Influenza virus evolution

Human immunity is the main driving force of the seasonal influenza viruses. Only when changing their antigenic properties, influenza viruses are able to re-infect previously infected humans. Mutation that prevent immune recognition often rapidly spread across the globe. For this reason, seasonal influenza vaccines need to be updated frequently. Vaccine strains are chosen among sampled virus strains, and the more closely this strain matches the future influenza virus population, the better the vaccine is going to be. Hence tracking influenza viruses is essential to maintain vaccine efficiency and accurate predictions of the composition of future populations could improve vaccines substantially.

Real-time tracking of influenza virus evolution

Together with Trevor Bedford, we have been working on an interactive tool to explore influenza evolution. It is up and running at In addition to a tree of the most recent influenza strains, users can explore the frequencies of mutations and clades of the tree. To facilitate data sharing and exploration during the recent ebola and MERS outbreaks, we have adapted nextflu and set up and

nextflu: Real-time tracking of seasonal influenza virus evolution in humans.
Richard A. Neher, Trevor Bedford. Bioinformatics, btv381

Predicting influenza evolution

In collaboration with Colin Russell and Boris Shraiman — we have shown that it is possible to predict which individual from a population is most closely related to future populations. The method uses the branching pattern of genealogical trees to estimate which part of the tree contains the “fittest” sequences. When applied to historical influenza data, the method makes informative predictions in about 80% of the time.

Predicting evolution from the shape of genealogical trees.
Richard A Neher, Colin A Russel, Boris I Shraiman. eLIFE, 03568

Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses.
Richard A. Neher,Trevor Bedford, Rodney S. Daniels, Colin A. Russell, Boris I. Shraiman.
PNAS, vol. 113, E1701-E1709. doi:10.1073/pnas.1525578113

Tracking spread and evolution of Zika virus

The Zika virus was first described in 1947 in Uganda and it typically causes only mild illness. In recent years the virus has spread rapidly through South Pacific Islands, South East Asia, and through parts of South and North America.
Sequencing Zika virus genomes from clinical specimens has been challenging due to very virus titers (see reports by the ZIBRA project and the lab of Kristian Andersen), but the 150 genomes available to date elucidate some aspects of Zika virus spread and evolution. We have adapted nextflu for Zika virus analysis and made it available at A screen shot of the Zika virus phylogeny (Oct 2, 2016) is shown below:



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