Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. They provide an updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. Their goal is to aid epidemiological understanding and improve outbreak response.
Nextstrain's philosophy is to track pathogen phylogenies in order to track genomic mutations in pathogens, find related infections and reconstruct a phylogeny to learn about epidemiological phenomena such as spatial spread, introduction timings and epidemic growth rate. They also look for actionable inferences they feel are hindered through the traditional scientific publishing practices. Their open online platform is meant to help inform public health interventions and synthesize data across research groups globally. The website aims to provide a real-time snapshot of evolving pathogen populations and interactive data visualizations to virologists, epidemiologists, public health officials and citizen scientists.
Nextstrain is working to collect and incorporate data on the Covid-19 and nCoV genomes as soon as they are publicly available and to provide analysis and situation reports as quickly as they are available. These reports are collected globally and the information is tracked. They built a database on the Genomic epidemiology of Covid-19 with data provided from GISAID.
Nextstrain: real-time tracking of pathogen evolution
James Hadfield, Colin Megill, Sidney M Bell, John Huddleston, Barney Potter, Charlton Callender, Pavel Sagulenko, Trevor Bedford, Richard A Neher
May 22, 2018
- PathogenIn biology, a pathogen (Greek: πάθος, pathos "suffering", "passion" and -γενής, -genēs "producer of") in the oldest and broadest sense, is any organism that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ. Pathogenic microorganisms are called parasitic microorganisms in relation to their host.