Genomic Epidemiology of SARS-CoV-2 in Peru from 2020 to 2024

This dataset compiles all code, scripts, supporting files, and figure outputs used for the analyses presented in Sobkowiak et al., Genomic Epidemiology of SARS-CoV-2 in Peru, 2020–2024 (Communications Medicine, 2025). <b>Contents:</b><b>1. Analysis Code</b>Core Python scripts used to curate metadata, process genomic data, perform lineage assignments, compute summary statistics, and prepare inputs for downstream phylogenetic and phylogeographic analyses. All primary analysis code was written by Ben Sobkowiak, Amy Langdon, Diego Villa-Almeida, and Renato Cava-Miller.<b>2. Figure-Specific Pipelines and Outputs</b><b>Figure 1: Epidemic overview of SARS-CoV-2 in Peru (2020–2024)</b>Scripts for generating national epidemic curves, cumulative incidence maps, and weekly incidence heatmaps.(a) Weekly COVID-19 positive cases and deaths.(b) Cumulative incidence and mortality rate at the province level.(c) Weekly incidence by department.<b>Figure 2: Phylogenetic analysis of 49,724 high-quality SARS-CoV-2 genomes</b>Pipelines for variant stratification, weekly lineage summaries, and timed phylogeny generation.(a) Weekly variant counts and proportions classified as VOC/VOI.(b) Time-calibrated phylogeny colored by Pango lineage assignment.Lineages are labeled “Other” if not classified as VOC/VOI, and “Unassigned” when Pango calling was inconclusive.<b>Figure 3: Inferred movements of SARS-CoV-2 within Peru</b>Python scripts for constructing subnational phylogeographic maps using Cartopy, GeoPandas, Matplotlib, Basemap, and Shapely.The map is projected in Plate Carrée at a scale of 200 km.Circles represent departments, scaled to the number of inferred outgoing movements.Arrows depict origin–destination transitions, with width proportional to event count.A population-density background is based on MINSA open data and INEI administrative boundaries.<b>Figure 4: International spread of Peruvian-origin SARS-CoV-2 sub-lineages</b>Scripts for generating global phylogeographic maps of international transitions.Visualizations represent inferred movements of Lambda C.37, Gamma P.1.12, Omicron XBB.2.6, and Omicron DJ.1.Arcs show cross-country transitions projected in Plate Carrée at 1,000 km scale.Arrow width corresponds to the number of inferred transitions; color denotes lineage identity.Basemaps were generated from Natural Earth Data, and geodesic arcs were computed using standard geospatial libraries.<b>Links to the source GitHub repositories:</b>https://github.com/healthinnovation/covid19trends/https://github.com/bensobkowiak/Peru_SARS-CoV-2/https://github.com/renatocava/inferred_dates_animation/Uploaded by Pablo Tsukayama on November 13, 2025.