Here's the full analysis of newly uncovered genetic data on COVID's origins - Ars Technica

The cache of data included metagenomic information from six samples, taken from two stalls, that had high levels of raccoon dog genetic material. Raccoon dogs are known to be susceptible to SARS-CoV-2 infections and known to shed high levels of viral particles. In particular, one sample, Q61, taken from a cart, contained 1,252 genetic fragments with 100 percent identity to the raccoon dog genome but contained zero sequences that had such a perfect match to the human genome. When the researchers took a closer look at the genetic fragments to see what was encoded, they found a mix of genes that are continuously active as well as tissue-specific genes, such as ones involved in mucus production and smell receptors. These findings hint that the swabs were picking up raccoon dog nasal excretions, which may have been more likely in animals sick with a respiratory virus, like SARS-CoV-2.

Such close commingling of genetic material from wild animals and SARS-CoV-2 in an area of the market with the highest density of virus-positive samples, and around which many of the earliest COVID-19 cases were identified, makes a compelling argument that a natural spillover occurred and, specifically, occurred in this area of the market, the researchers argue.

In the concluding remarks of their analysis, Worobey, Anderson, Débarre, and colleagues quickly summarize how this data fits into other data regarding the origin of the pandemic. They highlight again that the Huanan market was the initial epicenter of the pandemic, with most of the early cases having a direct link to the market or occurring in the close surrounding area. While SARS-CoV-2 samples and cases were found throughout the market, the highest concentration of positive samples centered around stalls with wild animals, many of which are known to be susceptible to the virus. Further, many of the earliest human cases also surrounded this area in the western zone of the market.

They also note that a separate genetic study published last year in Science found that there were two genetic lineages of SARS-CoV-2 in the early days of the pandemic—lineage A and lineage B. The two lineages suggest that the virus spilled over into humans on two separate occasions, days to weeks apart from each other. Both lineages were found in the market. The study authors, led by Jonathan Pekar at the University of California, San Diego, concluded that, based on a series of modeling, it was most likely that SARS-CoV-2 lineage B jumped into humans at the Huanan market in mid-November 2019, and lineage A jumped to humans in the Huanan market in late November.

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https://arstechnica.com/science/2023/03/heres-the-full-analysis-of-newly-uncovered-genetic-data-on-covids-origins/?utm_brand=ars