Cloning vectors and contamination in metagenomic datasets raise concerns over pangolin CoV genome authenticity

Jones, Adrian; Zhang, Daoyu; Deigin, Yuri; Quay, Steven C.

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. Finally, 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. 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 should be considered unreliable, and either substantial corrections and clarifications should be provided or the papers in question should be retracted.