This kind of data could quickly pinpoint the closest relatives of these viruses. A small number of wild raccoon dogs were sampled shortly after the pandemic around Wuhan. So let's rule in, or rule out, that population as a source of the mtDNA haplotypes we observe. 20/
Then let's sample populations of raccoon dogs, foxes, mustelids (weasels and close relatives) -- whatever the short list of possible intermediate hosts includes -- all over China, and perhaps elsewhere. There are more species to consider than just raccoon dogs. 21/
And although it is very unfortunate that this kind of supply chain reverse engineering via genetics was not initiated in January and February of 2020, when the metagenomic data was generated, I'm not one of the people who think all is lost in terms of maybe, just maybe... 22/
finding the source of the intermediate hosts at the market. Even the fact that farms supplying animals like masked palm civets and raccoon dogs were rapidly shut down in early 2020 is not necessarily a deal breaker. 23/
Let's go to as many former farms of susceptible hosts as possible and sample environmental DNA there - from cages, carts, feces - perhaps even dig up pits where I suspect many animals were buried in early 2020 when farms were rapidly liquidated. 24/
Do any show the former presence of animals closely related to what we now know for certain was sold at the Huanan market in late 2019, and for which we have genetic records? If a close match is found, then take two additional steps: 25/
(1) Try the Hail Mary pass of attempting to recover SARS-CoV-2-related viral sequences with very deep metagenomic sequencing and targeted approaches. (2) If local populations of horseshoe bats live nearby, sample them and see if they harbor SARS2-like viruses. 26/
Important to note, however, that we will never sample anything super close to SARS2 in bats now. Direct descendents of the progenitor virus will have accumulated something like 60 or 70 changes. Plus recombination is so frequent, such a direct descendent across... 27/
all genomic regions is very unlikely to exist. 28/
No matter what your view on the origin of the pandemic, I hope you might agree that given all the evidence supporting a Huanan market origin, entertaining at least the *possibility* that it did happen that way necessitates making these effort, ASAP. 29/
Now I want to say a few things about the controversy regarding our analyzing these data and communicating our findings, and GISAID's approach to date. First, here is an email I sent to Dr. Peipei Liu, at the CCDC, who was listed as the submitter of the metagenomic data. 30/
Next, here are passages from an email that I, and almost all the other co-signatories of the report, received from GISAID. I found a few things out of the ordinary with this letter. 31/