Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

The Ecological Niche of SARS-CoV-2-like Viruses in Bats, as Inferred from Phylogeographic Analyses of Rhinolophus Species

Version 1 : Received: 14 March 2021 / Approved: 16 March 2021 / Online: 16 March 2021 (09:39:15 CET)

A peer-reviewed article of this Preprint also exists.

Journal reference: Scientific Reports 2021, 11, 14276
DOI: 10.1038/s41598-021-93738-z


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 SARS-CoV-2-like viruses. Haplotype networks were constructed in order to investigate patterns of genetic diversity among bat populations of Southeast Asia. No strong geographic structure was found for the four Rhinolophus species, suggesting high dispersal capacity. The ecological niche of SARS-CoV-2 like viruses was predicted using the four localities of bat SARS-CoV-2-like viruses and the localities where bats showed identical or very similar CO1 haplotypes than virus-positive bats. The ecological niche of SARS-CoV-like viruses was deduced from the localities where bat SARS-CoV-like viruses were previously detected. The results show that the ecological niche of SARS-CoV2-like viruses includes several regions of mainland Southeast Asia whereas that of SARS-CoV-like viruses 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, and possibly Hainan and Taiwan), genomic recombination between highly divergent viruses is more likely to occur. Since recombinant viruses can threaten the benefit of vaccination campaigns, these regions should be under surveillance.


coronavirus; horseshoe bats; reservoir hosts; Indochina; China; herd immunity.


BIOLOGY, Animal Sciences & Zoology

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Received: 20 August 2021
The commenter has declared there is no conflict of interests.
Comment: Please note that the paper is now available as published version at
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