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

Alexandre Hassanin,Manon Curaudeau,Vuong Tan Tu,Gabor Csorba

doi:10.1038/s41598-021-93738-z

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.

Highlights

The Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is the causal agent of the coronavirus disease 2019 (COVID-19) pandemic
Viruses showing between 96.2 and 91.8% of genome identity with SARS-CoV-2 were identified from fecal samples of four horseshoe bat species: the RaTG13 virus (96.2%) was isolated from a R. affinis bat collected in Yunnan in 20131; the RmYN02 virus (93.7%) was found in a R. malayanus bat sampled in Yunnan in 20195; two variants of the same virus RshSTT200 (93.1%; other variant: RshSTT182) were detected in two R. shameli bats caught in northern Cambodia in 2 0106; and five variants of the same virus RacCS203 (91.8%; other variants: RacCS224, RacCS253, RacCS264, and RacCS271) were sequenced from five R. acuminatus bats collected in eastern Thailand in 20207
Since a virus related to SARS-CoV-2 (91.8% of genome identity), named RacCS203, was detected in five R. acuminatus bats caught in eastern Thailand in June 2 0206, the genetic pattern obtained for this species suggests that viruses closely related to RacCS203 may have circulated in most southern regions of mainland Southeast Asia

Summary

Introduction

The Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is the causal agent of the coronavirus disease 2019 (COVID-19) pandemic. The phylogeography of the four species R. acuminatus, R. affinis, R. malayanus and R. shameli was examined using the mitochondrial cytochrome c oxidase subunit 1 gene (CO1) from 343 georeferenced bats collected in 62 localities of Southeast Asia and China (Fig. 2).

Results

Conclusion