Following the Severe Acute Respiratory Syndrome (SARS) pandemic in 2002–03, caused by
the SARS coronavirus (SARS-CoV), intensive surveillance has detected a great diversity of
CoVs throughout the animal kingdom, especially in bats. The initial discovery of CoVs in
bats was made in China following the SARS outbreak [1-5]. The emergence of the Middle
Eastern Respiratory Syndrome (MERS) in 2012 renewed interest in bat-originated CoVs. The
molecular investigation in Saudi Arabia revealed one Taphozous perforatus bat whose virus
showed 100% nucleotide identity to the MERS virus found in the human index case [6].
Other subsequent studies have found MERS-related CoV lineages from a variety of bat
species globally [7-11]. CoVs are divided into four genera: Alphacoronavirus and
Betacoronavirus which largely infect mammals; and Gammacoronavirus and
Deltacoronavirus which primarily infect avian species [12]. CoVs in bats are generally of the
Alpha- and Betacoronavirus genus, and have been identified in bats of various species from
around the world. Thailand is home to 139 different bat species, of which two are endemic
species including Hipposideros pendleburyi and Murina balaensis (new species of genus
Murina) [13,14], however CoV surveillance has only been conducted on 25 (18%) of these
species [15]. The first report of bat CoVs in Thailand examined a total of 256 fecal specimens
and discovered 28 positive samples in H. larvatus and H. armiger [15]. Recently in a study in
Ratchaburi province, Thailand, we discovered lineage C betacoronavirus in dry bat guano
fertilizer, however the bat species was not identified as specimens were collected from a
mixed species roost [11]. As a result of the risk CoVs pose to human health, ecological
studies of CoVs in bats are warranted, particularly to understand the baseline viral diversity
circulating in wildlife hosts. Here we describe a comprehensive study of CoV diversity and
prevalence among bats in Eastern Thailand to explore CoV infections in bat populations