Possible Bat Origin of Severe Acute Respiratory Syndrome Coronavirus 2

We showed that severe acute respiratory syndrome coronavirus 2 is probably a novel recombinant virus. Its genome is closest to that of severe acute respiratory syndrome–related coronaviruses from horseshoe bats, and its receptor-binding domain is closest to that of pangolin viruses. Its origin and direct ancestral viruses have not been identified.

We showed that severe acute respiratory syndrome coronavirus 2 is probably a novel recombinant virus. Its genome is closest to that of severe acute respiratory syndrome-related coronaviruses from horseshoe bats, and its receptor-binding domain is closest to that of pangolin viruses. Its origin and direct ancestral viruses have not been identified.
Phylogenetic analysis showed that the RNA-dependent RNA polymerase gene of SARS-CoV-2 is most closely related to that of SARSr-Ra-BatCoV RaTG13, whereas its predicted RBD is closest to that of pangolin-SARSr-CoVs ( Figure 1). This finding suggests a distinct evolutionary origin for SARS-CoV-2 RBD, possibly as a result of recombination. Moreover, the SARS-CoV-2 RBD was also closely related to SARSr-Ra-BatCoV RaTG13 and the hACE2-using cluster containing human/civet-SARSr-CoVs and Yunnan SARSr-BatCoVs previously successfully cultured in VeroE6 cells (4,5).

Conclusions
Despite the close relatedness of SARS-CoV-2 to bat and pangolin viruses, none of the existing SARSr-CoVs represents its immediate ancestor. Most of the genome region of SARS-CoV-2 is closest to SARSr-Ra-BatCoV-RaTG13 from an intermediate horseshoe bat in Yunnan, whereas its RBD is closest to that of pangolin-SARSr-CoV/MP789/Guangdong/2019 from smuggled pangolins in Guangzhou. Potential recombination sites were identified around the RBD region, suggesting that SARS-CoV-2 might be a recombinant virus, with its genome backbone evolved from Yunnan bat virus-like SARSr-CoVs and its RBD region acquired from pangolin viruslike SARSr-CoVs. Because bats are the major reservoir of SARSr-CoVs and the pangolins harboring SARSr-CoVs were captured from the smuggling center, it is possible that pangolin SARSr-CoVs originated from bat viruses as a result of animal mixing, and there might be an unidentified bat virus containing an RBD nearly identical to that of SARS-CoV-2 and pangolin SARSr-CoV. Similar to SARS-CoV, SARS-CoV-2 is most likely a recombinant virus originated from bats.
The ability of SARS-CoV-2 to emerge and infect humans is likely explained by its hACE2-using RBD region, which is genetically similar to that of culturable Yunnan SARSr-BatCoVs and human/civet-SARSr-CoVs. Most SARSr-BatCoVs have not been successfully cultured in vitro, except for some Yunnan strains that had human/civet SARS-like RBDs and were shown to use hACE2 (4,5). For example, SARSr-Rp-BatCoV ZC45, which has an RBD that is more divergent from that of human/civet-SARSr-CoVs, did not propagate in VeroE6 cells (6). Factors that determine hACE2 use among SARSr-CoVs remain to be elucidated.
Although the Wuhan market was initially suspected to be the epicenter of the epidemic, the immediate source remains elusive. The close relatedness among SARS-CoV-2 strains suggested that the Wuhan outbreak probably originated from a point source with subsequent human-to-human transmission, in contrast to the polyphyletic origin of Middle East respiratory syndrome coronavirus (14). If the Wuhan market was the source, a possibility is that bats carrying the parental SARSr-BatCoVs were mixed in the market, enabling virus recombination. However, no animal samples from the market were reported to be positive. Moreover, the first identified case-patient and other early case-patients had not visited the market (15), suggesting the possibility of an alternative source.
Because the RBD is considered a hot spot for construction of recombinant CoVs for receptor and viral replication studies, the evolutionarily distinct SARS-CoV-2 RBD and the unique insertion of S1/S2 cleavage site among Sarbecovirus species have raised the suspicion of an artificial recombinant virus. However, there is currently no evidence showing that SARS-CoV-2 is an artificial recombinant, which theoretically might not carry signature sequences. Further surveillance studies in bats are needed to identify the possible source and evolutionary path of SARS-CoV-2. palm sap (tari) regularly before their illness, and 6 provided care to a person infected with NiV. The process of preparing date palm trees for tari production was similar to the process of collecting date palm sap for fresh consumtion. Bat excreta was reportedly found inside pots used to make tari. These findings suggest that drinking tari is a potential pathway of NiV transmission.