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From the paper: "The fact that such an informative data set was deleted has implications beyond those gleaned directly from the recovered sequences. Samples f
by rossdavidh 5y ago
From the paper:
"The fact that such an informative data set was deleted has implications beyond those gleaned directly from the recovered sequences.
Samples from early outpatients in Wuhan are a gold mine for anyone seeking to understand spread of the virus.
Even my analysis of the partial sequences is revealing, and it clearly would have been more scientifically informative to fully sequence the samples rather than surreptitiously delete the partial sequences.
There is no plausible scientific reason for the deletion: the sequences are perfectly concordant with the samples described in \citet{wang2020medRxiv,wang2020small}, there are no corrections to the paper, the paper states human subjects approval was obtained, and the sequencing shows no evidence of plasmid or sample-to-sample contamination.
It therefore seems likely the sequences were deleted to obscure their existence.
Particularly in light of the directive that labs destroy early samples~\citep{pinghui2020SCMP} and multiple orders requiring approval of publications on COVID-19~\citep{chinacdc2020, Kang2020}, this suggests a less than wholehearted effort to trace early spread of the epidemic.
Another important implication is that genomic epidemiology studies of early SARS-CoV-2 need to pay as much attention to the provenance and annotation of the underlying sequences as technical considerations.
There has been substantial scientific effort expended on topics such as phylogenetic rooting~\citep{pipes2021assessing, morel2021phylogenetic}, novel algorithms~\citep{kumar2021evolutionary}, and correction of sequencing errors~\citep{turakhia2020stability}.
Future studies should devote equal effort to going beyond the annotations in GISAID to carefully trace the location of patient infection and sample sequencing.
The potential importance of such work is revealed by the observation that many of the sequences closest to SARS-CoV-2's bat coronavirus relatives are from early patients who were infected in Wuhan, but then sequenced in and attributed to Guangdong."