Which flu strain will dominate 2015/2016?

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!

Building on two projects by Trevor Bedford to automatically construct influenza trees (augur) and visualize them using javascript (augur), I developed a tool for interactive exploration of seasonal influenza evolution and prediction.

The past 15 month of A/H3N2 visualized using our interactive tool. Isolates after the dates indicated in the panel are shown in grey, colors encode the genotype at 7 amino acid position with strong effects on antigenic properties. The clade designation is indicated in the right panel, big green dots correspond to recent vaccine strains.

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.

Our prediction for the 2015/2016 season as of Jan 05, 2015: 3C2a is most likely to take over, redder colors correspond to more rapid expansion. (Parameters tau = 0.0007 using data from 200 days prior to Jan 2015).


The tool also allows users to replay past evolution by ignoring all isolates past a certain date. Go ahead and explore the evolution of seasonal influenza A/H3N2 viruses.