Longitudinal Analysis of CD4 and CD8 T Cell Receptor Repertoires Associated with Newcastle Disease Virus Infection in Layer Birds

Velogenic Newcastle disease, also known as exotic Newcastle disease, is a contagious and fatal viral avian disease for both wild and domestic bird species. The World Health Organization for Animals (OIE) defined this disease as one of the most important avian diseases worldwide. This study used integrative genetics, genomics, and immunological approaches to study the chicken host response to Newcastle Disease Virus (NDV) with aim to sustainably enhance innate resistance in chickens. The T-cell receptor (TCR) is a highly polymorphic surface receptor on the T cells that recognize antigens presented by the major histocompatibility complex (MHC) molecules on the surface of antigen presenting cells (APCs). To investigate the temporal TCR dynamics under Newcastle disease virus infection, we performed high-throughput sequencing of CD4 and CD8 TCRβ chains on longitudinal peripheral blood mononuclear cell (PBMC) samples collected from pre-infection, 7-, 14-, and 21-days post infection (dpi), and the lung and harderian gland samples collected at 21 dpi from two commercial egg laying hens. From the Vβ and Jβ segment usage heatmap data, we found the most frequently used Vβ and Jβ segments are relatively common across all samples, reflecting a potential intrinsic bias in the VDJ rearrangement process. Repertoire overlap analysis revealed that in one bird the CD8 TCRβ sequences that were found with a high frequency at one time point were also found with a high frequency at all other time points, showing that frequencies of dominant TCRβs were largely consistent over time. Moreover, diversity rarefaction plot data indicated for both birds that CD4 TCRβ diversity at 21 dpi was lower than before infection, providing evidence for the appearance of clonally expanded repertoires during infection with NDV. In addition, at different timepoints the diversity of PBMC CD4 repertoires was higher than their counterparts in the CD8 groups. Finally, we tracked from pre-infection to 21 dpi the CD8 TCR clonotypes in the bird used for repertoire overlap analysis and found most of the TCR clonotypes are time persistent. For example, CAKRGNRNERLIF, CASSSTGSGTPLNF, and CAKQDNERLIF were observed at all these timepoints and had the highest clonotype abundance at 7 dpi. In general, our study will expand knowledge about antigen receptor repertoire functions in cell-mediated and humoral immunity to enable better understanding of the role of T cell immune repertoires in health and disease