N-linked glycosylation sites with low occupancy support sustained circulation of the A(H3N2) influenza A virus in the human population

Glycosylation of the influenza A virus hemagglutinin is crucial for viral fitness and immune evasion. The hemagglutinin of contemporary human A(H3N2) influenza A viruses is extensively glycosylated with up to 13 putative glycosylation sites. Glycan types and occupancy of these sites are not uniform: while most are nearly completely occupied by glycans, some, such as those at amino acid residues 45 and 144, are only partially occupied and are evolutionarily unstable. While the effects of highly occupied glycosylated sites of hemagglutinin on A(H3N2) influenza A virus biology are well studied, there is limited information on the functional impact of the low-occupancy glycosylation sites on the viral hemagglutinin. Here, by using reverse-genetics A(H3N2) influenza A viruses lacking glycans at either residue 45 or 144, or both in hemagglutinin, we demonstrate that, despite reduced receptor binding, thermal stability, and fusion, the presence of a low level of glycosylation at these positions does not impact virus growth in Madin-Darby canine kidney epithelial cell culture. In contrast, these low-occupancy sites do affect immune responses in mice, by reducing titers of antibodies that correlate with virus neutralization and protection against influenza disease. We suggest that the temporary introduction of sites with low glycosylation allows influenza viruses to reduce the immune pressure on antigenic and receptor binding sites of hemagglutinin without significantly compromising viral virulence. This mechanism may help support the sustained circulation of A(H3N2) influenza A virus in human populations. IMPORTANCE: Many of the glycosylation sites on the hemagglutinin of influenza A viruses are near antigenic sites, such that the glycans block antibody recognition and help evade population immunity. However, glycans may also reduce viral replication and virulence. Glycosylation sites at amino acid residues 45 and 144 of the hemagglutinin of contemporary A(H3N2) influenza A viruses are minimally occupied, with fewer than 10% of the sites containing glycans. This is still sufficient to partially evade antibody-based population immunity, while minimizing the impact on replication and virulence. Over time, A(H3N2) viruses have used both these sites only during limited periods, suggesting that even a low level of glycan occupancy may confer some negative selection pressure that is compensated by evasion of human population immunity. Data from this study provide a better understanding of the mechanisms that allow viruses to evade antibody-based immunity and maintain circulation in the human population.