Code: Inferred movements of SARS-CoV-2 infections between the 25 administrative regions of Peru (Figure 3) + International spread of four SARS-CoV-2 sub-lineages of Peruvian origin (Figure 4)

This repository contains the Python scripts used to visualize the inferred movements of respiratory virus lineages at the departmental level in Peru and internationally between countries. The visualizations were generated using the Cartopy, GeoPandas, Matplotlib, Basemap, and Shapely libraries.Figure 3. Inferred movements of SARS-CoV-2 infections between the 25 administrative regions of Peru. The map is projected in Plate Carrée at a scale of 200 km. Circles represent departments and are scaled to the number of inferred outgoing viral movements. Arrows represent the direction and intensity of viral transitions between regions, with width indicating the number of events. Population density is displayed as a blue choropleth background, based on open data from the Ministry of Health of Peru.Shapefiles from INEI were used for departmental boundaries.Nodes represent departments, and their size is proportional to the number of inferred outgoing transitions.Arrows indicate origin–destination routes, with thickness and transparency proportional to the number of events.Random grey circles (~10,000 inhabitants) were added to represent population density, based on MINSA data.Figure 4. International spread of four SARS-CoV-2 sub-lineages of Peruvian origin. Movements of Lambda C.37, Gamma P.1.12, Omicron XBB.2.6, and Omicron DJ.1 lineages inferred from phylogeographic analysis. Arcs represent transitions between countries of sample collection, projected in Plate Carrée at a scale of 1000 km. The width of each arrow indicates the number of inferred transitions, and the color denotes the viral lineage.Base maps from Natural Earth Data were used.Geodesic arrows represent inferred transitions between countries.The thickness of each arrow indicates the number of inferred transitions on that route.The color of each arrow represents the corresponding viral lineage.Github repository available at: https://github.com/renatocava/inferred_dates_animationUploaded November 13, 2025.