Analysis of pangolin metagenomic datasets reveals significant contamination, raising concerns for pangolin CoV host attribution

Code

• github.com/bioscienceresearch/pangolin_cov_sra_analysis
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Abstract

Metagenomic datasets from pangolin tissue specimens have previously yielded SARS-related coronaviruses which show high homology in their receptor binding domain to SARS-CoV-2, suggesting a potential zoonotic source for this feature of the human virus, possibly via recombination (Liu et al. 2019, Lam et al. 2020, Xiao et al. 2020, Liu et al. 2020). Here we re-examine these published datasets. We report that only a few pangolin samples were found to contain coronavirus reads, and even then in low abundance, while other non-pangolin hosted viruses were present in higher abundance. We also discovered extensive contamination with human, rodent, and other mammalian gene sequences, which was a surprising finding. Furthermore, we uncovered a number of pangolin CoV sequences embedded in standard laboratory cloning vectors, which suggests the pangolin specimens could have been contaminated with sequences derived from synthetic biology experiments. Finally, we discover a third pangolin dataset (He et al. 2022) with low levels of SARSr-CoV sequences and unambiguous extensive contamination of several pangolin samples. For these reasons, we find it unlikely that the pangolins in question had a coronavirus infection while alive, and all current versions of the cited papers claiming a zoonotic infection of pangolins with a SARS-r CoV require substantial corrections and should be retracted until such corrections are made.

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