Instead, I’ll focus on the substance of the Crits-Christoph analysis. Their analysis focused on the non-SARS2 metagenomic content of the deep sequenced environmental samples.
Key results are in Fig 1 of their analysis, shown below. Contour heatmap shows fraction of positive samples from different regions of market. Positive samples mostly from southwest corner, since that is where Chinese CDC mostly collected samples.
So contour plot just reflects where Chinese CDC collected samples (as shown in Fig 1A of their pre-print, mentioned earlier in this thread). In other words, contour does not show percent positivity of collected samples, but total positive samples not normalized by total samples.
The novel part of Fig 1 of Crits-Christoph et al is fraction of mammalian mtDNA reads in each analyzed sample that mapped to variety of mammalian species. These are pie chart circles. There are samples w mtDNA from humans, pigs, sheep, cows, Siberian weasels, raccoon dogs, etc.
The sample that has attracted the most attention is the mostly light green pie circle, for which the dominant mtDNA is from a raccoon dog. This has attracted attention because raccoon dogs are one of several species known to be susceptible to SARS2.
That green pie circle is sample Q61 from Chinese CDC pre-print, which was SARS2 negative by PCR but positive by deep sequencing. When data become available, I would like to quantify SARS2 reads in each sample, as it would be useful to know how much SARS2 was in each sample.
For instance, it is unclear whether there is enough SARS2 in the raccoon dog mtDNA dominated Q61 sample to actually infer a viral sequence, or if the undetectable Ct value for that sample means there are just trace levels of reads that are too low to obtain a viral sequence.
There are also lots of pie circles where the dominant mtDNA is from humans, & also from animals that were probably only sold as meat (eg, cow, sheep, pig). And although not shown in figure (since it’s not a mammal), the text reports some samples had fish mtDNA.
So as Crits-Christoph et al note in text, fact that mtDNA from a species is found in a sample doesn’t mean that species was infected w SARS2. It just means material from that animal ended up in the same place as viral RNA, which was widespread in the Huanan Market by Jan 2020.
They also analyze a few samples in more detail, including assembling near-complete mtDNA for some animals, and some genomic / cDNA contigs for sample Q61. This could be useful for learning more details about animals from which genetic material in the market was derived.
Overall, main thing we learn is details of which animals or products (eg, meats) were in market before it closed on Jan-1-2020. This doesn’t tell us if any infected w SARS2. But knowing more about animals could help trace supply chain, which is valuable line of investigation.
However, human SARS2 infections started in Wuhan no later than Nov 2019. So we have to be circumspect about environmental samples from Jan 2020. Eg, raccoon dog sample Q61 was collected on Jan-12-2020, which is at least 6 and probably >8 weeks after first human infections.
@jbloom_lab Some comment (by drastic) which seems relevant: the B5 'ground' sample had low CT (29) and was one of the 3 succesfully cultured, yet it has 20 times more beef and sheep mtDNA reads than human. On the other hand the WHO map shows 3 human cases at this stall.