Breakthrough infection elicits hypermutated IGHV3-53/3-66 public antibodies with broad and potent neutralizing activity against SARS-CoV-2 variants including the emerging EG.5 lineages

The rapid emergence of SARS-CoV-2 variants of concern (VOCs) calls for efforts to study broadly neutralizing antibodies elicited by infection or vaccination so as to inform the development of vaccines and antibody therapeutics with broad protection. Here, we identified two convalescents of breakthrough infection with relatively high neutralizing titers against all tested viruses. Among 50 spike-specific monoclonal antibodies (mAbs) cloned from their B cells, the top 6 neutralizing mAbs (KXD01-06) belong to previously defined IGHV3-53/3-66 public antibodies. Although most antibodies in this class are dramatically escaped by VOCs, KXD01-06 all exhibit broad neutralizing capacity, particularly KXD01-03, which neutralize SARS-CoV-2 from prototype to the emerging EG.5.1 and FL.1.5.1. Deep mutational scanning reveals that KXD01-06 can be escaped by current and prospective variants with mutations on D420, Y421, L455, F456, N460, A475 and N487. Genetic and functional analysis further indicates that the extent of somatic hypermutation is critical for the breadth of KXD01-06 and other IGHV3-53/3-66 public antibodies. Overall, the prevalence of broadly neutralizing IGHV3-53/3-66 public antibodies in these two convalescents provides rationale for novel vaccines based on this class of antibodies. Meanwhile, KXD01-06 can be developed as candidates of therapeutics against SARS-CoV-2 through further affinity maturation. The greatest challenge for the development of effective vaccines and antibody therapeutics against SARS-CoV-2 is the rapid emergence of variants. Broadly neutralizing antibodies (bnAbs) and vaccines that can elicit those antibodies are promising strategies to meet the challenge. Therefore, we focus on identification and characterization of bnAbs elicited by infection or vaccination in this study. From two convalescents of breakthrough infection, we discovered a serial of bnAbs (KXD01-06), which are able to neutralize SARS-CoV-2 from prototype to XBB lineages, and even to the emerging EG.5. Notably, these bnAbs are prevalent in the two convalescents and their neutralization breadth is developed through extensive affinity maturation. Overall, our study is an important support for vaccine development aiming at eliciting those bnAbs. Moreover, those bnAbs have potential to be developed as candidates of therapeutics against SARS-CoV-2 through further optimization.