  RaTG13 is the closest related coronavirus genome phylogenetically to
SARS-CoV-2, consequently understanding its provenance is of key importance to
understanding the origin of the COVID-19 pandemic. The RaTG13 NGS dataset is
attributed to a fecal swab from the intermediate horseshoe bat Rhinolophus
affinis. However, sequence analysis reveals that this is unlikely. Metagenomic
analysis using Metaxa2 shows that only 10.3 % of small subunit (SSU) rRNA
sequences in the dataset are bacterial, inconsistent with a fecal sample, which
are typically dominated by bacterial sequences. In addition, the bacterial taxa
present in the sample are inconsistent with fecal material. Assembly of
mitochondrial SSU rRNA sequences in the dataset produces a contig 98.7 %
identical to R.affinis mitochondrial SSU rRNA, indicating that the sample was
generated from this or a closely related species. 87.5 % of the NGS reads map
to the Rhinolophus ferrumequinum genome, the closest bat genome to R.affinis
available. In the annotated genome assembly, 62.2 % of mapped reads map to
protein coding genes. These results clearly demonstrate that the dataset
represents a Rhinolophus sp. transcriptome, and not a fecal swab sample.
Overall, the data show that the RaTG13 dataset was generated by the Wuhan
Institute of Virology (WIV) from a transcriptome derived from Rhinolophus sp.
tissue or cell line, indicating that RaTG13 was in live culture. This raises
the question of whether the WIV was culturing additional unreported
coronaviruses closely related to SARS-CoV-2 prior to the pandemic. The
implications for the origin of the COVID-19 pandemic are discussed.
