this study and from other coronaviruses. Phylogenetic trees were constructed by using the neighbor joining method and bootstrap values were determined by 3000 replicates. Scale bar the estimated genetic distance of these viruses. Black circle sequences from oral swabs Black up-pointing triangle sequences from fecal samples. White up-pointing triangle sequences from carcass

Fig. 3

Phylogenetic tree of Korean bat coronaviruses detected by Kim et al. [13] and in this study, based on 355-nt sequences. Phylogenetic trees were constructed by using the neighbor joining method and bootstrap values were determined by 3000 replicates. Scale bar the estimated genetic distance of these viruses. Black circle sequences from oral swabs. Black up-pointing triangle sequences from fecal samples. White up-pointing triangle sequences from carcass