Human immunity is the main driving force of evolution of 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.
Together with Trevor Bedford, we have been working on an interactive tool to explore influenza evolution. It is up and running at nextflu.org. 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 ebola.nextflu.org and mers.nextflu.org.
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.
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 nextstrain.org. A screen shot of the Zika virus phylogeny (Oct 2, 2016) is shown below:
Dylan H. Morris, Katelyn M. Gostic, Simone Pompei
Trends in Microbiology, 10.1016/j.tim.2017.09.004 bibtex
Richard A. Neher, Trevor Bedford, Rodney S. Daniels, Colin A. Russell and Boris I. Shraiman
Proceedings of the National Academy of Sciences of the United States of America, 113 E1701--1709. 10.1073/pnas.1525578113 bibtex
Richard A. Neher and Trevor Bedford
Bioinformatics (Oxford, England), 31 3546--3548. 10.1093/bioinformatics/btv381 pdf bibtex
Richard A. Neher, Colin A. Russell and Boris I. Shraiman
eLife, 3 10.7554/eLife.03568 pdf bibtex