LAUSR

Significance Influenza virus and some other human pathogens evolve to evade herd immunity and, hence, to reinfect previously immune individuals. Individual humoral immune responses also evolve, through somatic mutation and selection in a process known as affinity maturation. We describe a detailed molecular “case history” of this coevolution (to our knowledge, the most thorough such study so far) through structural and biophysical analysis of a lineage of human antibodies directed at the influenza hemagglutinin receptor binding site. We show how affinity maturation in this lineage has maintained adaptability (“breadth” of neutralizing activity) by generating a branched and, hence, diversifying phylogeny. The mechanisms underlying affinity maturation appear to ensure such diversification while also enhancing affinity of the most potent resulting antibodies. Affinity maturation of the B cell antigen receptor (BCR) is a conserved and crucial component of the adaptive immune response. BCR lineages, inferred from paired heavy- and light-chain sequences of rearranged Ig genes from multiple descendants of the same naive B cell precursor (the lineages’ unmutated common ancestor, “UCA”), make it possible to reconstruct the underlying somatic evolutionary history. We present here an extensive structural and biophysical analysis of a lineage of BCRs directed against the receptor binding site (RBS) of subtype H1 influenza virus hemagglutinin (HA). The lineage includes 8 antibodies detected directly by sequencing, 3 in 1 principal branch and 5 in the other. When bound to HA, the heavy-chain third complementarity determining region (HCDR3) fits with an invariant pose into the RBS, but in each of the 2 branches, the rest of the Fab reorients specifically, from its position in the HA-bound UCA, about a hinge at the base of HCDR3. New contacts generated by the reorientation compensate for contacts lost as the H1 HA mutated during the time between the donor’s initial exposure and the vaccination that preceded sampling. Our data indicate that a “pluripotent” naive response differentiated, in each branch, into 1 of its possible alternatives. This property of naive BCRs and persistence of multiple branches of their progeny lineages can offer broader protection from evolving pathogens than can a single, linear pathway of somatic mutation.