Jiwon Lee¹, Daniel R Boutz², Veronika Chromikova³, M Gordon Joyce⁴, Christopher Vollmers⁵, Kwanyee Leung⁴, Andrew P Horton², Brandon J DeKosky^1,15, Chang-Han Lee¹, Jason J Lavinder¹, Ellen M Murrin¹, Constantine Chrysostomou¹, Kam Hon Hoi^6,15, Yaroslav Tsybovsky⁷, Paul V Thomas⁴, Aliaksandr Druz⁴, Baoshan Zhang⁴, Yi Zhang⁴, Lingshu Wang⁴, Wing-Pui Kong⁴, Daechan Park¹, Lyubov I Popova^8,15, Cornelia L Dekker⁹, Mark M Davis^10,11, Chalise E Carter¹², Ted M Ross¹², Andrew D Ellington^2,13, Patrick C Wilson⁸, Edward M Marcotte^2,13, John R Mascola⁴, Gregory C Ippolito¹³, Florian Krammer³, Stephen R Quake^5,10,14, Peter D Kwong⁴ & George Georgiou<sup>1,2,6,13

1</sup>Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA. ²Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA. ³Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA. ⁴Vaccine Research Center, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA. ⁵Department of Bioengineering, Stanford University, Stanford, California, USA. ⁶Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA. ⁷Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA. ⁸Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA. ⁹Department of Pediatrics, Stanford University, Stanford, California, USA. ¹⁰Howard Hughes Medical Institute, Stanford University, Stanford, California, USA. ¹¹Department of Microbiology and Immunology, Stanford University, Stanford, California, USA. ¹²Center for Vaccines and Immunology, Department of Infectious Diseases, University of Georgia, Athens, Georgia, USA. ¹³Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA. ¹⁴Department of Applied Physics, Stanford University, Stanford, California, USA. ¹⁵Present addresses: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA (B.J.D.); Antibody Engineering Department, Genentech, Inc., South San Francisco, California, USA (K.H.H.); Division of Infectious Diseases, SRI International, Harrisonburg, Virginia, USA (L.I.P.).

Correspondence to : George Georgiou
 
Abstract
Molecular understanding of serological immunity to influenza has been confounded by the complexity of the polyclonal antibody response in humans. Here we used high-resolution proteomics analysis of immunoglobulin (referred to as Ig-seq) coupled with high-throughput sequencing of transcripts encoding B cell receptors (BCR-seq) to quantitatively determine the antibody repertoire at the individual clonotype level in the sera of young adults before and after vaccination with trivalent seasonal influenza vaccine. The serum repertoire comprised between 40 and 147 clonotypes that were specific to each of the three monovalent components of the trivalent influenza vaccine, with boosted pre-existing clonotypes accounting for ~60% of the response. An unexpectedly high fraction of serum antibodies recognized both the H1 and H3 monovalent vaccines. Recombinant versions of these H1 + H3 cross-reactive antibodies showed broad binding to hemagglutinins (HAs) from previously circulating virus strains; several of these antibodies, which were prevalent in the serum of multiple donors, recognized the same conserved epitope in the HA head domain. Although the HA-head-specific H1 + H3 antibodies did not show neutralization activity in vitro, they protected mice against infection with the H1N1 and H3N2 virus strains when administered before or after challenge. Collectively, our data reveal unanticipated insights regarding the serological response to influenza vaccination and raise questions about the added benefits of using a quadrivalent vaccine instead of a trivalent vaccine.