Phylogenetic trees of the coronavirus (CoV) RNA-dependent RNA polymerase (RdRp) gene at the nucleotide level. Maximum-likelihood tree of a 353 bp fragment of the RdRp gene from bat CoVs found in this study are colored according to their roost (Dark blue = Chakarn cave, CK; Pink = Rad cave, RD; Red = Chonburi province, CB; Pale blue = Ang Aed, AA; Green = Sarika cave, SK) and previously found in bats and other animals (black). A Bulbul deltacoronavirus HKU11-934 was used as outgroup. Alignments were constructed using Multiple Alignment Fast Fourier Transform, MAFFT. Bootstrap values were determined using 1000 replicates via MEGA 5. The tree was visualised using the FigTree program, version 1.4.0. Taxa are named according to the following pattern: identification code/strain or isolate/typical host/country/collection year/accession number. Cyn_bra, Cynopterus brachyotis; Cyn_sph, Cynopterus sphinx; Tap_mel, Taphozous melanopogon; Hip_arm, Hipposideros armiger; Hip_lar, Hipposideros larvatus; Hip_lek, Hipposideros lekaguli; Meg_lyr, Megaderma lyra; Rhi_sha, Rhinolophus shameli; Min_mag, Miniopterus magnater; Min_pus, Miniopterus pusillus; Min_sch, Miniopterus schreibersii; Sco_kuh, Scotophilus kuhlii; Sco_hea, Scotophilus heathii. There were 7, 4, 6, and 3 different sequences obtained from samples no. B128 (B128-1 to B128-7), B311 (B311-1 to B311-4), BFE55593 (BFE55593-1 to BFE55593-6, and B55700 (B55700-1 to B44700-3), respectively. Representative sequences where the same exact CoV species (>99% nucleotide similarity) was found in different individuals of the same bat species at the same site show in italic. Clades 1–6 of alphacoronavirus were categorized based on the CoVs previously reported in China; bat-CoV1A/B, −HKU7, −HKU8, −CoV512, −HKU10 and -HKU2, respectively while clade 7–8 and 9 of betacoronavirus were categorized based on HKU9 and SARS CoV, respectively. The percent nucleotide similarity within each clade is shown in parentheses under the clade name.