Within the family Coronaviridae, the subgenus Sarbecovirus includes two human viruses, SARS-CoV-2 and SARS-CoV (which was responsible for the SARS epidemic in 2002–2004)4. The genomes of these two viruses share only 80% of nucleotide identity, and whole-genome phylogenies have shown that they belong to two divergent lineages1,5–7, which we refer to herein as SARS-CoV related coronaviruses (SCoVrCs) and SARS-CoV-2 related coronaviruses (SCoV2rCs). Most SCoVrCs were discovered in bats collected in China after the SARS epidemic, and the great majority were found in horseshoe bat species of the genus Rhinolophus (family Rhinolophidae), suggesting that this taxon is the natural reservoir host of sarbecoviruses8. More recently, several 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 20106; 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. The bat species R. acuminatus and R. shameli are endemic to Southeast Asia whereas the two other bat species, R. affinis and R. malayanus, are distributed in both Southeast Asia and China (Fig. 1), suggesting that Southeast Asia is the main region where bat SCoV2rCs diversified. In addition, these recent data confirmed that the genus Rhinolophus is the natural reservoir host of all sarbecoviruses3,8. Note that this hypothesis was already corroborated by the discovery of two divergent sarbecovirus genomes (< 80% of genomic identity with SARS-CoV and SARS-CoV-2) in horseshoe bat species collected out of Asia: one in Rhinolophus blasii from Bulgaria (BM48-31)9 and another in an unidentified Rhinolophus species from Kenya (BtKY72)10.
Figure 1 Geographic distribution of the four Rhinolophus species found positive for viruses closely related to SARS-CoV-2 in southern China and Southeast Asia. Map from Google Earth Pro (version 7.3.3.7786) US Dept of State Geographer
© 2020 Google—Image Landsat/Copernicus—Data SIO, NOAA, U.S. Navy, NGA, GEBCO. For each of the four Rhinolophus species, the geographic distribution was extracted from the IUCN website11. The figure was drawn in Adobe Photoshop CS5 (version 12.0) and Microsoft PowerPoint (version 16.16.27). The coloured dots show the four geographic locations where bats found positive for SCoV2rCs were collected.