So, Flo Debarre et al’s raccoon dog analysis that has caused such a media frenzy has been released and what does it show ?
Not much 🧵
Not much 🧵
2/ Essentially, it confirms Gao et al’s preprint analysis that there was nuc acid from animals in addition to humans in the samples 👇 (no surprise there)
It adds some species specific info
It adds some species specific info
3/ The analysis is crude, and taxonomic attribution method naïve
They rely on seq assembly, which miss a lot of info
They use numbers of assembled contigs as a metric for quantity of species specific material
This is semi-quantitative at best (due to the vagaries of assembly)
They rely on seq assembly, which miss a lot of info
They use numbers of assembled contigs as a metric for quantity of species specific material
This is semi-quantitative at best (due to the vagaries of assembly)
4/ Even then, they fail to see if the species specific material correlates with numbers of SARS2 reads, which is inexplicable
5/ They apparently identify a potentially new subspecies of raccoon dog – this would worth following up for forensic purposes, but bafflingly they fail to do so
6/ But they also seem to identify new subspecies of masked palm civet, hoary bamboo rat, Malayan porcupine and Amur hedgehog. This could be interesting, or more likely indicates problems with their assembly. Oddly, they fail to follow this up and validate their assembly qualities
7/ Bizarrely, they seem unable to differentiate between DNA and RNA (hint, trying mapping reads to annotated mito genome or nuc genome). This has importance as it can affect estimates of relative species proportions
8/ Tellingly, none of the stalls with raccoon dog nuc acid have a human SARS2 case linked to it (which puzzlingly they fail to mention)
(figure on left from our HSM Zoonosis critique, on right from Debarre et al)
(figure on left from our HSM Zoonosis critique, on right from Debarre et al)
9/ This saga is a case study in the perils of making grandiose claims without having completed the analysis, and of the hubris to embark into a new subject area without specialists (metagenomic) to scrutinize and suggest robust analyses
8/ (that disappeared above)
Tellingly, none of the stalls with raccoon dog nuc acid have a human SARS2 case linked to it (which puzzlingly they fail to mention)
(fig on left from our HSM Zoonosis preprint, on right from Debarre et al)
Tellingly, none of the stalls with raccoon dog nuc acid have a human SARS2 case linked to it (which puzzlingly they fail to mention)
(fig on left from our HSM Zoonosis preprint, on right from Debarre et al)
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