During outbreaks of emerging diseases such as COVID-19, efficiently collecting, sharing, and integrating data is critical to scientific research.
outbreak.info is a standardized, searchable platform to discover and explore COVID-19 and SARS-CoV-2 data from the Center for Viral Systems Biology at Scripps Research. It contains three parts: a standardized searchable database of COVID-19 research; customizable real-time surveillance reports on SARS-CoV-2 variants and mutations; and an explorable interface to examine changes in epidemiological data.
Disclaimer: This project is a work-in progress. Please submit an issue if you notice any bugs or want to suggest features.
src
directory of this repository.npm install
.npm run dev
.outbreak.info maintains a curated list of VOCs/VOIs/VUMs based on classifications by public health agencies. Additionally, the sublineages associated with a variant are determined using data from the Pango team and are maintained here.
pangolin_lineage
: the primary, parent pangolin lineage for the variant. Can also be an array (e.g. ["B.1.427", "B.1.429"]
-- specify as a yaml array)who_name
: (if available) the WHO alias for the variantdateModified
: date which outbreak.info classifies it as a VOC/VOI/VUMclassifications
: array containing classifications as per CDC, WHO, PHE, ECDCpython curated_reports_prep/generate_curated_lineages_json.py
. This updates the curated .json file used by outbreak.info.updates
admin.js to add a note that a variant has been classified, reclassified, or downgraded.python curated_reports_prep/generate_curated_lineages_json.py
. This updates the curated .json file used by outbreak.info.