Current Biology
Volume 30, Issue 7, 6 April 2020, Pages 1346-1351.e2
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Report
Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak

https://doi.org/10.1016/j.cub.2020.03.022Get rights and content
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Highlights

  • Pangolin-CoV is 91.02% identical to SARS-CoV-2 at the whole-genome level

  • Pangolin-CoV is the second closest relative of SARS-CoV-2 behind RaTG13

  • Five key amino acids in the RBD are consistent between Pangolin-CoV and SARS-CoV-2

  • Only SARS-CoV-2 contains a potential cleavage site for furin proteases

Summary

An outbreak of coronavirus disease 2019 (COVID-19) caused by the 2019 novel coronavirus (SARS-CoV-2) began in the city of Wuhan in China and has widely spread worldwide. Currently, it is vital to explore potential intermediate hosts of SARS-CoV-2 to control COVID-19 spread. Therefore, we reinvestigated published data from pangolin lung samples from which SARS-CoV-like CoVs were detected by Liu et al. [1]. We found genomic and evolutionary evidence of the occurrence of a SARS-CoV-2-like CoV (named Pangolin-CoV) in dead Malayan pangolins. Pangolin-CoV is 91.02% and 90.55% identical to SARS-CoV-2 and BatCoV RaTG13, respectively, at the whole-genome level. Aside from RaTG13, Pangolin-CoV is the most closely related CoV to SARS-CoV-2. The S1 protein of Pangolin-CoV is much more closely related to SARS-CoV-2 than to RaTG13. Five key amino acid residues involved in the interaction with human ACE2 are completely consistent between Pangolin-CoV and SARS-CoV-2, but four amino acid mutations are present in RaTG13. Both Pangolin-CoV and RaTG13 lost the putative furin recognition sequence motif at S1/S2 cleavage site that can be observed in the SARS-CoV-2. Conclusively, this study suggests that pangolin species are a natural reservoir of SARS-CoV-2-like CoVs.

Keywords

pangolin
SARS-CoV-2
COVID-19
origin

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2

These authors contributed equally

3

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