Antigenic and virological properties of an H3N2 variant that continues to dominate the 2021-22 Northern Hemisphere influenza season

Abstract

Influenza viruses circulated at very low levels during the beginning of the COVID-19 pandemic, and population immunity against these viruses is low. An H3N2 strain (3C.2a1b.2a2) with a hemagglutinin (HA) that has several substitutions relative to the 2021-22 H3N2 vaccine strain is dominating the 2021-22 Northern Hemisphere influenza season. Here, we show that one of these substitutions eliminates a key glycosylation site on HA and alters sialic acid binding. Using glycan array profiling, we show that the 3C.2a1b.2a2 H3 maintains binding to an extended biantennary sialoside and replicates to high titers in human airway cells. We find that antibodies elicited by the 2021-22 Northern Hemisphere influenza vaccine poorly neutralize the 3C.2a1b.2a2 H3N2 strain. Together, these data indicate that 3C.2a1b.2a2 H3N2 viruses efficiently replicate in human cells and escape vaccine-elicited antibodies.

Keywords: CP: Microbiology; antibody; antigenic mismatch; influenza vaccine; influenza virus.

Graphical abstract

Figure 1

H3N2 variant lineage 2a2 replicates efficiently in human cells despite changes in HA receptor specificity (A) Nextstrain phylogenetic analysis of the HA gene of contemporary (2019–21) H3N2 viruses. (B) Amino acid differences at residues 158–160 are denoted (red), and glycan loss is modeled on the crystal structure of an H3 HA trimer (PDB: 4O5I) for 2a1 and 2a2 HAs. (C and D) Binding of wild-type (C) and mutant (D) recombinant HAs to a sialoside microarray. Printed glycans include those with α2,3 sialic acid linkages (yellow), α2,6 sialic acid linkages (green), or no sialic acid linkage (gray). Bars represent the mean fluorescent intensity with standard error bars. Mutant 2a1 HA proteins (D) had N159 and I160 substitutions to remove glycosylation motif, and mutant 2a2 HA proteins (D) had Y159 and T160 substitutions to add glycosylation motif. Glycan numbers are shown on the x axes. (E) Infectious virus production after an MOI = 0.01 infection of primary differentiated human nasal epithelial cell (hNEC) cultures incubated at 37°C (top) or 32°C (bottom). Virus titers were measured by TCID₅₀ assay using MDCK cells. Data at each time point are the mean/SEM of three separate wells. Curves are representative of two independent experiments. A repeated measures MANOVA followed by a Bonferonni post-test was completed (^∗p ≤ 0.05).

Figure 2

Potential H3N2 antigenic mismatch for the 2021–22 Northern Hemisphere influenza season (A) Amino acid residues encoded by egg-adapted and wild-type circulating strains at HA positions 158, 159, and 160, an N-linked glycosylation site. (B and C) Virus neutralization titers to the vaccine virus and circulating viruses prior to vaccination (B) and 27–28 days following vaccination (C) in a group of vaccinees in Oct–Nov 2021 (n = 40). Neutralization titers are plotted as the geometric mean titer (GMT) of two independent experiments. Lines represent the GMT and standard deviation among vaccinees. A Kruskal-Wallis one-way ANOVA with Dunn’s multiple comparisons test was completed on log₂ transformed titers (^∗p ≤ 0.05). (D) Fold-reduction in neutralizing antibodies to circulating strains when compared to the vaccine virus in a group of vaccinees (n = 40).