T cells are defined by a heterodimeric surface receptor (the T cell receptor or TCR) that mediates recognition of pathogen-associated epitopes via interactions with peptide-major histocompatibility complexes (pMHC). TCRs are generated by genomic rearrangements of the germline TCR locus, a process termed V(D)J recombination that has the potential to generate a staggering diversity of TCRs (estimated to range from 1015 1 to as high as 1061 2 possible receptors). Despite this potential diversity, TCRs from T cells that recognize the same pMHC epitope often share conserved sequence features, suggesting that it may be possible to predictively model epitope specificity. Here we report the in-depth characterization of ten epitope-specific CD8+ TCR repertoires from mice and humans representing 4600+ in-frame, single cell-derived TCRαβ sequence pairs from 110 subjects. We developed novel analytical tools to characterize these epitope-specific repertoires: a distance measure on the space of TCRs that permits clustering and visualization (TCRdist), a robust repertoire diversity metric (TCRdiv) that accommodates the low number of paired public receptors observed when compared to single chain analyses, and a distance-based classifier capable of assigning previously unobserved TCRs to characterized repertoires with robust sensitivity and specificity. Our analysis demonstrates that each epitope-specific repertoire contains a clustered group of receptors that share core sequence similarities, together with a dispersed set of diverse “outlier” sequences. By identifying shared motifs in core sequences, we were able to highlight key conserved residues driving essential elements of TCR recognition. These analyses provide insights into the generalizable, underlying features of epitope-specific repertoires and adaptive immune recognition.

Influenza A viruses that circulate normally in the human population cause a debilitating, though generally transient, illness that is sometimes fatal, particularly in the elderly. Severe complications arising from pandemic influenza or the highly pathogenic avian H5N1 viruses are often associated with rapid, massive inflammatory cell infiltration, acute respiratory distress, reactive hemophagocytosis and multiple organ involvement. Histological and pathological indicators strongly suggest a key role for an excessive host response in mediating at least some of this pathology. Here, we review the current literature on how various effector arms of the immune system can act deleteriously to initiate or exacerbate pathological damage in this viral pneumonia. Generally, the same immunological factors mediating tissue damage during the anti‐influenza immune response are also critical for efficient elimination of virus, thereby posing a significant challenge in the design of harmless yet effective therapeutic strategies for tackling influenza virus.