Measures of Population Immunity Can Predict the Dominant Clade of Influenza A (H3N2) in the 2017-2018 Season and Reveal Age-Associated Differences in Susceptibility and Antibody-Binding Specificity

Abstract

Background: For antigenically variable pathogens such as influenza, strain fitness is partly determined by the relative availability of hosts susceptible to infection with that strain compared with others. Antibodies to the hemagglutinin (HA) and neuraminidase (NA) confer substantial protection against influenza infection. We asked if a cross-sectional antibody-derived estimate of population susceptibility to different clades of influenza A (H3N2) could predict the success of clades in the following season.

Methods: We collected sera from 483 healthy individuals aged 1 to 90 years in the summer of 2017 and analyzed neutralizing responses to the HA and NA of representative strains using focus reduction neutralization tests (FNRT) and enzyme-linked lectin assays (ELLA). We estimated relative population-average and age-specific susceptibilities to circulating viral clades and compared those estimates to changes in clade frequencies in the following 2017-2018 season.

Results: The clade to which neutralizing antibody titers were lowest, indicating greater population susceptibility, dominated the next season. Titer correlations between viral strains varied by age, suggesting age-associated differences in epitope targeting driven by shared past exposures. Yet substantial unexplained variation remains within age groups.

Conclusions: This study indicates how representative measures of population immunity might improve evolutionary forecasts and inform selective pressures on influenza.

FIGURE 1

Reference viruses representing co‐circulating H3N2 clades during the 2016–2017 season. (A) Genealogies of H3N2 HA through the 2016–2017 (left) and 2017–2018 season (right). Tips are colored by similarity to reference viruses. For clades with multiple representative viruses, branches are colored the same as one of those viruses, chosen arbitrarily. Tips are shown as filled circles if collected in North America during the most recent season. (B) Amino acid and glycosylation site variation among reference viruses. Clades 3C.3a and 3C.2a diverge at additional non‐epitope sites (not shown). Residue 128 belongs to antigenic site B, but the substitution T128A results in loss of glycosylation on residue 126 of epitope A. Therefore, we show residue 128 in epitope A and in the glycosylation site involving residues 126–128, following [20]. (C) Variable residues among the reference viruses are shown on the H3 structure of A/Aichi/2/1968 (Protein Data Bank: 1HGG) and colored by epitope as in panel (B). For each strain, residues differing from 3C.2a are numbered and darker in color. (D) Glycosylation sites used in the model shown on the H3 structure. (E) Monthly clade frequencies among GISAID isolates from North America collected between the 2016–2017 and the 2018–2019 seasons. Gray bars represent isolates that do not belong to the focal clades in this study.

FIGURE 2

Antibody titers and inferred relative susceptibilities to co‐circulating H3 strains show variability by strain and age group. (A) FRNT titers with points jittered slightly along the $x$‐ and $y$‐axes. Lines are locally estimated scatterplot smoothing (LOESS) curves of geometric mean titers (smoothing parameter $\alpha =0.75$, degree $=2$). (B) Inferred relative susceptibility to each reference strain for the whole population (left) and by age group (right). The bars indicate 95% CIs obtained from bootstrapping. Separately for the overall population and each age group, we ranked strains in decreasing order of susceptibility using pairwise bootstrap tests (e.g., a strain had rank 1 if susceptibility to it was significantly higher than susceptibility to all other strains in pairwise tests, 2 if significantly higher for all but one strain, and so on. Strains are tied in rank and appear in the same color if their relative susceptibilities do not differ significantly. The gray arrows show how the clades changed in frequency in North America between the 2016/17 and 2017/2018 seasons.

FIGURE 3

Antibody titers and relative susceptibilities to co‐circulating N2 strains show differences by strain and age group. (A) ELLA titers with points jittered slightly along the $x$‐ and $y$‐axes. Lines are locally estimated scatterplot smoothing (LOESS) curves of geometric mean titers (smoothing parameter $\alpha =0.75$, degree $=2$). (B) Inferred relative susceptibility and its rank for each NA for the whole population (left) and by age group (right). A lower rank indicates significantly higher susceptibility. Strains are tied in rank and appear in the same color if their relative susceptibilities do not differ significantly.

FIGURE 4

Host age distribution of H3N2 isolates sampled in the United States during the 2017/18 season. We obtained isolate data from GISAID. Viruses from clade 3C.2a2 are shown in purple, and viruses from all other clades combined are shown in gray (bars are overplotted). 3C.2a2 isolates were more common across all ages than viruses from other clades combined, but viruses from other clades were proportionally more common in children relative to adults.

FIGURE 5

Correlations in titers to different clades. (A) Schematics demonstrating how we calculated the correlation in titers to each strain pair across people in each age group. For these analyses, we randomly imputed continuous titer values between consecutive dilutions (e.g., a titer of 160 was replaced by a continuous value between 160 and 320 drawn with uniform probability). For each pair of viruses and each age group, we report the average Spearman correlation coefficient across 1000 replicate imputations. We removed individuals with undetectable titers across all reference viruses. (B) Correlations between titers to different strains differ by age group, suggesting age‐dependent patterns of epitope targeting.