Outbreak.info

Outbreak.info integrates SARS-CoV-2 genomic data, metadata, publications, clinical trials, datasets, and protocols to support genomic surveillance and research of COVID-19.

Key Features:

• Standardized metadata schema and reusable framework: A rigorous schema links related information across diverse resource types to ensure consistent representation of publications, datasets, protocols, and metadata.
• Dynamic variant surveillance: Tracks over 40 million combinations of Pango lineages and individual mutations across more than 7,000 locations using data from over 11 million sequenced genomes shared through GISAID.
• Scalable data ingestion pipelines: Robust pipelines ingest heterogeneous sources of variant and genomic data to support scalability and adaptability as new information becomes available.
• High-performance API: An API-based dissemination layer provides programmatic access to processed genomic and metadata outputs for downstream analysis.
• Interpretable visualizations: Generates visualizations that summarize genomic surveillance metrics across geographic and temporal scales to aid interpretation and hypothesis generation.

Scientific Applications:

• Genomic surveillance: Monitoring the prevalence and geographic spread of SARS-CoV-2 Pango lineages and specific mutations over time.
• Variant and mutation analysis: Quantifying combinations of lineages and mutations to support studies of viral evolution and phenotype associations.
• Public health situational awareness: Providing data to inform surveillance priorities and assess emerging variant dynamics across locations.
• Research support: Integrating publications, datasets, and protocols with genomic data to enable cross-disciplinary COVID-19 research.

Methodology:

Robust pipelines ingest heterogeneous variant and genomic sources into a reusable framework with a rigorous schema that links related information; variant surveillance tracks Pango lineages and individual mutations across locations using sequenced genomes from GISAID; processed outputs are served via a high-performance API and visualized for interpretation.