Revised Preprint of Huanan Seafood Market Samples

The preprint reporting the results from 923 environmental and 457 animal samples from the Huanan Seafood market has been extensively revised, expanded and polished. The raw genomic data is also publicly available.
1/https://t.co/emTsXgNXI3

— Prof Francois Balloux (@BallouxFrancois) March 29, 2023

I enjoyed reading it. The write-up is nuanced and much clearer, and there's a lot of information to digest, even if there's no smoking gun either way. The samples may have been collected too late (January) to capture a clear pattern that may inform on the origin of SARS-CoV-2.
2/

— Prof Francois Balloux (@BallouxFrancois) March 29, 2023

In short, none of the animal samples analysed were found to be infected with SARS-CoV-2. There is evidence for a large number of wild and domestic animals at the market (including many susceptible to SARS-CoV-2), but no obvious pattern of mammalian and viral co-occurrence.
3/

— Prof Francois Balloux (@BallouxFrancois) March 29, 2023

There is a 'mini-glitch of sorts' that many may obsess over. In figure 4F, the 'raccoon dog sample' (Q61 - Env_0660 in this preprint) is given as containing mostly domestic dog (Canis) mitochondrial reads, rather than raccoon dog (Nyctereutes).
4/ pic.twitter.com/e0ABIUd0is

— Prof Francois Balloux (@BallouxFrancois) March 29, 2023

This likely stems from the raccoon dog's genome not having been included in Liu's reference panel. In the supplementary material, they also use another approach based on a single mitochondrial gene, which points to the sample carrying a lot of raccoon dog mitochondrial reads.
5/ pic.twitter.com/HlTmosoU0r

— Prof Francois Balloux (@BallouxFrancois) March 29, 2023