Allelic polymorphism gates vaccine amplification of a human broadly neutralizing response against influenza virus

Abstract A major goal of universal influenza vaccine design is to elicit high titer antibody responses against functionally conserved but immunologically subdominant sites of vulnerability. Using a transgenic mouse model where antibodies develop with human-like CDRH3 diversity but are otherwise restricted to single VH-genes of interest, we have demonstrated that human IGHV1-69 endows for pathway-amplifiable broadly neutralizing antibody (bnAb) responses targeting the hemagglutinin (HA) stalk of group 1 influenza A viruses following vaccination with an engineered HA nanoparticle. However, IGHV1-69 is polymorphic with alleles containing either a phenylalanine (F54) or leucine (L54) within the contacting CDRH2 loop at germline, the latter which is correlated with dampened IGHV1-69 usage in human stalk bnAbs. To experimentally test the consequence of this, we applied our transgenic model to assess the capacity for both alleles to vaccine expand bnAbs through pathway-amplification. We found that while both VH forms endow germline targeting solutions to the same bnAb site on HA, only the F54 allele is productive following sequential immunization with a stalk-only nanoparticle immunogen. By contrast, L54 BCRs, while initially expanded, were autoreactive and rapidly tolerized upon boosting. While globally most humans utilize at least one copy of the F54 allele and would be predicted to support bnAb expansion, certain ethnicities show heightened usage of the L54 allele and may be unable to support such pathway-amplification. Thus, we find that allele usage gates the ability to pathway expand productive bnAb responses through immune tolerance.