Novel Antibody Genetic Diversity in an African Population Alters Gene Expression
Antibodies are a critical part of the adaptive immune response that are expressed by B-cells as identical pairs of heavy and light chains. These chains are the product of the somatic recombination of different immunoglobulin genes which form part of the germline repertoire. The full antibody then circulates around the body as part of the expressed antibody repertoire. The IGHV (immunoglobulin heavy chain variable) genes play the largest role in mediating antigen binding and are incredibly polymorphic. These genes also exhibit copy number variation (CNV) through the insertion, deletion and/or duplication of genes. In this study we compared Next-Generation Sequencing (NGS) approaches of expressed antibody repertoire and germline targeted sequencing methods. Germline IGHV gene usage and polymorphic diversity was inferred from expressed antibody repertoires of 13 HIV infected donors from rural and urban KwaZulu Natal. Furthermore, individual haplotypes and CNV were examined using Bayesian inference with heterozygous gene anchors. IGHV germline sequencing was performed using targeted amplicon sequencing on MiSeq and PacBio. 70 donors from the same cohorts were sequenced, revealing vast novel genetic diversity. Overall, 22 novel alleles identified in germline sequencing were found in the expressed repertoires, with a further 12 alleles being entirely novel. Furthermore, expressed data confirmed the duplication of 48 genes observed in germline sequencing. There were also duplications on both haplotypes for 11 genes, indicating the high prevalence of CNV. The combination of these data verify that the novel allelic variants and CNV described by genomic sequencing are expressed as part of the functional antibody repertoire. Categorising novel IGHV diversity enhances our understanding of differential immune responses that may arise during infection and vaccination.