Data and Code for "Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic"

This repository provides data, sequences, and analyses of the metagenomic detection of mammalian wildlife at the Huanan Market in early 2020.

**Article sections:**

- (R1): SARS-CoV-2 genetic diversity linked to the Huanan market is consistent with market emergence
- (R2): Increased High SARS-CoV-2 positivity rate in and near a wildlife stall in the Huanan market
- (R3): Mammalian wildlife species detected in five SARS-CoV-2 positive samples from a wildlife stall and in other wildlife stalls
- (R4): Wildlife stalls and SARS-CoV-2 positive samples contain other mammalian viruses associated with the animal trade
- (R5): Reconstruction of mitochondrial genotypes of potential intermediate host species of SARS-CoV-2 within the Huanan market

## Contents by folder
- `metadata/`: sample and species metadata (R)
- `mitochondrial_mappings/`: Read mapping counts and covered bases (breadth) for animal mtDNA. (R3, R5)
- `mitochondrial_genotypes/`: Animal mtDNA consensus genotypes and SNV VCFs. (R3, R5)
- `sars2_mappings/`: identification and quantification of SARS-CoV-2 reads. (R1, R2)
- `sars2_phylogenetics/`: SARS-CoV-2 phylogeny. (R1)
- `viruses`: identification and quantification of other viruses in the market. (R4)
- `correlations/`: computations of correlations between viruses and animals (R3)
- `fastq_processing/`: code for sample (pre)processing (R)
- `figs/`: directory where figure outputs are stored (R)
- `figures_R/`: R code to generate figures (R)
- `summary_and_tables/`: Supplementary tables (R)

Crits-Christoph, A., Levy, J., Pekar, J., Goldstein, S., Singh, R., Hensel, Z., Gangavarapu, K., Rogers, M. B., Moshiri, N., Garry, R. F., Holmes, E. C., Koopmans, M. P. G., Lemey, P., Peacock, T. P., Popescu, S., Rambaut, A., Robertson, D. L., Suchard, M. A., Wertheim, J. O., … Débarre, F. (2024). Data and Code for "Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic" [Data set]. Zenodo. https://doi.org/10.5281/zenodo.12571327