Fig. 3.

Increasing sequon densities of HA of A/H3N2 (Left) and A/H1N1 (Center) strains of influenza virus with antigenic drift results from an increased conditional probability that Asn, Thr, and Ser will be present in sequons rather than elsewhere in HA. Selection for sequons (solid arrow) based on this mechanism, which is determined by comparing actual (solid pink triangles) versus calculated or expected (open pink triangles) sequon densities for HA, increases with time. As a control, there is no selection for sequons in viral capsid and polymerases (capsidic proteins), where the observed density of sequons (solid blue circles) equals the expected density (open blue circles). In contrast, amino acid composition bias (white arrow), which is determined by comparing the expected sequon density of HA (open pink triangles) with that of capsid and polymerases of influenza viruses (open blue circles), remains the same with time. The HA proteins of A/H5N1 and 2009 A/H1N1 (Right) show modest selection based on amino acid composition bias but do not show selection based on an increased conditional probability of Asn, Thr, and Ser being present in sequons rather than elsewhere in HA (20, 25). Changes in the amino acid sequences of A/H3N2 influenza proteins with time is shown in Fig. S3.