Recovery of Deleted Deep Sequencing Data Sheds More Light on the Early Wuhan SARS-CoV-2 Epidemic
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Abstract
The origin and early spread of SARS-CoV-2 remains shrouded in mystery. Here, I identify a data set containing SARS-CoV-2 sequences from early in the Wuhan epidemic that has been deleted from the NIH’s Sequence Read Archive. I recover the deleted files from the Google Cloud and reconstruct partial sequences of 13 early epidemic viruses. Phylogenetic analysis of these sequences in the context of carefully annotated existing data further supports the idea that the Huanan Seafood Market sequences are not fully representative of the viruses in Wuhan early in the epidemic. Instead, the progenitor of currently known SARS-CoV-2 sequences likely contained three mutations relative to the market viruses that made it more similar to SARS-CoV-2’s bat coronavirus relatives.
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SciScore for 10.1101/2021.06.18.449051: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Archiving of key weblinks: I have digitally archived key weblinks in the Wayback Machine, including a subset of the SRA files from PRJNA612766 on the Google Cloud: Recovery of SRA files from deleted project PRJNA612766: I parsed the first supplementary table of Farkas et al. (2020) to extract the accessions for sequencing runs for deleted SRA BioProject PRJNA612766. BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)I processed the resulting alignments with samtools and pysam to determine the coverage at each site by aligned nucleotides with a quality score of at least 20. samtoolssugge…SciScore for 10.1101/2021.06.18.449051: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Archiving of key weblinks: I have digitally archived key weblinks in the Wayback Machine, including a subset of the SRA files from PRJNA612766 on the Google Cloud: Recovery of SRA files from deleted project PRJNA612766: I parsed the first supplementary table of Farkas et al. (2020) to extract the accessions for sequencing runs for deleted SRA BioProject PRJNA612766. BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)I processed the resulting alignments with samtools and pysam to determine the coverage at each site by aligned nucleotides with a quality score of at least 20. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)I then used IQ-Tree (Minh et al. 2020) to infer a maximum-likelihood phylogenetic tree using a GTR nucleotide substitution model with empirical nucleotide frequencies, and collapsing zero-length branches to potentially allow a multifurcating tree. IQ-Treesuggested: (IQ-TREE, RRID:SCR_017254)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:There are several caveats to this study. Most obviously, the sequences recovered from the deleted data set are partial and lack full metadata. Therefore, it is impossible to unambiguously place them phylogenetically, or determine exactly when they were collected. However, little can be done to mitigate this caveat beyond my failed attempt to contact the corresponding authors of Wang et al. (2020a). It is also important to note that my phylogenetic analyses use relatively simple methods to draw qualitative conclusions without formal statistical testing. Further application of more advanced methods would be a welcome advance. However, qualitative and visual analyses do have advantages when the key questions relate more to the underlying data than the sophistication of the inferences. Finally, both plausible putative progenitors require that an early mutation to SARS-CoV-2 was a reversion towards the bat coronavirus outgroups (either C18060T or C29095T) on a branch that subsequently gave rise to multiple distinct descendants. Such a scenario can only be avoided by invoking recombination very early in the pandemic, which is not entirely implausible for a coronavirus (Boni et al. 2020). However, because the outgroups have ~4% nucleotide divergence from SARS-CoV-2, a mutation towards the outgroup is also entirely possible. Of course, future identification of additional early sequences could fully resolve these questions. More broadly, the approach taken here suggests it may be poss...
Results from TrialIdentifier: No clinical trial numbers were referenced.
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Results from scite Reference Check: We found no unreliable references.
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