Broadly neutralizing human antibody that recognizes the receptor-binding pocket of influenza virus hemagglutinin

Abstract

Seasonal antigenic drift of circulating influenza virus leads to a requirement for frequent changes in vaccine composition, because exposure or vaccination elicits human antibodies with limited cross-neutralization of drifted strains. We describe a human monoclonal antibody, CH65, obtained by isolating rearranged heavy- and light-chain genes from sorted single plasma cells, coming from a subject immunized with the 2007 trivalent influenza vaccine. The crystal structure of a complex of the hemagglutinin (HA) from H1N1 strain A/Solomon Islands/3/2006 with the Fab of CH65 shows that the tip of the CH65 heavy-chain complementarity determining region 3 (CDR3) inserts into the receptor binding pocket on HA1, mimicking in many respects the interaction of the physiological receptor, sialic acid. CH65 neutralizes infectivity of 30 out of 36 H1N1 strains tested. The resistant strains have a single-residue insertion near the rim of the sialic-acid pocket. We conclude that broad neutralization of influenza virus can be achieved by antibodies with contacts that mimic those of the receptor.

Fig. 1.

(A) Inferred lineage of clone 860. (Left) The unmutated common ancestor (UCA) of the three antibodies (shown by their numbers, Right) isolated from the donor. (B) Alignment of heavy-chain (Upper) and light-chain (Lower) sequences in the lineage. Positions at which CH65 differs from the UCA are highlighted in green; those at which one of the other antibodies differs are boxed in blue; residues that contact HA in the complex are underscored in red. (C) Contact of the Fab from CH65 with HA1. Heavy chain in dark blue; light chain in light blue; CDRs in colors as labeled in B; and HA in red, with the atomic surface shown as a partly transparent overlay. Residues that have mutated from the UCA are marked at Cα positions by green spheres.

Fig. 2.

(A) HA trimer with bound CH65 Fab. One HA chain is in red (HA1) and green (HA2); the other two chains are in gray; glycans are in yellow. The Fab bound to the colored HA chain is in dark blue (heavy chain) and light blue (light chain), with the contacting CDRs in colors as in Fig. 1. Glycans modeled with GlyProt server. (B) Blow-up of the variable region and its contact with HA1. Colors as in Fig. 1. Note that the heavy-chain CDR3 (magenta) projects into the receptor-binding pocket on HA1, whereas the remaining CDRs have more limited surface contacts. (C and D) Surface representation of the contact between Fab CH65 and HA1, opened up as shown by the arrows. The sialic-acid pocket on one HA subunit is in dark red; the rest of the subunit, in dull red; the remaining two subunits, in gray; and glycans, in yellow. (D) Worm representations of the CH65 CDRs are shown superimposed on the HA surface. The H1 epitopes (Sa, Sb, etc.) are labeled.

Fig. 3.

Comparison of interactions from CH65 (A) and LSTc (B). Hydrogen bonds in the receptor site are shown as dashed lines.