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Single source of pangolin CoVs with a near identical Spike RBD to SARS-CoV-2

View ORCID ProfileYujia Alina Chan, View ORCID ProfileShing Hei Zhan
doi: https://doi.org/10.1101/2020.07.07.184374
Yujia Alina Chan
1Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
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  • ORCID record for Yujia Alina Chan
  • For correspondence: alinac@broadinstitute.org zhan@zoology.ubc.ca
Shing Hei Zhan
2Department of Zoology & Biodiversity Research Centre, the University of British Columbia, Vancouver BC, Canada
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  • For correspondence: alinac@broadinstitute.org zhan@zoology.ubc.ca
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Abstract

Multiple publications have independently described pangolin CoV genomes from the same batch of smuggled pangolins confiscated in Guangdong province in March, 2019. We analyzed the three metagenomic datasets that sampled this batch of pangolins and found that the two complete pangolin CoV genomes, GD_1 by Xiao et al. Nature and MP789 by Liu et al. PLoS Pathogens, were both built primarily using the 2019 dataset first described by Liu et al. Viruses. Other publications, such as Zhang et al. Current Biology and Lam et al. Nature, have also relied on this same dataset by Liu et al. Viruses for their assembly of pangolin CoV sequences and comparisons to SARS-CoV-2. To our knowledge, all of the published pangolin CoV genome sequences that share a nearly identical Spike receptor binding domain with SARS-CoV-2 originate from this single batch of smuggled pangolins. This raises the question of whether pangolins are truly reservoirs or hosts of SARS-CoV-2-related coronaviruses in the wild, or whether the pangolins may have contracted the CoV from another host species during trafficking. Our observations highlight the importance of requiring authors to publish their complete genome assembly pipeline and all contributing raw sequence data, particularly those supporting epidemiological investigations, in order to empower peer review and independent analysis of the sequence data.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 07, 2020.
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Single source of pangolin CoVs with a near identical Spike RBD to SARS-CoV-2
Yujia Alina Chan, Shing Hei Zhan
bioRxiv 2020.07.07.184374; doi: https://doi.org/10.1101/2020.07.07.184374
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Single source of pangolin CoVs with a near identical Spike RBD to SARS-CoV-2
Yujia Alina Chan, Shing Hei Zhan
bioRxiv 2020.07.07.184374; doi: https://doi.org/10.1101/2020.07.07.184374

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