Sequence and Structural Analyses Reveal Distinct and Highly Diverse Human CD8+ TCR Repertoires to Immunodominant Viral Antigens

A diverse T cell receptor (TCR) repertoire is essential for controlling viral infections. However, information about TCR repertoires to defined viral antigens is limited. We performed a comprehensive analysis of CD8(+) TCR repertoires for two dominant viral epitopes: pp65(495-503) (NLV) of cytomegalovirus and M1(58-66) (GIL) of influenza A virus. The highly individualized repertoires (87-5,533 alpha or beta clonotypes per subject) comprised thousands of unique TCRa and TCRb sequences and dozens of distinct complementary determining region (CDR) 3 alpha and CDR3 beta motifs. However, diversity is effectively restricted by preferential V-J combinations, CDR3 lengths, and CDR3a/ CDR3b pairings. Structures of two GIL-specific TCRs bound to GIL-HLA-A2 provided a potential explanation for the lower diversity of GIL-specific versus NLV-specific repertoires. These anti-viral TCRs occupied up to 3.4% of the CD8(+) TCRb repertoire, ensuring broad T cell responses to single epitopes. Our portrait of two anti-viral TCR repertoires may inform the development of predictors of immune protection.