Vaccine-elicited antibody that neutralizes H5N1 influenza and variants binds the receptor site and polymorphic sites

Abstract

Antigenic drift of circulating seasonal influenza viruses necessitates an international vaccine effort to reduce the impact on human health. A critical feature of the seasonal vaccine is that it stimulates an already primed immune system to diversify memory B cells to recognize closely related, but antigenically distinct, influenza glycoproteins (hemagglutinins). Influenza pandemics arise when hemagglutinins to which no preexisting adaptive immunity exists acquire the capacity to infect humans. Hemagglutinin 5 is one subtype to which little preexisting immunity exists and is only a few acquired mutations away from the ability to transmit efficiently between ferrets, and possibly humans. Here, we describe the structure and molecular mechanism of neutralization by H5.3, a vaccine-elicited antibody that neutralizes hemagglutinin 5 viruses and variants with expanded host range. H5.3 binds in the receptor-binding site, forming contacts that recapitulate many of the sialic acid interactions, as well as multiple peripheral interactions, yet is not sensitive to mutations that alter sialic acid binding. H5.3 is highly specific for a subset of H5 strains, and this specificity arises from interactions to the periphery of the receptor-binding site. H5.3 is also extremely potent, despite retaining germ line-like conformational flexibility. structural biology | immunity | antigen recognition | affinity maturation | influenza I nfluenza remains a major public health concern because seasonal influenza infects 600 million to 1.1 billion people annually, resulting in 3-5 million cases of severe disease, and 250,000-500,000 deaths (1). By comparison, the four influenza pandemics of the 20th century, caused by novel influenza strains infecting the immunologically naive human population, resulted in 50-100 million deaths (1-4). Influenza A immunity is principally mediated by the antibody response to the viral glycoprotein, hemagglutinin (HA) (5). HA is expressed as a preprotein, HA0, assembled as a trimer on the viral envelope, and cleaved by host proteases into HA1 and HA2. HA1 is a largely globular domain responsible for receptor binding, and HA2 is a rod-shaped helical bundle responsible for membrane fusion (Fig. 1A) (5). There are 18 genetically distinct subtypes of influenza A HA (H1-H18), of which only H1 and H3 currently circulate among humans (1,(6)(7)(8)(9).Despite the widespread presence of H5N1 influenza viruses in wild birds, the virus is not currently transmissible within the human population. Human-to-human transmission is inefficient and is partially restricted by the receptor specificity of the virus; human-type HAs preferentially recognize α2,6-linked sialic acid whereas avian-type HAs prefer α2,3-linked sialic acid (1, 10-12). However, there have been >600 human cases of H5N1 infection since 2004, resulting from the direct transmission of the virus from birds to humans, associated with an ∼60% mortality rate. There is the potential for a significant pandemic if H5 viruses develop the ability to spread efficiently b...

Identification of antibodies targeting the H3N2 hemagglutinin receptor binding site following vaccination of humans

“…Most HA RBS-targeting antibodies are not broadly reactive because their large binding footprints require contacts outside of the narrow RBS. However, several broadly reactive HA RBS-targeting antibodies have been identified (Ekiert et al, 2012; Krause et al, 2011; Lee et al, 2014; Lee et al, 2012; McCarthy et al, 2018; Schmidt et al, 2015b; Tsibane et al, 2012; Whittle et al, 2011; Winarski et al, 2015; Xu et al, 2013). A common feature of these broadly reactive HA RBS-targeting antibodies is that they all have relatively long HCDR3s, which allow them to minimize contacts on the rim of the RBS and maximize contacts with conserved RBS residues.…”

“…Several broadly neutralizing antibodies that target conserved residues in the HA RBS have been identified (Ekiert et al, 2012; Krause et al, 2011; Lee et al, 2014; Lee et al, 2012; McCarthy et al, 2018; Schmidt et al, 2015b; Tsibane et al, 2012; Whittle et al, 2011; Winarski et al, 2015; Xu et al, 2013). These antibodies can arise from a number of V H gene segments (McCarthy et al, 2018; Schmidt et al, 2015b).…”

Principles of Broad and Potent Antiviral Human Antibodies: Insights for Vaccine Design

“…Such antibodies bind near the top surface of the head domain of the HA protein that mediates attachment to the cellular receptor sialic acid. Antibodies that block receptor binding for diverse influenza type A viruses including those of subtype H1 (Krause et al, 2010, 2011a, 2011b; Tsibane et al, 2012; Xu et al, 2010; Yu et al, 2008b), H2 (Krause et al, 2012; Xu et al, 2013), H3 (Bangaru et al, 2016), H5 (Thornburg et al, 2013; Winarski et al, 2015), and H7 (Thornburg et al, 2016) have been isolated and characterized. High-resolution crystal structures of these antibodies in complex with soluble trimeric forms of HA (or recombinant HA head domain) have proven very useful for defining the chemical and physical principles underlying the molecular recognition of the RBD.…”

“…A large number of antibodies with this residue have been identified and visualized in high-resolution structures as achieving important critical interactions (Figures 3C and 3D; see also Hong et al, 2013; Schmidt et al, 2013; Whittle et al, 2011; Wu and Wilson, 2017). Interestingly, although presentation of an aspartate residue in this position seems to be a rule that satisfies interaction, the neutralizing human antibody designated H5.3 has the aspartate in the right position in a CDR3, but the loop does not use the aspartate to interact in the canonical fashion (Thornburg et al, 2013; Winarski et al, 2015) (Figure 3E). Thus, although structural rules of engagement for antibodies can be identified, the structural features are not simply short sequences or single residues, but rather are elements that function as predicted only in proper context.…”

“…H5.3 is indicated in green; conventional Asp containing antibodies is indicated in red. Figure is based on Winarski et al, 2015.…”