The ecological niche of bat SCoV2rCs was firstly predicted using the four localities where bat viruses were previously detected1,6–8 (Fig. 5a). The highest probabilities of occurrence (highlighted in green in Fig. 5a) were found in Southeast Asia rather than in China. However, the AUC was only 0.58, and the value was < 95% CI null-model’s AUCs (0.74), indicating that the model was not statically supported at a significance level of 0.05 (see on line supplementary Fig. S2). As expected, these preliminary results confirmed that more than four records are needed to increase the accuracy of the distribution model22. For that reason, we used a genetic approach to determine geographic localities where bat SCoV2rCs are more likely to be found. The CO1 sequences of the nine bats in which a SCoV2rC was detected are shown by red arrows in Fig. 3. For R. affinis, the CO1 haplotype sequenced for the bat found positive for a SCoV2rC in southern Yunnan (site named Ch1 in Figs. 2, 3) was not found in other sampled localities. For the three other bat species found positive for SCoV2rCs, identical CO1 sequences were detected in bats from 17 other geographic localities (see online supplementary Table S1). For R. acuminatus, the four CO1 haplotypes sequenced for the bats found positive for SCoV2rCs in eastern Thailand (site named T4 in Figs. 2, 3) were also found in four localities in Cambodia (C2, C4, C5, and C6), two localities in southern Laos (L10 and L11), and three localities in southern Vietnam (V13, V14, and V17). The results indicate high connectivity among R. acuminatus populations from eastern Thailand, Cambodia, southern Laos and southern Vietnam. For R. malayanus, the CO1 haplotype sequenced for the bat found positive for a SCoV2rC in southern Yunnan (site named Ch3 in Figs. 2, 3) was also found in another locality in southern Yunnan (Ch2) and two localities in northern Laos (L1 and L3). The results indicate high connectivity among R. malayanus populations from southern China and northern Laos. For R. shameli, the single CO1 haplotype sequenced for the two bats found positive for SCoV2rCs in northern Cambodia (site named C3 in Figs. 2, 3) was also found in three other localities in Cambodia (C1, C2, and C5) and five localities in Laos (L4, L6, L8, L9, and L10). The results indicate high connectivity among R. shameli populations from Cambodia and Laos. Based on these genetic data, the ecological niche of bat SCoV2rCs was predicted using 21 records corresponding to the four localities where bat viruses were previously detected1,6–8 and the 17 localities where bats showed the same CO1 haplotype than virus-positive bats (data set B: 21 points; see online supplemntary Table S1 for details). The AUC was 0.96. The value was > 95% CI null-model’s AUCs (0.81), indicating that the model performs significantly better than a random model (see online supplementary Fig. S3). The areas showing the highest probabilities of occurrence (highlighted in green in Fig. 5b) include four main geographic areas: (i) southern Yunnan, northern Laos and bordering regions in northern Thailand and northwestern Vietnam; (ii) southern Laos, southwestern Vietnam, and northeastern Cambodia; (iii) the Cardamom Mountains in southwestern Cambodia and the East region of Thailand; and (iv) the Dawna Range in central Thailand and southeastern Myanmar.
Figure 5 Ecological niches of bat viruses closely related to SARS-CoV-2 (SCoV2rCs) predicted using 4 points (a) (AUC = 0.58) and 21 points (b) (AUC = 0.96). The geographic distributions of suitable environments were predicted using the Maxent algorithm in ENMTools (see “Methods” section for details). Black circles indicate localities used to build the distribution model (see geographic coordinates in online supplementary Table S1).