The phylogenetic analysis for the partial RdRp region revealed the presence of distinct BtCoVs in both the bats. The genomic sequences retrieved from the Indian sequences form a distinct cluster. The three CoV_BtRtBetaCoV/GX2018 sequences retrieved from the Indian Rousettus bats were 5.8-6.7 per cent different from the reference sequence, which was retrieved from Rhinolophus affinis. The two CoV_BtRtBetaCoV/GX2018 sequences retrieved from different bats were 1.2 per cent different from each other. The effect of host influence on the nt usage of the virus cannot be denied; however, it needs to be explored further in detail.