Detection of Severe Acute Respiratory Syndrome-Like, Middle East Respiratory Syndrome-Like Bat Coronaviruses and Group H Rotavirus in Faeces of Korean Bats

Abstract

Bat species around the world have recently been recognized as major reservoirs of several zoonotic viruses, such as severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), Nipah virus and Hendra virus. In this study, consensus primer-based reverse transcriptase polymerase chain reactions (RT-PCRs) and high-throughput sequencing were performed to investigate viruses in bat faecal samples collected at 11 natural bat habitat sites from July to December 2015 in Korea. Diverse coronaviruses were first detected in Korean bat faeces, including alphacoronaviruses, SARS-CoV-like and MERS-CoV-like betacoronaviruses. In addition, we identified a novel bat rotavirus belonging to group H rotavirus which has only been described in human and pigs until now. Therefore, our results suggest the need for continuing surveillance and additional virological studies in domestic bat.

Keywords: Korea; Middle East respiratory syndrome; bat; coronavirus; group H rotavirus; severe acute respiratory syndrome.

Figure 1

Phylogenetic trees constructed from bat coronavirus sequences detected in this study and from other coronaviruses. (a) bootstrap consensus tree inferred from 1000 replicates with the UPGMA method (evolutionary distance parameter: maximum composite likelihood method) based on 351 bases of the RNA‐dependent RNA polymerase gene, (b) bootstrap consensus tree inferred from 1000 replicates using the neighbour‐joining method (evolutionary distance parameter: maximum composite likelihood method) based on 163 bases of the spike gene. The box indicates the bat CoV sequences obtained in this study.

Figure 2

Phylogenetic trees constructed from Group H rotavirus‐related sequences detected in bat faeces in this study and sequences of other, representative rotavirus strains. The bootstrap consensus tree inferred from 1000 replicates using the neighbour‐joining method (evolutionary distances were computed using the Kimura 2‐parameter method). (a) 275 bases of the VP1 region, (b) 347 bases of the VP3 region, (c) 202 bases of the VP4 region. The box indicates the group H bat rotavirus sequences obtained in this study.