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The current outbreak of coronavirus disease-2019 (COVID-19) poses unprecedented challenges to global health
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. The new coronavirus responsible for this outbreak—severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)—shares high sequence identity to SARS-CoV and a bat coronavirus, RaTG13
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. Although bats may be the reservoir host for a variety of coronaviruses
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,
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, it remains unknown whether SARS-CoV-2 has additional host species. Here we show that a coronavirus, which we name pangolin-CoV, isolated from a Malayan pangolin has 100%, 98.6%, 97.8% and 90.7% amino acid identity with SARS-CoV-2 in the E, M, N and S proteins, respectively. In particular, the receptor-binding domain of the S protein of pangolin-CoV is almost identical to that of SARS-CoV-2, with one difference in a noncritical amino acid. Our comparative genomic analysis suggests that SARS-CoV-2 may have originated in the recombination of a virus similar to pangolin-CoV with one similar to RaTG13. Pangolin-CoV was detected in 17 out of the 25 Malayan pangolins that we analysed. Infected pangolins showed clinical signs and histological changes, and circulating antibodies against pangolin-CoV reacted with the S protein of SARS-CoV-2. The isolation of a coronavirus from pangolins that is closely related to SARS-CoV-2 suggests that these animals have the potential to act as an intermediate host of SARS-CoV-2. This newly identified coronavirus from pangolins—the most-trafficked mammal in the illegal wildlife trade—could represent a future threat to public health if wildlife trade is not effectively controlled.
A newly identified coronavirus found in Malayan pangolins shares considerable sequence identity with SARS-CoV-2, which suggests that the latter may have originated from a recombination event involving SARS-related coronaviruses from bats and pangolins.