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

Richard A Neher,Trevor Bedford

doi:10.1093/bioinformatics/btv381

Abstract

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

Highlights

Every year, seasonal influenza infects between 10 and 20% of the global population, resulting in substantial human morbidity and mortality (World Health Organization, 2009)
The particular choice of vaccine strain plays a major role in determining vaccine efficacy and so it is of critical importance to develop tools to analyze the ongoing evolution of the influenza virus population in order to aid vaccine strain selection
Influenza sequence data for the hemagglutinin (HA) gene is downloaded from the GISAID EpiFlu database (Bogner et al, 2006), which contains the most up-to-date collection of seasonal influenza viruses

Summary

Introduction

Seasonal influenza infects between 10 and 20% of the global population, resulting in substantial human morbidity and mortality (World Health Organization, 2009). The seasonal influenza vaccine needs frequent updating to remain effective. The program nextflu presents a near real-time display of genetic relationships among influenza viruses and allows investigation of currently available sequence data. By visualizing many different genetic and epidemiological features, we hope that nextflu will help vaccine strain selection.

Results

Conclusion