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Structure–function analysis of neutralizing antibodies to H7N9 influenza from naturally infected humans

Abstract

Little is known about the specificities and neutralization breadth of the H7-reactive antibody repertoire induced by natural H7N9 infection in humans. We have isolated and characterized 73 H7-reactive monoclonal antibodies from peripheral B cells from four donors infected in 2013 and 2014. Of these, 45 antibodies were H7-specific, and 17 of these neutralized the virus, albeit with few somatic mutations in their variable domain sequences. An additional set of 28 antibodies, isolated from younger donors born after 1968, cross-reacted between H7 and H3 haemagglutinins in binding assays, and had accumulated significantly more somatic mutations, but were predominantly non-neutralizing in vitro. Crystal structures of three neutralizing and protective antibodies in complex with the H7 haemagglutinin revealed that they recognize overlapping residues surrounding the receptor-binding site of haemagglutinin. One of the antibodies, L4A-14, bound into the sialic acid binding site and made contacts with haemagglutinin residues that were conserved in the great majority of 2016–2017 H7N9 isolates. However, only 3 of the 17 neutralizing antibodies retained activity for the Yangtze River Delta lineage viruses isolated in 2016–2017 that have undergone antigenic change, which emphasizes the need for updated H7N9 vaccines.

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Fig. 1: Neutralization titres of convalescent sera from donors with laboratory-confirmed H7N9 infection.
Fig. 2: Structures of L4A-14/H7, L3A-44/H7 and L4B-18/H7 complexes.
Fig. 3: Comparison of epitope residues recognized by L4A-14, L3A-44 and L4B-18 antibodies.
Fig. 4: Protection against lethal infection with H7N9 in mice by antibodies.

Data availability

The data that support the findings of this study are available from the corresponding authors upon request. Atomic coordinates for the H7-FabL4A-14, H7-FabL4B-18 and H7-FabL3A-44 complex as well as structure factors have been deposited to the Protein Data Bank under accession codes 6II4, 6II8 and 6II9.

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Acknowledgements

The authors acknowledge support from the laboratories that provided the sequences of reference antibody MEDI885221 for the comparisons in the tables and figures. The authors also acknowledge the BD FACSAria cell sorter service provided by the Core Instrument Center of Chang Gung University, and C. Waugh for FACS sorting B cells and MDCK-SIAT1 cell lines at WIMM Oxford. These studies were funded by the Townsend-Jeantet Charitable Trust (registered charity no. 1011770), the Emergency Technology Research Issue on Prevention and Control for Human infection with A (H7N9) Avian Influenza Virus (10600100000015001206), the Strategic Priority Research Program of the Chinese Academy of Sciences (CAS) (XDB29010000), the National Science and Technology Major Project (2018ZX10101004), the Human Immunology Unit (MRC), Oxford University, Chang Gung Medical Research Program (CMRPG3G0921, CMRPG3G0922) and the Ministry of Science and Technology of Taiwan (MOST 104-2320-B-182A-002-MY2, MOST 105-2320-B-182A-008- and MOST 107-2321-B-182A-003-). G.F.G. is supported partly as a leading principal investigator of the NSFC Innovative Research Group (81621091). Y.S. is supported by the Excellent Young Scientist Program from the National Natural Science Foundation of China (81622031), the Excellent Young Scientist Program of CAS and the Youth Innovation Promotion Association CAS (2015078).

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K.-Y.A.H., G.F.G., Y.S. and A.R.T. conceived and designed the study. K.-Y.A.H., P.R., H.J., B.W., L.S., T.D., Y.-M.L., P.C., M.I., M.-C.W., Z.C., R.S., C.-C.H., J.-H.Y., J.Q., T.-Y.L., A.L., T.J.P., J.-T.J., C.M., G.F.G., Y.S. and A.R.T. carried out the experiments. K.-Y.A.H., P.R., H.J., B.W., L.S., T.D., Y.-M.L., J.-T.J., C.M., G.F.G., Y.S. and A.R.T. performed data analysis and figure/table preparation. K.-Y.A.H., P.R., G.F.G., Y.S. and A.R.T. wrote the manuscript.

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Correspondence to Kuan-Ying A. Huang, George F. Gao, Yi Shi or Alain R. Townsend.

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Supplementary Information

Supplementary Figures 1–8, Supplementary Tables 1–6.

Reporting Summary

Supplementary Table 1

Binding and neutralizing activities of of 73 H7-reactive monoclonal antibodies isolated from donors.

Supplementary table 2

Details of 73 H7-reactive monoclonal antibodies variable domain sequences isolated from donors.

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Huang, KY.A., Rijal, P., Jiang, H. et al. Structure–function analysis of neutralizing antibodies to H7N9 influenza from naturally infected humans. Nat Microbiol 4, 306–315 (2019). https://doi.org/10.1038/s41564-018-0303-7

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