Fig. 2

Phylogenetic tree of novel coronaviruses based on the nucleotide sequence of the partial RdRp gene. Maximum-likelihood tree of 348 bp fragment of the RdRp gene from bat CoVs found in this study are colored according to their subgenera (Yellow  = Borneo Beta-1 and Borneo Beta-2; Green  = Borneo Alpha-1 and Borneo Alpha-2). Microhyla letovirus 1 (MLeV) (GVEC01031551) was used as the outgroup. Individual nodes are considered well supported when ML bootstrap values (BS) are at least 70% and Bayesian inference (PP) are at least 0.95% and tree with the highest log likelihood is shown (− 8794.58). Taxa are named according to the following pattern: Accension Number CoV Genus/Source or host/Country/Lab code/Year. The following are the names in full of species, M.nip, Megaerops niphanae; C.sph, Cynopterus sphinx; C.bra, Cynopterus brachyotis; P.jag, Ptenochirus jagori; M.dau, Myotis daubentonii; P.cor. Pipistrellus coromandra; H.pom, Hipposideros pomona; H.gal, Hipposideros galeritus; H.pra, Hipposideros pratti; H.lar, Hipposideros larvatus; H.dia, Hipposideros diadema; H.lek, Hipposideros lekaguli; R.hip, Rhinolophus hipposideros; R.fer, Rhinolophus ferrumequinum; R.sha, Rhinolophus shameli; S.kuh, Scotophilus heathii and S.hea, Scotophilus heathii. Accension Numbers of positive bat guano samples are MZ574065–MZ574074