Two different ecological niches for bat viruses related to either SARS-CoV or SARS-CoV-2
In the wild, sarbecoviruses were generally detected after examining fecal samples collected on dozens of bats. For instance, two sarbecoviruses were found7 among the total 59 bats collected at the same cave entrance in northern Cambodia in 2010 (unpublished data). However, this does not mean necessarily that sarbecoviruses were absent in negative samples, as degradation of RNA molecules and very low viral concentrations may prevent the detection of RNA viruses. Despite these difficulties, full genomes of Sarbecovirus have been sequenced from a wide diversity of horseshoe bat species collected in Asia, Africa and Europe5–10. Therefore, there is no doubt that Rhinolophus species constitute the natural reservoir host of all sarbecoviruses3,8. The genus Rhinolophus currently includes between 9211 and 10916 insectivorous species that inhabit temperate and tropical regions of the Old World, with a higher biodiversity in Asia (63–68 out of the 92–109 described species) than in Africa (34–38 species), Europe (5 species) and Oceania (5 species). Although some Rhinolophus species are solitary, most of them are gregarious and live in large colonies or small groups generally in caves and hollow trees, but also in burrows, tunnels, abandonned mines, and old buildings11,16. However, they prefer large caves with total darkness, where temperatures are stable and less affected by diurnal and seasonal climatic variations. Importantly, all Rhinolophus species in which sarbecoviruses were detected in previous studies1,5–9,17 are cave species that form small groups or colonies (up to several hundreds)11,18,19.
In China, many SCoVrCs were previously detected in several horseshoe bat species, including Rhinolophus sinicus, Rhinolophus ferrumequinum (currently R. nippon)16, Rhinolophus macrotis (currently R. episcopus)16, Rhinolophus pearsoni, and Rhinolophus pusillus, and it has been shown that they circulate not only among conspecific bats from the same colony, but also between bat species inhabiting the same caves17,20,21. The ecological niche predicted for bat SCoVrCs using a data set of 19 points (see online supplementary Table S2) is shown in Fig. 4. The AUC was 0.81. The value was > 95% CI null-model’s AUCs (0.68), indicating that the model performs significantly better than a random model (see online supplementary Fig. S1). The highest probabilities of occurrence (highlighted in green in Fig. 4) were found in Nepal, Bhutan, Bangladesh, northeastern India, northern Myanmar, northern Vietnam, most regions of China south of the Yellow River, Taiwan, North and South Korea, and southern Japan.
Figure 4 Ecological niche of bat viruses related to SARS-CoV (SCoVrCs). The geographic distribution of suitable environments was predicted using the Maxent algorithm in ENMTools (see “Methods” section for details). AUC = 0.81. Black circles indicate localities used to build the distribution model (see geographic coordinates in online supplementary Table S2).
In Southeast Asia and southern China, SCoV2rCs have currently been found in four Rhinolophus species (R. acuminatus, R. affinis, R. malayanus and R. shameli)1,6–8, but the greatest diversity of horseshoe bat species in mainland Southeast Asia (between 28 and 36 species)11,16 suggests that many sarbecoviruses will be discovered soon. Despite the limited data currently available on SCoV2rCs, several arguments support that bat intraspecific and interspecific transmissions also occur with SCoV2rCs. Firslty, recent genomic studies have revealed that SCoV2rCs circulate and evolve among horseshoe bats of the same colony, as five very similar genomes (nucleotide distances between 0.03% and 0.10%) were sequenced from five R. acuminatus bats collected from the same colony in eastern Thailand6, and as two genomes differing at only three nucleotide positions (distance = 0.01%) were sequenced from two R. shameli bats collected at the same cave entrance on the same night7. Secondly, the discovery of four viruses closely related to SARS-CoV-2 (between 96.2 and 91.8% of genome identity) in four different species of Rhinolophus is a strong evidence that interspecific transmission occurred several times in the past. As detailed in online supplementary Table S1, these species were collected together in several localities of Cambodia (three species in C1, C2, and C5; two species in C8), Laos (four species in L10; three species in L9; two species in L1, L5, L8, L11), and Vietnam (two speciess in V10, V9, V17, V18). These data corroborate previous studies suggesting that sarbecoviruses can be transmitted, at least occasionally, between Rhinolophus species sharing the same caves.
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).
Our results show that bat SCoVrCs and SCoV2rCs have different ecological niches: that of SCoVrCs covers mainly China and several adjacent countries and extends to latitudes between 18° and 43°N, whereas that of SCoV2rCs covers northern mainland Southeast Asia and extends to latitudes between 10° and 24°N. Most Rhinolophus species involved in the ecological niche of SCoVrCs have to hibernate in winter when insect populations become significantly less abundant. This may be different for most Rhinolophus species involved in the ecological niche of SCoVrC2s. Since this ecological difference may be crucial for the dynamics of viral transmission among bat populations, it needs to be further studied through comparative field surveys in different regions of China and Southeast Asia. The ecological niches of SCoVrCs and SCoV2rCs slightly overlap in the zone including southern Yunnan, northern Laos, and northern Vietnam (Figs. 4, 5b). This zone corresponds to the northern edge of tropical monsoon climate23. Highly divergent sarbecoviruses of the two main lineages SCoVrCs and SCoV2rCs are expected to be found in sympatry in this area. This is confirmed by the discovery of both SCoVrCs and SCoV2rCs in horseshoe bats collected in southern Yunnan1,6,21. Collectively, these data suggest that genomic recombination between viruses of the two divergent lineages are more likely to occur in bats roosting, at least seasonally, in the caves of these regions. Since highly recombinant viruses can threaten the benefit of vaccination campaigns, southern Yunnan, northern Laos, and northern Vietnam should be the targets of closer surveillance.