nextstrain.org

nextstrain.org visualizes and analyzes pathogen genome sequences to infer phylogenetic relationships and monitor pathogen evolution for epidemiological surveillance.

Key Features:

• Real-Time Tracking: Monitors pathogen evolution and transmission in real time using continuously updated public genomic data.
• Phylogenetic Analysis: Performs phylogenetic analysis to infer evolutionary relationships among pathogen isolates.
• Transmission Cluster Detection: Identifies transmission clusters and estimates introduction dates and cluster dynamics from genomic data.
• Retrospective Phylogenetic Methods: Applies multiple phylogenetic methods for retrospective identification of clusters, definition of epidemiological characteristics, and calculation of cluster cut-off points.
• Clade Surveillance: Monitors endemic and emerging clades in pathogen populations.
• Integration of Genomic and Clinical Data: Integrates genomic data with clinical and epidemiological metadata to support surveillance and intervention planning.
• Visualization: Visualizes evolutionary relationships and temporal-spatial changes via phylogenetic trees and maps.
• High-Resolution Sequencing Support: Incorporates high-resolution viral sequencing data to help identify infection sources and timing.

Scientific Applications:

• Hepatitis C Virus (HCV) Transmission Research: Characterizing HCV transmission dynamics among HIV/HCV co-infected men who have sex with men (MSM).
• Molecular Surveillance: Real-time molecular surveillance of endemic and emerging clades and transmission clusters to inform public health responses.
• Retrospective Cluster Analysis: Retrospective phylogenetic analyses to define cluster cut-offs, epidemiological characteristics, and introduction dates.
• Informing Targeted Interventions: Informing targeted interventions, testing strategies, and outbreak response planning based on genomic and epidemiological evidence.

Methodology:

Uses continuously updated public genomic data, high-resolution viral sequencing, phylogenetic analysis using multiple phylogenetic methods, real-time phylogenetic monitoring with phylogenetic tools and open-source software, retrospective cluster identification, and integration of genomic with clinical and epidemiological metadata.