Abstract The first encounter with influenza virus biases later immune responses. This “immune imprinting”, formerly from infection within a few years of birth, is in the U.S. now largely from immunization with a quadrivalent, split vaccine (IIV4). In a pilot study of IIV4 imprinting, we characterized, by single-B-cell cultures, NextGen sequencing, and plasma antibody proteomics, the primary antibody responses to influenza in two infants during their first two years of seasonal influenza vaccination. One infant, who received only a single vaccination in Year 1, contracted an influenza B (IBV) infection between the two years, allowing us to compare imprinting by infection and vaccination. That infant had a shift in hemagglutinin (HA)-reactive B-cell specificity from largely influenza A (IAV)-specific in Year 1 to IBV-specific in Year 2, both before and after vaccination. HA-reactive B cells from the other infant maintained a more evenly distributed specificity. In Year 2, class-switched HA-specific B cell IGHV somatic hypermutation (SHM) levels reached average levels seen in adults. The HA-reactive plasma antibody repertoires of both infants comprised a relatively small number of antibody clonotypes, with one or two very abundant clonotypes. Thus, after the Year 2 boost, both infants had overall B cell profiles that resembled those of adult controls. Importance Influenza virus is a moving target for the immune system. Variants emerge that escape protection from antibodies elicited by a previously circulating variant (“antigenic drift”). The immune system usually responds to a drifted influenza virus by mutating existing antibodies rather than by producting entirely new ones. Thus, immune memory of the earliest influenza exposure has a major influence on later responses to infection or vaccination (“immune imprinting”). In the many studies of influenza immunity in adult subjects, imprinting has been from an early infection, since only in the past two decades have infants received influenza immunizations. The work reported in this paper is a pilot study of imprinting in two infants by the flu vaccine, which they received before experiencing an influenza infection. The results suggest that a quadrivalent (four-subtype) vaccine may provide an immune imprint less dominated by one subtype than does a monovalent infection.

Infant antibody repertoires during the first two years of influenza vaccination