A critical reexamination of recovered SARS-CoV-2 sequencing data

SARS-CoV-2 genomes collected at the onset of the Covid-19 pandemic are valuable because they could help understand how the virus entered the human population. In 2021, Jesse Bloom reported on the recovery of a dataset of raw sequencing reads that had been removed from the NCBI SRA database at the request of the data generators, a scientific team at Wuhan University (Wang et al., 2020b). Bloom suggested that the data may have been removed in order to obfuscate the origin of SARS-CoV-2, and he questioned the generating authors' statements that the samples had been collected on and after January 30, 2020. Here, we show that sample collection dates were published in 2020 by Wang et al. together with the sequencing reads, and match the dates given by the authors in 2021. We examine mutations in these sequences and confirm that they are entirely consistent with the previously known genetic diversity of SARS-CoV-2 of late January 2020. Finally, we explain how an apparent phylogenetic rooting paradox described by Bloom was resolved by subsequent analysis. Our reanalysis demonstrates that allegations of cover-up or of metadata manipulation were unwarranted. ### Competing Interest Statement The authors have declared no competing interest.