Association between SARS-CoV-2 and metagenomic content of environmental samples from the Huanan Seafood Market

Analysis by Jesse Bloom of the SARS-CoV-2 and mitochondrial DNA content of metagenomic samples collected in early 2020 from the Huanan Seafood Market by Liu et al (2023), with the data taken from NGDC project CRA010170.

The metagenomic content of some samples was also analyzed by Crits-Christoph et al (2023).

This page links to interactive plots of key results:

• Correlation of read counts aligned to mitochondria of different species in current study vs Crits-Christoph et al
• Composition of mitochondrial DNA in each sample for all chordates and just mammals
• Composition of genomic contigs in each sample
• Percent of high-quality reads aligning to SARS-CoV-2 in each metagenomic sample
• Percent of high-quality reads aligning to SARS-CoV-2 in each metagenomic sample (vertically oriented plot)
• Correlation of mitochondrial composition with SARS-CoV-2 reads for all species
• Correlation of mitochondrial composition with SARS-CoV-2 reads for individual species
• Overall correlation of mitochondrial DNA and SARS-CoV-2 across all species
• Overall correlation of mitochondrial DNA and SARS-CoV-2 across all samples using Theil-Sen estimator
• Correlation of RT-qPCR and SARS-CoV-2 reads in deep sequencing

See Bloom et al, bioRxiv, DOI 10.1101/2023.04.25.538336 for a paper describing this analysis.

See https://github.com/jbloom/Huanan_market_samples for results files and a fully reproducible computational pipeline.

See https://jbloom.github.io/Huanan_market_samples for links to all interactive plots.