Post by Nadica (She/Her) on Sept 21, 2024 2:13:05 GMT
Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic - Published Sept 19, 2024
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
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.
Graphical abstract
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
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.
Graphical abstract