- Published
- 27 June 2024
- Dataset
Data and Code for "Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic"
- Authors
-
- Source
- Zenodo
Full text
Abstract
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)
Cite as
Crits-Christoph, A., Levy, J., Pekar, J., Goldstein, S., Singh, R., Hensel, Z., Gangavarapu, K., Rogers, M., Moshiri, N., Garry, R., Holmes, E., Koopmans, M., Lemey, P., Peacock, T., Popescu, S., Rambaut, A., Robertson, D., Suchard, M., Wertheim, J., Rasmussen, A., Worobey, M., Andersen, K. & Débarre, F. 2024, 'Data and Code for "Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic"', Zenodo. https://doi.org/10.5281/zenodo.12571327