TreeFix-TP

TreeFix-TP corrects errors in phylogenetic trees to improve transmission network inference for viral and bacterial pathogens by leveraging intra-host strain diversity and host information.

Key Features:

• Error-Correction Framework: Employs an error-correction framework that leverages intra-host strain diversity and host information, balancing parsimonious evaluation of implied transmission networks with statistical hypothesis testing using sequence data likelihood.
• Scalability and Accuracy: Designed to scale to larger outbreaks while reconstructing phylogenies that minimize inferred disease transmissions and retain support comparable to maximum likelihood phylogenies.
• Utilization of Intra-host Diversity: Incorporates within-host diversity and supports sampling of multiple strain sequences per infected host to improve phylogenetic reconstruction and transmission inference.
• Simulation and Real-Data Validation: Validated using a simulation framework for viral transmission and evolution and with real data from ten Hepatitis C Virus (HCV) outbreaks demonstrating improved source detection.

Scientific Applications:

• Epidemiological Reconstruction: Improves reconstruction of transmission phylogenies for studies of infectious disease spread and evolution.
• Outbreak Source Detection: Enhances identification of outbreak sources, as demonstrated on HCV outbreak datasets.
• Transmission Pathway Inference: Aids tracing of transmission pathways and assessments that inform public health intervention strategies.

Methodology:

Uses an error-correction framework that leverages intra-host strain diversity and host information, balances parsimony of implied transmission networks with statistical hypothesis testing based on sequence data likelihood, reconstructs phylogenies by minimizing inferred transmissions while maintaining support comparable to maximum likelihood phylogenies, and has been validated with simulation of viral transmission/evolution and ten HCV outbreak datasets.