Nextstrain

Nextstrain is an open-source project that provides a continually updated view of publicly available data on pathogen evolution. It is a powerful tool used by researchers, epidemiologists, and public health officials to track the spread and evolution of infectious diseases, such as SARS-CoV-2, Influenza, and Ebola virus.

Overview

Nextstrain integrates data from genomic sequencing with powerful visualization tools to provide insights into the dynamics of pathogen spread. The platform is designed to be accessible and informative, offering a real-time view of how pathogens are evolving and spreading across the globe.

History

Nextstrain was developed by a team led by Trevor Bedford and Richard Neher. The project began as a response to the need for real-time tracking of pathogen evolution during outbreaks. It gained significant attention during the 2014 West Africa Ebola outbreak and has since been applied to numerous other pathogens.

Features

Real-time Tracking

Nextstrain provides real-time tracking of pathogen evolution by integrating genomic data from various sources. This allows for the visualization of how a pathogen is spreading geographically and temporally.

Phylogenetic Analysis

The platform uses phylogenetic trees to show the evolutionary relationships between different strains of a pathogen. This helps in understanding how different strains are related and how they have evolved over time.

Interactive Visualizations

Nextstrain offers interactive visualizations that allow users to explore data in detail. Users can zoom in on specific regions, view metadata associated with each strain, and observe changes in the pathogen's genetic makeup.

Open Source and Community Driven

Nextstrain is open-source, meaning that its code is freely available for anyone to use, modify, and contribute to. The project encourages collaboration and contributions from the global scientific community.

Applications

Nextstrain has been used in various public health contexts, including:

• Tracking the global spread of COVID-19 and identifying new variants of concern.
• Monitoring seasonal influenza and aiding in vaccine strain selection.
• Understanding the dynamics of Zika virus outbreaks.

Impact

Nextstrain has had a significant impact on the field of epidemiology and public health. By providing a platform for real-time data sharing and analysis, it has improved the ability of researchers and public health officials to respond to outbreaks more effectively.

Also see

• Genomic epidemiology
• Phylogenetics
• Pathogen evolution
• Public health informatics