Single B cell transcriptomics identifies multiple isotypes of broadly neutralizing antibodies against flaviviruses

Sequential dengue virus (DENV) infections often generate neutralizing antibodies against all four DENV serotypes and sometimes, Zika virus. Characterizing cross-flavivirus broadly neutralizing antibody (bnAb) responses can inform countermeasures that avoid enhancement of infection associated with non-neutralizing antibodies. Here, we used single cell transcriptomics to mine the bnAb repertoire following repeated DENV infections. We identified several new bnAbs with comparable or superior breadth and potency to known bnAbs, and with distinct recognition determinants. Unlike all known flavivirus bnAbs, which are IgG1, one newly identified cross-flavivirus bnAb (F25.S02) was derived from IgA1. Both IgG1 and IgA1 versions of F25.S02 and known bnAbs displayed neutralizing activity, but only IgG1 enhanced infection in monocytes expressing IgG and IgA Fc receptors. Moreover, IgG-mediated enhancement of infection was inhibited by IgA1 versions of bnAbs. We demonstrate a role for IgA in flavivirus infection and immunity with implications for vaccine and therapeutic strategies. A central challenge for developing clinical interventions for dengue virus or the closely related Zika virus is the ability of IgG antibodies to enhance, rather than neutralize infection under certain conditions. When present prior to infection, as in the case of vaccination, these antibodies can worsen disease outcome. In this study, we analyzed B cells of individuals who experienced dengue or Zika infection to identify those expressing antibodies that can potently neutralize these viruses with minimal potential to enhance infection. We used a method that captured a larger number and wider variety of antibodies than previous approaches. We discovered several potent antibodies that simultaneously neutralized dengue and Zika viruses, including those of IgG isotype, which are common, and one of IgA isotype, which had never been described against this group of viruses. Although IgG antibodies enhanced infection in certain cases, the IgA antibody did not. We further showed that modifying a region of IgG antibodies to convert them to IgA antibodies eliminated their ability to enhance infection. Moreover, the modified IgA versions inhibited the ability of IgG versions to enhance infection. These results suggest that inducing IgA antibodies may be an attractive goal for safe and effective vaccines.