Genetic ghosts suggest Covid's market origins

[muriel_volestrangler]

A team of scientists say it is “beyond reasonable doubt” the Covid pandemic started with infected animals sold at a market, rather than a laboratory leak.
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"We are seeing the DNA and RNA ghosts of these animals in the environmental samples, and some are in stalls where [the Covid virus] was found too," says Prof Florence Débarre, of the French National Centre for Scientific Research.
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It shows Covid virus and susceptible animals were detected in the same location, with some individual swabs collecting both animal and coronavirus genetic code. This is not evenly distributed across the market and points to very specific hotspots.
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The depth of the genetic analysis was able to identify the specific types of raccoon dogs being sold. They were those more commonly found in the wild in South China rather than those farmed for their fur. This gives scientists clues about where to look next.

https://www.bbc.co.uk/news/articles/cy8095xjg4po

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic

Highlights
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Common ancestor of SARS-CoV-2 linked to Huanan market matches the global common ancestor
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Wildlife mitochondrial DNA identified in samples from stalls positive for SARS-CoV-2
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DNA from raccoon dogs, civets, and other wildlife species detected in market samples
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Genotypes of potential hosts were reconstructed for retracing animal geographic origins

Summary
Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that market-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistent with market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identify wildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboo rats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them with those from farms and other markets. This analysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritize for serological and viral sampling.

https://www.cell.com/cell/fulltext/S0092-8674%2824%2900901-2