nextflu: real-time tracking of seasonal influenza virus evolution in humans

Seasonal influenza viruses evolve rapidly, allowing them to evade immunity in their human hosts and reinfect previously infected individuals. Similarly, vaccines against seasonal influenza need to be updated frequently to protect against an evolving virus population. We have thus developed a process...

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Bibliographic Details
Published in:Bioinformatics Vol. 31; no. 21; pp. 3546 - 3548
Main Authors: Neher, Richard A., Bedford, Trevor
Format: Journal Article
Language:English
Published: England Oxford University Press 01.11.2015
Subjects:
Applications Notes
Evolution
Evolution, Molecular
Human
Humans
Influenza
Influenza virus
Influenza, Human - virology
Java (programming language)
Mutation
Orthomyxoviridae - classification
Orthomyxoviridae - genetics
Orthomyxoviridae - isolation & purification
Phylogeny
Sampling
Seasons
Software
Source code
Statistics
Viruses
ISSN:1367-4803, 1367-4811, 1367-4811, 1460-2059
Online Access:Get full text
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Description
Summary:Seasonal influenza viruses evolve rapidly, allowing them to evade immunity in their human hosts and reinfect previously infected individuals. Similarly, vaccines against seasonal influenza need to be updated frequently to protect against an evolving virus population. We have thus developed a processing pipeline and browser-based visualization that allows convenient exploration and analysis of the most recent influenza virus sequence data. This web-application displays a phylogenetic tree that can be decorated with additional information such as the viral genotype at specific sites, sampling location and derived statistics that have been shown to be predictive of future virus dynamics. In addition, mutation, genotype and clade frequency trajectories are calculated and displayed. Availability and implementation: Python and Javascript source code is freely available from https://github.com/blab/nextflu, while the web-application is live at http://nextflu.org. Contact:  tbedford@fredhutch.org
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Associate Editor: David Posada
ISSN:1367-4803
1367-4811
1367-4811
1460-2059
DOI:10.1093/bioinformatics/btv381