chainchecker

chainchecker visualizes, curates, and verifies transmission chain data for Ebola virus disease (EVD) and other viral hemorrhagic fevers (VHFs) to support epidemiological link determination during outbreak investigations.

Key Features:

• Visualization and curation: Supports integration and curation of VHF case linelists and metadata to identify and correct inconsistencies within putative epidemiological links.
• Transmission tree visualization: Generates transmission trees that highlight inconsistent links to assist mapping of disease spread.
• Exposure window calculation: Calculates exposure windows for individual EVD cases using defined incubation periods and symptom profiles.
• Cluster analysis: Performs cluster analysis to detect epidemiological clusters and patterns, including indications of nosocomial transmission.
• Nosocomial transmission highlighting: Identifies and highlights potential hospital-acquired (nosocomial) transmission events within transmission chains.

Scientific Applications:

• Outbreak investigation: Supports reconstruction and verification of transmission chains during EVD and other VHF outbreaks.
• Epidemiological link assessment: Facilitates evaluation of putative infector–infectee links using exposure windows and transmission trees.
• Cluster detection: Enables detection of transmission clusters and patterns that inform epidemiological analyses.
• Infection control assessment: Highlights nosocomial transmission events to inform targeted infection prevention and control measures.

Methodology:

Implemented as a Shiny application written in R, with capability to integrate with VHF databases or linelists.