Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic, 2024, Crits-Christoph et al.

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic
Alexander Crits-Christoph; Joshua I. Levy; Jonathan E. Pekar; Stephen A. Goldstein; Reema Singh; Zach Hensel; Karthik Gangavarapu; Matthew B. Rogers; Niema Moshiri; Robert F. Garry; Edward C. Holmes; Marion P.G. Koopmans; Philippe Lemey; Thomas P. Peacock; Saskia Popescu; Andrew Rambaut; David L. Robertson; Marc A. Suchard; Joel O. Wertheim; Angela L. Rasmussen; Kristian G. Andersen; Michael Worobey; Florence Débarre

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.

HIGHLIGHTS

• Common ancestor of SARS-CoV-2 linked to Huanan market matches the global common ancestor

• Wildlife mitochondrial DNA identified in samples from stalls positive for SARS-CoV-2

• DNA from raccoon dogs, civets, and other wildlife species detected in market samples

• Genotypes of potential hosts were reconstructed for retracing animal geographic origins

Link | PDF (Cell) [Open Access]

 

An updated dataset of early SARS-CoV-2 diversity supports a wildlife market origin (Preprint 2025)
Zach Hensel; Florence Débarre

The origin of SARS-CoV-2 has been intensely scrutinized, and epidemiological and genomic evidence has consistently pointed to Wuhan9s Huanan Seafood Wholesale Market as the epicenter of the COVID-19 pandemic. Early cases were associated with this market, and environmental sequencing placed the common ancestor of SARS-CoV-2 genomic diversity within the market. Phylogenetic analysis also suggested separate introductions of lineages A and B into the human population, a finding that can be tested with additional data. Here, we curated an expanded sequence dataset of early SARS-CoV-2 viral genomes, including newly available sequences from mid-January 2020.

In this dataset, we found no additional support for previously proposed alternative progenitor sequences, or for any evolutionary intermediates between lineages A and B in the human population. Instead, we identified SARS-CoV-2 lineages that may have spread from the market, and additional samples of a sublineage of lineage A with three mutations, including one found in closely related bat coronaviruses. Although our analysis of early pandemic genomes suggests that this mutation is unlikely to characterize the immediate SARS-CoV-2 ancestor, it is more plausible than two previously proposed ancestral genomes.

These findings reinforce the proposed emergence of SARS-CoV-2 from the wildlife trade at the Huanan market, demonstrating how new data continues to both solidify and clarify our understanding of how the pandemic began.


Link | PDF (Preprint: BioRxiv) [Open Access]