Analyses of CO1 sequences
Our sequences were aligned with 199 additional CO1 sequences downloaded from GenBank. Note that the CO1 sequences of seven bats found positive for viruses closely related to SARS-CoV-21,5,6 were assembled on Geneious Prime 2020.0.3 (Biomatters Ltd., Auckland, New Zealand) by mapping available SRA data to a CO1 reference. Sequences were aligned using AliView 1.2230. Our final CO1 alignments contain 37 sequences for R. acuminatus, 44 sequences for R. malayanus, 82 sequences for R. shameli, and 180 sequences for R. affinis. These four alignments were analysed in PopART 1.513 to construct haplotype networks using the median joining method with equal weights for all mutations. The 62 localities where bats were sampled are shown in the map of Fig. 2 and their geographic coordinates are detailed in online supplementary Table S1.