Geometric constraints dominate the antigenic evolution of influenza H3N2 hemagglutinin

Austin G Meyer, Claus O Wilke
doi: http://dx.doi.org/10.1101/014183

We have carried out a comprehensive analysis of the determinants of human influenza A H3 hemagglutinin evolution, considering three distinct predictors of evolutionary variation at in- dividual sites: solvent accessibility (as a proxy for protein fold stability and/or conservation), experimental epitope sites (as a proxy for host immune bias), and proximity to the receptor- binding region (as a proxy for protein function). We have found that these three predictors individually explain approximately 15% of the variation in site-wise dN/dS. However, the sol- vent accessibility and proximity predictors seem largely independent of each other, while the epitope sites are not. In combination, solvent accessibility and proximity explain 32% of the variation in dN/dS. Incorporating experimental epitope sites into the model adds only an ad- ditional 2 percentage points. We have also found that the historical H3 epitope sites, which date back to the 1980s and 1990s, show only weak overlap with the latest experimental epi- tope data, and we have defined a novel set of four epitope groups which are experimentally supported and cluster in 3D space. Finally, sites with dN/dS > 1, i.e., the sites most likely driving seasonal immune escape, are not correctly predicted by either historical or experimental epitope sites, but only by proximity to the receptor-binding region. In summary, proximity to the receptor-binding region, rather than host immune bias, seems to be the primary determinant of H3 immune-escape evolution.