ArticleVirus evolution2023
Association between SARS-CoV-2 and metagenomic content of samples from the Huanan Seafood Market.
Article in Virus evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- The Data are Insufficient to Confidently Root the SARS-CoV-2 Phylogenetic Tree.Molecular biology and evolution · 2025Article
- Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.Cell · 2024Article
- Importance of quantifying the number of viral reads in metagenomic sequencing of environmental samples from the Huanan Seafood Market.Virus evolution · 2024Article
- What we can and cannot learn from SARS-CoV-2 and animals in metagenomic samples from the Huanan market.Virus evolution · 2024Article
- Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.bioRxiv : the preprint server for biology · 2023Article
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1 author.
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Abstract
The role of the Huanan Seafood Market in the early severe acute respiratory syndrome virus 2 (SARS-CoV-2) outbreak remains unclear. Recently, the Chinese Centers for Disease Control (CDC) released data from deep sequencing of environmental samples collected from the market after it was closed on 1 January 2020. Prior to this release, Crits-Christoph et al. analyzed data from a subset of the samples. Both that study and the Chinese CDC study concurred that the samples contained genetic material from a variety of species, including some like raccoon dogs that are susceptible to SARS-CoV-2. However, neither study systematically analyzed the relationship between the amount of genetic material from SARS-CoV-2 and different animal species. Here I implement a fully reproducible computational pipeline that jointly analyzes the number of reads mapping to SARS-CoV-2 and the mitochondrial genomes of chordate species across the full set of samples. I validate the presence of genetic material from numerous species and calculate mammalian mitochondrial compositions similar to those reported by Crits-Christoph et al. However, the SARS-CoV-2 content of the environmental samples is generally very low: only 21 of 176 samples contain more than ten SARS-CoV-2 reads, despite most samples being sequenced to depths exceeding 10
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