A novel SARS-CoV-2 related coronavirus in bats from Cambodia

Abstract

Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID-19 pandemic is still fragmentary. To date, the closest relatives to SARS-CoV-2 have been detected in Rhinolophus bats sampled in the Yunnan province, China. Here we describe the identification of SARS-CoV-2 related coronaviruses in two Rhinolophus shameli bats sampled in Cambodia in 2010. Metagenomic sequencing identified nearly identical viruses sharing 92.6% nucleotide identity with SARS-CoV-2. Most genomic regions are closely related to SARS-CoV-2, with the exception of a small region corresponding to the spike N terminal domain. The discovery of these viruses in a bat species not found in China indicates that SARS-CoV-2 related viruses have a much wider geographic distribution than previously understood, and suggests that Southeast Asia represents a key area to consider in the ongoing search for the origins of SARS-CoV-2, and in future surveillance for coronaviruses.

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

“…Could it have been in their natural Southeast Asian environment, before being captured? The discovery of two new viruses close to SARS-CoV-2 in bats from Cambodia and Thailand [7,8] supports this hypothesis, as Rhinolophus bats and pangolins can meet, at least occasionally, in forests of Southeast Asia, possibly in caves, tree hollows or burrows. Further substantiating this hypothesis, the geographic distribution of Manis javanica [28] overlaps the ecological niche here predicted for bat SARS-CoV-2 viruses (Figures 4a and 4b), and SARS-CoV-2 neutralizing antibodies have been recently detected in a Sunda pangolin collected in eastern Thailand [8].…”

“…The ecological niche of bat SARS-CoV-2 like viruses was predicted using the four localities where bat SARS-CoV-2-like viruses were previously detected [1,[6][7][8] and the 16 localities where bats showed the same CO1 haplotype than virus-positive bats (dataset A: 20 points; see Table S1 for details). The areas showing the highest probabilities of occurrence (highlighted in green in Figure 4a) include northern and southern Laos, northeastern and southwestern Cambodia, northwestern and southern Vietnam, eastern, northern and western Thailand, southern Myanmar, and western Philippines.…”

“…The great majority of sarbecoviruses related to SARS-CoV were found in several horseshoe bat species of the genus Rhinolophus (family Rhinolophidae), suggesting that this taxon is the natural reservoir host of these viruses [5]. 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 was isolated from a Rhinolophus affinis bat collected in Yunnan in 2013 [1]; the RmYN02 virus was found in a Rhinolophus malayanus bat sampled in Yunnan in 2019 [6]; two variants of the same virus RshSTT200 (other variant: RshSTT182) were detected in two Rhinolophus shameli bats caught in northern Cambodia in 2010 [7]; and five variants of the same virus RacCS203 (other variants: RacCS224, RacCS253, RacCS264, and RacCS271) were sequenced from five Rhinolophus acuminatus bats collected in eastern Thailand in 2020 [8]. These data confirmed that the genus Rhinolophus is the natural reservoir host of all viruses of the subgenus Sarbecovirus [3,5].…”

Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses

“…Although several SARS-CoV-2-like viruses have been identified from different wildlife species that display high sequence similarity to SARS-CoV-2 in some genomic regions, none are highly similar (e.g. >95%) to SARS-CoV-2 in the spike gene in terms of both the overall sequence identity and the amino acid residues at critical receptor binding sites (Zhou et al, 2020b;Lam et al, 2020;Xiao et al, 2020;Zhou et al, 2020a;Murakami et al, 2020;Hul et al, 2021;Wacharapluesadee et al, 2021). Indeed, the spike protein sequences of three of the novel coronaviruses described here (RsYN04, RmYN05, RmYN08) formed an independent lineage separated from known sarbecoviruses by a relatively long branch.…”

“…The copyright holder for this preprint this version posted March 8, 2021. ; https://doi.org/10.1101/2021.03.08.434390 doi: bioRxiv preprint the viral genome as a whole (Zhou et al, 2020b); (ii) the bat (R. malayanus) derived coronavirus RmYN02 that is the closest relative of SARS-CoV-2 in the long ORF1ab gene and which contains a similar nucleotide insertion at the S1/S2 cleavage site of the spike gene (Zhou H et al, 2020a); (iii) viruses from the Malayan pangolin (Manis javanica) that comprised two lineages reflecting their Chinese province of collection by local customs authorities (Guangdong and Guangxi), with the pangolins from Guangdong possessing identical amino acids at the six critical residues of the receptor binding domain (RBD) to human SARS-CoV-2 (Lam et al, 2020;Xiao et al, 2020); and (iv) a more distant SARS-CoV-2 related coronavirus from a bat (R. cornutus) sampled in Japan (Murakami et al, 2020). More recently, two novel betacoronaviruses (STT182 and STT200) were described in R. shameli bats sampled from Cambodia in 2010 that share 92.6% nucleotide identity with SARS-CoV-2 as well as five of the six critical RBD sites observed in SARS-CoV-2 (Hul et al, 2021).…”