I am very excited to announce that my lab will join the Biozentrum Basel in Februar 2017! The Biozentrum and the Basel life science community is a great place to do science and I am looking forward to working with my new colleagues at the Biozentrum, the D-BSSE, and other institutes in Basel.
In November, Boris Shraiman, Colin Russell and myself published a paper on predicting evolution. The method uses the shape of genealogical trees to spot expanding clades which will likely dominate the future population. We demonstrated the method by applying it to historical data of seasonal influenza A/H3N2 virus evolution and predicted the majority years well. However, those “predictions” were for past events. It is time to predict the future!
The dynamics of A/H3N2 viruses over the last 3 years are illustrated in the above figure. There are two big clades that emerged almost 3 years ago and have been dominating A/H3N2 since (3C2 and 3C3 in WHO nomenclature). Of these, 3C3 is bigger and has dominated the 13/14 season. In the past 8 months, however, 3C2 has come back to life evolving a new subclade, 3C2a, while 3C3 has also evolved a new subclade, 3C3a. Importantly, these subclades differ at critical amino acids of HA1 from the precursor (F159Y, 3C2a in green, F159S, 3C3a in red) and are far from the current vaccine for the northern hemisphere (lower green dot). The updated H3N2 vaccine choice for the southern hemisphere (the upper green dot) is part of the 3C3a. The question now is whether 3C3a or 3C2a is taking over?
The interactive tool allows users to color the tree by our prediction using the local branching index we developed. Given the data up until 5 January 2015, our algorithm predicts 3C2a as the strain that expands and dominates the future (see screen shot below). To be concrete, the method predicts that viruses from 3C2a will be the dominant progenitors of the 2015/2016 northern hemisphere winter epidemic.
Emmanuel Benard, a computer scientist/bioinformaticien from France, joined our lab as a post-doc in July. For his PhD at the University of Strasbourg, Emmanuel worked on substitution models for genetic motives.