joshuailevy/outbreak.info

During outbreaks of emerging diseases such as COVID-19, efficiently collecting, sharing, and integrating data is critical to scientific research. outbreak.info is a resource to aggregate all this information into a single location.

outbreak.info

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.

Data sources

• See outbreak.info sources

Related projects

• Outbreak.api -- repo for the back-end API
• outbreak.info-resources -- data schemas and harvesters for COVID-19 resources

Deploying a local version of the site

1. Clone the repository
2. Make sure you have [node & npm] (https://nodejs.org/en/) and Vue & Vue CLI installed.
3. In terminal, navigate to the src directory of this repository.
4. Install node_modules by running npm install.
5. Launch a local server with hot-reloads by running npm run serve.

Updating curated Variants of Concern (VOCs) / Variants of Interest (VOIs) / Variants under Monitoring (VUMs).

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 maintained by accessing the data file from the Pango team.

Adding, removing, or changing the list of VOCs/VOIs/VUMs.

1. Edit the curated yaml file. Do not manually edit the curated .json file used by outbreak.info; this file will be dynamically generated by the python script below. Essential components:
   • 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 variant
   • dateModified: date which outbreak.info classifies it as a VOC/VOI/VUM
   • classifications: array containing classifications as per CDC, WHO, PHE, ECDC
   • Make sure to nest the yaml object under the appropriate section (VOC, VOI, VUM) to ensure it gets classified as the appropriate level of concern.
2. Run python curated_reports_prep/generate_curated_lineages_json.py. This updates the curated .json file used by outbreak.info.
3. Edit updates admin.js to add a note that a variant has been classified, reclassified, or downgraded.
4. Commit to the GitHub repo and rebuild the site.

Updating only the Pango sublineages associated with each tacked variant.

1. Run python curated_reports_prep/generate_curated_lineages_json.py. This updates the curated .json file used by outbreak.info.
2. Commit to the GitHub repo and rebuild the site.