Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape

Abstract

Antigenic drift of influenza virus hemagglutinin (HA) is enabled by facile evolvability. However, HA antigenic site B, which has become immunodominant in recent human H3N2 influenza viruses, is also evolutionarily constrained by its involvement in receptor binding. Here, we employ deep mutational scanning to probe the local fitness landscape of HA antigenic site B in six different human H3N2 strains spanning from 1968 to 2016. We observe that the fitness landscape of HA antigenic site B can be very different between strains. Sequence variants that exhibit high fitness in one strain can be deleterious in another, indicating that the evolutionary constraints of antigenic site B have changed over time. Structural analysis suggests that the local fitness landscape of antigenic site B can be reshaped by natural mutations via modulation of the receptor-binding mode. Overall, these findings elucidate how influenza virus continues to explore new antigenic space despite strong functional constraints.

Structural Biology of Influenza Hemagglutinin: An Amaranthine Adventure

“…Consistently, subsequent studies demonstrated that major antigenic drift in seasonal influenza viruses is mostly driven by mutations within or near the RBS [83,84]. It is therefore not surprising that some of the mutations that arise during natural evolution of human influenza virus can alter both HA antigenicity and receptor binding [47,48,85,86]. Furthermore, egg-based seasonal influenza vaccines often carry egg-adaptive mutations in the HA RBS that allow the vaccine strain to bind to α2-3 linkage sialylated glycans on the chorioallantoic membrane but can also alter the antigenicity of HA, thereby decreasing vaccine effectiveness [49,[87][88][89].…”

“…Structural studies have also shown that the receptor-binding mode of human H3N2 HA has changed over time and is associated with mutations in all four structural elements of the RBS [46][47][48][49]. Specifically, natural mutations in the 130-loop and 220-loop have introduced additional hydrogen bonds (H-bonds) to Sia-1 and Gal-2 of the receptor [47][48][49], whereas a number of other mutations in the 190-helix and 150-loop allow the subsequent sugar moieties (GlcNAc-3, Gal-4, and GlcNAc-5) to move closer to the RBS [47][48][49] (Figure 1). Such changes in receptor binding can alter the amino acid preference at particular positions in the RBS [47,48].…”

“…Specifically, natural mutations in the 130-loop and 220-loop have introduced additional hydrogen bonds (H-bonds) to Sia-1 and Gal-2 of the receptor [47][48][49], whereas a number of other mutations in the 190-helix and 150-loop allow the subsequent sugar moieties (GlcNAc-3, Gal-4, and GlcNAc-5) to move closer to the RBS [47][48][49] (Figure 1). Such changes in receptor binding can alter the amino acid preference at particular positions in the RBS [47,48]. For example, residue 190 in the RBS of H3N2 HA was almost exclusively Glu before the 1992-1993 influenza season but mutated to Asp in almost all strains from then on.…”

“…Interestingly, reverting the Asp back to Glu in strains from year 2007 onward abolished receptor binding, due to the concomitant change in the receptor-binding mode [47]. In fact, evolutionary contingency, which describes sequence variants that were previously fit but then become unfit and extinct, as well as evolutionary entrenchment, which describes sequence variants that were previously unfit and then become fit and emerge, are common in the HA RBS of human H3N2 viruses [48]. As seasonal influenza viruses continue to evolve in the human population, it will be fascinating to observe how the receptor-binding mode is able to change (or not) in the future, which would allow the H3N2 virus to continue its over 50 years of sustained circulation in the human population.…”

“…This phenomenon has recently been reported in human H3N2 viruses, which have evolved a preference for long, branched sialylated glycans with extended poly-N-acetyl-lactosamine (poly-LacNAc) [ 45 ]. Structural studies have also shown that the receptor-binding mode of human H3N2 HA has changed over time and is associated with mutations in all four structural elements of the RBS [ 46 , 47 , 48 , 49 ]. Specifically, natural mutations in the 130-loop and 220-loop have introduced additional hydrogen bonds (H-bonds) to Sia-1 and Gal-2 of the receptor [ 47 , 48 , 49 ], whereas a number of other mutations in the 190-helix and 150-loop allow the subsequent sugar moieties (GlcNAc-3, Gal-4, and GlcNAc-5) to move closer to the RBS [ 47 , 48 , 49 ] ( Figure 1 ).…”