Outbreak.info

Outbreak.info aggregates SARS-CoV-2 genomic variant data and COVID-19 research resources to support genomic surveillance and integrative analyses.

Key Features:

• Genomic surveillance: Tracks over 40 million combinations of PANGO lineages and individual mutations across more than 7,000 locations worldwide.
• Interpretable visualizations: Produces variant- and location-focused visual summaries of genomic trends and mutation dynamics.
• Scalable data ingestion pipelines: Ingests heterogeneous sources of SARS-CoV-2 variant data using robust, scalable pipelines.
• High-performance API: Exposes genomic and metadata outputs via a high-performance API with programmatic access, including an R package.
• Research Library: Aggregates over 350,000 COVID-19-related resources (peer-reviewed publications, clinical trials, datasets, protocols, etc.) as of October 2022 from sixteen repositories.
• Unified metadata schema: Applies a standardized metadata schema to ensure consistency across diverse resource types and to link related materials.

Scientific Applications:

• Real-time genomic surveillance: Monitor geographic and temporal distributions of SARS-CoV-2 lineages and mutations for epidemiological analyses.
• Evolutionary and variant tracking: Analyze mutation emergence and lineage dynamics to study viral evolution and variant spread.
• Integrative research aggregation: Combine genomic data with aggregated publications, datasets, and protocols to support multidisciplinary COVID-19 research.
• Hypothesis generation and public-health analysis: Enable data-driven generation of hypotheses and evidence synthesis for public-health decision-making.

Methodology:

Tracking of PANGO lineages and individual mutations across locations; scalable pipelines for ingesting heterogeneous SARS-CoV-2 variant data; aggregation of >350,000 COVID-19 resources from sixteen repositories; application of a unified metadata schema; data dissemination via a high-performance API and an R package.