Longitudinal analysis of the peripheral B cell repertoire reveals unique effects of immunization with a new influenza virus strain

Abstract

BackgroundDespite the potential to produce antibodies that can neutralize different virus (heterotypic neutralization), there is no knowledge of why vaccination against influenza induces protection predominantly against the utilized viral strains (homotypic response). Identification of structural patterns of the B cell repertoire associated to heterotypic neutralization may contribute to identify relevant epitopes for a universal vaccine against influenza.MethodsBlood samples were collected from volunteers immunized with 2008/2009 trivalent inactivated vaccine (TIV), pandemic H1N1 (pdmH1N1) monovalent inactivated vaccine (MIV) and the 2014/2015 TIV. Neutralization was assessed by hemagglutination and microneutralization test. IgG VH amplicons derived from peripheral blood RNA from pre-immune and 7 days post vaccination were subjected to 454-Roche sequencing. Full reconstruction of the sampled repertoires was done with ImmunediveRsity.ResultsThe TIV induced a predominantly homotypic neutralizing serologic response, while the 09 MIV induced a heterotypic neutralizing seroconversion in 17 % of the individuals. Both the 08/09 and the 14/15 TIV were associated with a reduction in clonotypic diversity, whereas 09 MIV was the opposite. Moreover, TIV and MIV induced distinctive patterns of IGHV segment use that are consistent with B cell selection by conserved antigenic determinants shared by the pre-pandemic and the pandemic strains. However, low somatic hypermutation rates in IgG after 09 MIV immunization, but not after 08/09 and 14/15 TIV immunization were observed. Furthermore, no evidence of the original antigenic sin was found in the same individuals after vaccination with the three vaccines.ConclusionsImmunization with a new influenza virus strain (2009 pdmH1N1) induced unique effects in the peripheral B cell repertoire clonal structure, a stereotyped response involving distinctive IGHV segment use and low somatic hypermutation levels. These parameters were contrastingly different to those observed in response to pre-pandemic and post-pandemic vaccination, and may be the result of clonal selection of common antigenic determinants, as well as germinal center-independent responses that wane as the pandemic strain becomes seasonal. Our findings may contribute in the understanding of the structural and cellular basis required to develop a universal influenza vaccine.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-015-0239-y) contains supplementary material, which is available to authorized users.

Repertoire comparison of the B‐cell receptor‐encoding loci in humans and rhesus macaques by next‐generation sequencing

“…In addition, the repertoires that we report here are in good agreement with those reported in previous studies for both humans and RMs. 34, 40, 52, 57, 58, 59, 60, 61 Taken together, these findings provide confidence that the BCR repertoires we report here are representative of actual average circulating repertoires in both species, although the collection of more repertoire data will be needed to confirm this.…”

The pipeline repertoire of Ig-Seq analysis

“…The latter, can be visualized either through heatmaps, histograms or pie charts. Furthermore, if a 3ʹ primer was set to cover the C region during the library construction, it is possible to perform an analysis to identify the most abundant isotype; this is especially relevant when conducting protocols for "before-and-after" vaccination and their respective repertoire analysis (3,9,12,14,(40)(41)(42). The statistical quantification and comparison of clonotype diversity is primarily calculated using the generalized diversity index -a general mathematical formulation commonly used in ecology to assess diversity, developed by Hill in 1973(43).…”

“…When the immune system encounters an antigen, memory cells may be activated to produce already existent antibodies or naive B cells may hypermutate the variable regions of the antibody thus forming a B cell lineage with new plasma cells producing new antibodies (3). Analyzing how the antibody repertoire evolves throughout time provides an insight into how pathogens, vaccines, and even self-epitopes shape our humoral response (3,9,12,14,(40)(41)(42)52,53). Although the evolution of repertoires can be studied at one single time point with phylogenetic trees that portray clonal dynamics, multiple time points help to generate more accurate and robust ontogenic analysis and these can be portrayed as stream graphs, longitudinal phylogenetic "birthday" trees, stack-plots or clonotype tracking heatmaps.…”

“…As new discoveries arise in the immunology field, novel computational tools have emerged to adapt their algorithms to provide more accurate and statistically robust analyses (6,7). Furthermore, computational pipelines have also helped to unveil details previously unknown about the antibody repertoire; exhibiting the intertwined relationship that exists between modern antibody repertoire analysis and computational immunology (4,(8)(9)(10)(11)(12)(13)(14)(15). Since the study of antibody repertoires can be addressed from many biological aspects, there is a concomitant diverse set of computational algorithms tailored to many purposes.…”

High Affinity Maturated Human Antibodies from Naïve and Synthetic Antibody Repertoires

“…Subsequently, the region will be cleaved and replaced by the gBlock [109]. This method has allowed the design and generation of antibody libraries [117,118].…”