StrainHub

StrainHub reconstructs pathogen transmission networks by integrating phylogenetic trees with associated metadata to map character state changes and quantify node importance in transmission dynamics.

Key Features:

• Integration of Phylogenetic Trees and Metadata: Maps metadata-derived characters such as host species or place of isolation onto phylogenetic trees constructed from genetic or other data.
• Transmission Network Reconstruction: Generates transmission networks by translating mapped character state changes on phylogenies into links between metadata states.
• Centrality Metrics Calculation: Computes betweenness, closeness, degree, and the source/hub ratio for network nodes to assess their roles in transmission dynamics.
• Flexible Methodology: Supports parsimony ancestry reconstruction of character states or the use of BEAST phylogeography to produce a maximum clade credibility (MCC) tree for downstream network generation.
• Exportable Outputs: Exports constructed networks with node metrics and annotated phylogenetic trees for downstream analysis.

Scientific Applications:

• Epidemiological Investigation: Reconstructs transmission pathways to identify sources, hubs, and routes of pathogen spread in epidemiological studies.
• Prioritization for Intervention: Provides centrality-based quantitative metrics to prioritize nodes and locations for targeted interventions and infection control measures.

Methodology:

Maps metadata onto phylogenetic trees; performs parsimony ancestry reconstruction of character states or uses BEAST phylogeography to generate a maximum clade credibility (MCC) tree; reconstructs transmission networks from character state changes; calculates centrality metrics (betweenness, closeness, degree, source/hub ratio); exports networks and annotated phylogenies.