Inferring the ecological niche of bat viruses closely related to SARS-CoV-2 using phylogeographic analyses of Rhinolophus species

Abstract

The Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is the causal agent of the coronavirus disease 2019 (COVID-19) pandemic. To date, viruses closely related to SARS-CoV-2 have been reported in four bat species: Rhinolophus acuminatus, Rhinolophus affinis, Rhinolophus malayanus, and Rhinolophus shameli. Here, we analysed 343 sequences of the mitochondrial cytochrome c oxidase subunit 1 gene (CO1) from georeferenced bats of the four Rhinolophus species identified as reservoirs of viruses closely related to SARS-CoV-2. Haplotype networks were constructed in order to investigate patterns of genetic diversity among bat populations of Southeast Asia and China. No strong geographic structure was found for the four Rhinolophus species, suggesting high dispersal capacity. The ecological niche of bat viruses closely related to SARS-CoV-2 was predicted using the four localities in which bat viruses were recently discovered and the localities where bats showed the same CO1 haplotypes than virus-positive bats. The ecological niche of bat viruses related to SARS-CoV was deduced from the localities where bat viruses were previously detected. The results show that the ecological niche of bat viruses related to SARS-CoV2 includes several regions of mainland Southeast Asia whereas the ecological niche of bat viruses related to SARS-CoV is mainly restricted to China. In agreement with these results, human populations in Laos, Vietnam, Cambodia, and Thailand appear to be much less affected by the COVID-19 pandemic than other countries of Southeast Asia. In the climatic transitional zone between the two ecological niches (southern Yunnan, northern Laos, northern Vietnam), genomic recombination between highly divergent viruses is more likely to occur. Considering the limited data and the risk of recombinant bat-CoVs emergence as the source of new pandemics in humans, the bat populations in these regions should be under surveillance.

Variation in synonymous nucleotide composition among genomes of sarbecoviruses and consequences for the origin of COVID-19

“…The available data suggest therefore that Rhinolophus sinicus could be the main reservoir species for SCoVrC. In support of this hypothesis, the distribution of Rhinolophus sinicus (Burgin et al 2020;IUCN 2021) fits well with the ecological niche recently inferred for SCoVrC (Hassanin et al 2021b). It appears much more difficult to determine the main reservoir host species (if any) for SCoV2rC.…”

“…In agreement with previous studies (Hu et al 2018;Boni et al 2020;Li et al 2021), these results indicate that the three RecSar viruses (RspPrC31, RsZC45, and RsZXC21) have emerged through recombination between SCoVrC and SCoV2rC genomes. The genomic recombination between these two divergent Sarbecovirus lineages may have occurred preferrentially in the geographic area including southern Yunnan, northern Laos and northern Vietnam, where the ecological niches of SCoVrC and SCoV2rC slightly overlap (Hassanin et al 2021b). It can be also proposed that divergent or recombined variants of Sarbecovirus may have dispersed from Yunnan to eastern China through several generations of bats via occasional contacts in caves between populations usually found in different regions.…”

“…Biogeographically, the most striking result of this study is that the first dimension of all PCAs of Figures 2-4 allowed to separate temperate versus tropical groups of Sarbecovirus. Indeed, two latitudinal groups can be separated in Asia (Figure 5): the tropical group contains SCoV2rC, for which the ecological niche was inferred to include southern Yunnan and several regions of minaland Southeast Asia (Hassanin et al 2021b), and PangSar, for which the most likely origin is Southeast Asia (Hassanin et al 2021a); and the temperate group is composed of SCoVrC, for which the ecological niche was inferred to contain most southern and eastern provinces of China, as well as the Korean Peninsula, Japan, Taiwan, northeastern India, and northern regions of Myanmar and Vietnam (Hassanin et al 2021b), Rc-o319, which is virus from Japan, and YunSar, which is currently endemic to Yunnan. Similarily, two latitudinal groups can be separated in the western Old World (Figure 5): RspKY72 from Kenya in East Africa versus RbBM48-31 from Bulgaria in Europe.…”

“…Five SARS-CoV-2 related coronaviruses (SCoV2rC), sharing between 92 and 96% of genomic identity with SARS-CoV-2, were recently sequenced from five horseshoe bat species sampled in Yunnan (Rhinolophus affinis, Rhinolophus malayanus, and Rhinolophus pusillus), Cambodia (Rhinolophus shameli) and Thailand (Rhinolophus acuminatus) (Zhou H. et al 2020;Zhou P. et al 2020;Hul et al 2021;Wacharapluesadee et al 2021;Zhou et al 2021). Based on these discoveries, the ecological niche of bat SCoV2rC was inferred using phylogeographic analyses of Rhinolophus species and it was found to include the four following geographic areas (Hassanin et al 2021b): (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. Importantly, the distribution of Sunda pangolin (Manis javanica) covers all these four geographic areas, as well as most other regions of mainland Southeast Asia, Borneo, Sumatra and Java (IUCN 2021).…”

The continuing search for the origins of SARS-CoV-2

“…To date, all SARS-CoV-2-related viruses from bats are detected in Rhinolophus sp , the majority in Southeast Asia. SARS-CoV-2-related positive Rhinolophid species are diverse; however, their ranges and behaviors intertwine, promoting viral transmission, spread, and recombination ( Hassanin et al., 2021 ). This viral diversity and prevalence, coupled with high population density and a richness of other potential bridge species, makes Southeast Asia a hotspot for emerging infectious diseases.…”