Haplotype Explorer

Haplotype Explorer visualizes and analyzes haplotype networks to enable spatiotemporal dissection of epidemic spread using genomic sequences and associated metadata.

Key Features:

• Interactive Visualization: Generates interactive haplotype network visualizations to explore network topology and temporal changes.
• Spatiotemporal Analysis: Provides spatiotemporal filtering and time-dependent snapshots to examine introductions, outbreaks, expansion, and containment phases.
• Metadata Integration: Integrates metadata including GISAID IDs, locations, and collection dates to correlate genetic variation with geographic and temporal information.
• HTML Distribution Files: Produces HTML distribution files that embed visualizations and comprehensive node-level metadata for dissemination.
• Case Study (SARS-CoV-2): Applied to 4,282 SARS-CoV-2 genome sequences to generate time-dependent haplotype network snapshots.

Scientific Applications:

• Viral Phylogenetics: Resolve phylogenetic relationships between viral genomes through haplotype network structure.
• Transmission Mapping: Identify transmission patterns and potential introduction events using temporal and geographic metadata.
• Epidemic Dynamics: Characterize outbreak phases (introduction, expansion, containment) via time-resolved network analysis.
• Public Health Surveillance: Inform containment strategies and public health responses by linking genomic data with spatiotemporal trends.

Methodology:

Constructs haplotype networks from genomic data, integrates GISAID IDs, locations, and collection dates, and generates time-resolved visualizations and HTML distribution files.