TY - DATA
AU - Crits-Christoph, Alexander
AU - Levy, Joshua I.
AU - Pekar, Jonathan E.
AU - Goldstein, Stephen A.
AU - Singh, Reema
AU - Hensel, Zach
AU - Gangavarapu, Karthik
AU - Rogers, Matthew B.
AU - Moshiri, Niema
AU - Garry, Robert F.
AU - Holmes, Edward C.
AU - Koopmans, Marion P. G.
AU - Lemey, Philippe
AU - Peacock, Thomas P.
AU - Popescu, Saskia
AU - Rambaut, Andrew
AU - Robertson, David L.
AU - Suchard, Marc A.
AU - Wertheim, Joel O
AU - Rasmussen, Angela L.
AU - Worobey, Michael
AU - Andersen, Kristian G.
AU - Débarre, Florence
PY - 2024
DA - June
TI - Data and Code for "Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic"
DO - https://doi.org/10.5281/zenodo.12571327
AB - 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)
PB - Zenodo
UR - https://www.research.ed.ac.uk/en/datasets/5d21cb45-7614-40e5-9d8c-d55c7653028e
KW - Coronavirus (COVID-19)
KW - Digital health and technology
ER