Geometric constraints dominate the antigenic evolution of influenza H3N2 hemagglutinin

Abstract

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 individual 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 found that these three predictors individually explain approximately 15% of the variation in site-wise dN/dS. The solvent accessibility and proximity predictors were largely independent of each other, while the epitope sites were not. In combination, solvent accessibility and proximity explained 32% of the variation in dN/dS. Incorporating experimental epitope sites into the model added only an additional 2 percentage points. We also found that the historical H3 epitope sites, which date back to the 1980s and 1990s, showed only weak overlap with the latest experimental epitope data. 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, and not host immune bias, seems to be the primary determinant of H3 evolution.\n\nAuthor summaryThe influenza virus is one of the most rapidly evolving human viruses. Every year, it accumulates mutations that allow it to evade the host immune response of previously infected individuals. Which sites in the virus genome allow this immune escape and the manner of escape is not entirely understood, but conventional wisdom states that specific \"immune epitope sites\" in the protein hemagglutinin are preferentially attacked by host antibodies and that these sites mutate to directly avoid host recognition; as a result, these sites are commonly targeted by vaccine development efforts. Here, we combine influenza hemagglutinin sequence data, protein structural information, experimental immune epitope data, and historical epitopes to demonstrate that neither the historical epitope groups nor epitopes based on experimental data are crucial for predicting the rate of influenza evolution. Instead, we find that a simple geometrical model works best: sites that are closest to the location where the virus binds the human receptor are the primary driver of hemagglutinin evolution. There are two possible explanations for this result. First, the existing historical and experimental epitope sites may not be the real antigenic sites in hemagglutinin. Second, alternatively, hemagglutinin antigenicity may not the primary driver of influenza evolution.