Influenza hemagglutinin stem-fragment immunogen elicits broadly neutralizing antibodies and confers heterologous protection

Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza virus hemagglutinin to generate multidomain antibodies with impressive breadth and potency. Multidomain antibody MD3606 protects mice against influenza A and B infection when administered intravenously or expressed locally from a recombinant adeno-associated virus vector. Crystal and single-particle electron microscopy structures of these antibodies with hemagglutinins from influenza A and B viruses reveal binding to highly conserved epitopes. Collectively, our findings demonstrate that multidomain antibodies targeting multiple epitopes exhibit enhanced virus cross-reactivity and potency. In combination with adeno-associated virus–mediated gene delivery, they may provide an effective strategy to prevent infection with influenza virus and other highly variable pathogens.

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Structure of the apo anti-influenza CH65 Fab

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x14027599 ◽

2015 ◽

Vol 71 (2) ◽

pp. 145-148 ◽

Cited By ~ 2

Author(s):

Peter S. Lee ◽

Ashley J. Arnell ◽

Ian A. Wilson

Keyword(s):

Neutralizing Antibodies ◽

Affinity Maturation ◽

Influenza Viruses ◽

Antigenic Drift ◽

Human Antibody ◽

Broadly Neutralizing Antibodies ◽

High Affinity ◽

Influenza Hemagglutinin ◽

Universal Influenza Vaccine ◽

Complementarity Determining Region

Influenza viruses remain a persistent challenge to human health owing to their inherent ability to evade the immune response by antigenic drift. However, the discovery of broadly neutralizing antibodies (bnAbs) against divergent viruses has sparked renewed interest in a universal influenza vaccine and novel therapeutic opportunities. Here, a crystal structure at 1.70 Å resolution is presented of the Fab of the human antibody CH65, which has broad neutralizing activity against a range of seasonal H1 isolates. Previous studies proposed that affinity maturation of this antibody lineage pre-organizes the complementarity-determining region (CDR) loops into an energetically favorable HA-bound conformation. Indeed, from the structural comparisons of free and HA-bound CH65 presented here, the CDR loops, and in particular the heavy-chain CDR3, adopt the same conformations in the free and bound forms. Thus, these findings support the notion that affinity maturation of the CH65 lineage favorably preconfigures the CDR loops for high-affinity binding to influenza hemagglutinin.

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Influenza A virus hemagglutinin stem fragment to induce broadly neutralizing antibodies

Science-Business eXchange ◽

10.1038/scibx.2014.811 ◽

2014 ◽

Vol 7 (27) ◽

pp. 811-811

Keyword(s):

Influenza A Virus ◽

Neutralizing Antibodies ◽

Influenza A ◽

Broadly Neutralizing Antibodies ◽

Stem Fragment

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Quantifying the effects of single mutations on viral escape from broad and narrow antibodies to an H1 influenza hemagglutinin

10.1101/210468 ◽

2017 ◽

Cited By ~ 1

Author(s):

Michael B. Doud ◽

Juhye M. Lee ◽

Jesse D. Bloom

Keyword(s):

Influenza Virus ◽

Neutralizing Antibodies ◽

Viral Escape ◽

Effect Sizes ◽

Single Amino Acid ◽

Broadly Neutralizing Antibodies ◽

Receptor Binding Site ◽

Influenza Hemagglutinin ◽

Amino Acid Mutations ◽

Do So

ABSTRACTInfluenza virus can completely escape most antibodies with single mutations. However, rare antibodies broadly neutralize many viral strains. It is unclear how easily influenza virus might escape such antibodies if it was under strong pressure to do so. Here we map all single amino-acid mutations that increase resistance to broad antibodies targeting an H1 hemagglutinin. Crucially, our approach not only identifies antigenic mutations but also quantifies their effect sizes. All antibodies select mutations, but the effect sizes vary widely. The virus can escape a broad antibody that targets residues in hemagglutinin’s receptor-binding site the same way it escapes narrow strain-specific antibodies: via single mutations with huge effects. In contrast, broad antibodies targeting hemagglutinin’s stalk only select mutations with small effects. Therefore, among the antibodies we have examined, breadth is an imperfect indicator of the potential for viral escape via single mutations. Broadly neutralizing antibodies targeting the H1 hemagglutinin stalk are quantifiably harder to escape than the other antibodies tested here.

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A glycan cluster on the SARS-CoV-2 spike ectodomain is recognized by Fab-dimerized glycan-reactive antibodies

10.1101/2020.06.30.178897 ◽

2020 ◽

Cited By ~ 6

Author(s):

Priyamvada Acharya ◽

Wilton Williams ◽

Rory Henderson ◽

Katarzyna Janowska ◽

Kartik Manne ◽

...

Keyword(s):

Fusion Proteins ◽

Neutralizing Antibodies ◽

Cell Entry ◽

List Type ◽

Viral Fusion ◽

Broadly Neutralizing Antibodies ◽

S Protein ◽

Influenza Hemagglutinin ◽

Viral Fusion Proteins ◽

Hiv 1

SummaryThe COVID-19 pandemic caused by SARS-CoV-2 has escalated into a global crisis. The spike (S) protein that mediates cell entry and membrane fusion is the current focus of vaccine and therapeutic antibody development efforts. The S protein, like many other viral fusion proteins such as HIV-1 envelope (Env) and influenza hemagglutinin, is glycosylated with both complex and high mannose glycans. Here we demonstrate binding to the SARS-CoV-2 S protein by a category of Fab-dimerized glycan-reactive (FDG) HIV-1-induced broadly neutralizing antibodies (bnAbs). A 3.1 Å resolution cryo-EM structure of the S protein ectodomain bound to glycan-dependent HIV-1 bnAb 2G12 revealed a quaternary glycan epitope on the spike S2 domain involving multiple protomers. These data reveal a new epitope on the SARS-CoV-2 spike that can be targeted for vaccine design.HighlightsFab-dimerized, glycan-reactive (FDG) HIV-1 bnAbs cross-react with SARS-CoV-2 spike.3.1 Å resolution cryo-EM structure reveals quaternary S2 epitope for HIV-1 bnAb 2G12.2G12 targets glycans, at positions 709, 717 and 801, in the SARS-CoV-2 spike.Our studies suggest a common epitope for FDG antibodies centered around glycan 709.

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Isolation of anin VitroAffinity-Matured, Thermostable “Headless” HA Stem Fragment That Binds Broadly Neutralizing Antibodies with High Affinity

Biochemistry ◽

10.1021/acs.biochem.8b00267 ◽

2018 ◽

Vol 57 (26) ◽

pp. 3817-3829 ◽

Cited By ~ 1

Author(s):

Tariq Ahmad Najar ◽

Uddipan Kar ◽

Jessica A. Flynn ◽

Raghavan Varadarajan

Keyword(s):

Neutralizing Antibodies ◽

Broadly Neutralizing Antibodies ◽

High Affinity ◽

Stem Fragment

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Cross-neutralization of SARS-CoV-2 by HIV-1 specific broadly neutralizing antibodies and polyclonal plasma

PLoS Pathogens ◽

10.1371/journal.ppat.1009958 ◽

2021 ◽

Vol 17 (9) ◽

pp. e1009958

Author(s):

Nitesh Mishra ◽

Sanjeev Kumar ◽

Swarandeep Singh ◽

Tanu Bansal ◽

Nishkarsh Jain ◽

...

Keyword(s):

Monoclonal Antibodies ◽

Neutralizing Antibodies ◽

Cross Reactivity ◽

Type I ◽

Broadly Neutralizing Antibodies ◽

Human Monoclonal Antibodies ◽

Influenza Hemagglutinin ◽

Cd4 Binding Site ◽

Antigenic Profile ◽

Hiv 1

Cross-reactive epitopes (CREs) are similar epitopes on viruses that are recognized or neutralized by same antibodies. The S protein of SARS-CoV-2, similar to type I fusion proteins of viruses such as HIV-1 envelope (Env) and influenza hemagglutinin, is heavily glycosylated. Viral Env glycans, though host derived, are distinctly processed and thereby recognized or accommodated during antibody responses. In recent years, highly potent and/or broadly neutralizing human monoclonal antibodies (bnAbs) that are generated in chronic HIV-1 infections have been defined. These bnAbs exhibit atypical features such as extensive somatic hypermutations, long complementary determining region (CDR) lengths, tyrosine sulfation and presence of insertions/deletions, enabling them to effectively neutralize diverse HIV-1 viruses despite extensive variations within the core epitopes they recognize. As some of the HIV-1 bnAbs have evolved to recognize the dense viral glycans and cross-reactive epitopes (CREs), we assessed if these bnAbs cross-react with SARS-CoV-2. Several HIV-1 bnAbs showed cross-reactivity with SARS-CoV-2 while one HIV-1 CD4 binding site bnAb, N6, neutralized SARS-CoV-2. Furthermore, neutralizing plasma antibodies of chronically HIV-1 infected children showed cross neutralizing activity against SARS-CoV-2 pseudoviruses. Collectively, our observations suggest that human monoclonal antibodies tolerating extensive epitope variability can be leveraged to neutralize pathogens with related antigenic profile.

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Accurate measurement of the effects of all amino-acid mutations to influenza hemagglutinin

10.1101/047571 ◽

2016 ◽

Cited By ~ 7

Author(s):

Michael B. Doud ◽

Jesse D. Bloom

Keyword(s):

Amino Acid ◽

Neutralizing Antibodies ◽

Viral Evolution ◽

Point Mutations ◽

Helper Virus ◽

Broadly Neutralizing Antibodies ◽

Amino Acid Mutation ◽

Influenza Hemagglutinin ◽

Amino Acid Mutations ◽

Evolutionary Paths

AbstractInfluenza genes evolve mostly via point mutations, and so knowing the effect of every amino-acid mutation provides information about evolutionary paths available to the virus. We previously used high-throughput mutagenesis and deep sequencing to estimate the effects of all mutations to an H1 influenza hemagglutinin on viral replication in cell culture (Thyagarajan and Bloom, 2014); however, these measurements suffered from sub-stantial noise. Here we describe advances that greatly improve the accuracy and reproducibility of our measurements. The largest improvements come from using a helper virus to reduce bottlenecks when generating viruses from plasmids. Our measurements confirm that antigenic sites on the globular head of hemagglutinin are highly tolerant of mutations. However, other regions – including stalk epitopes targeted by broadly neutralizing antibodies – have a limited capacity to evolve. The ability to accurately measure the effects of all influenza mutations should enhance efforts to understand and predict viral evolution.

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