title: Clonotype tracking of TCR repertoires during chronic virus infections.
abstract: Human viral infections such as HIV and EBV typically evoke a strong and diverse CD8(+) T cell response. Relatively little is known about the extent to which TCR repertoire evolution occurs during viral infection or how repertoire evolution affects the efficacy of the CD8(+) T cell response. In this study we describe a general approach for tracking TCR repertoire evolution during viral infection. IFNgamma surface capture and MHC class I tetramer staining were independently used to isolate EBV-specific CD8(+) T cells from peripheral blood. Anchored RT-PCR and clonotype TCR repertoire analysis were performed immediately after isolating the cells. We find that the TCR repertoires of the IFNgamma-secreting and MHC class I tetramer staining populations were similar. In one subject a detailed analysis of the TCR repertoire during the first year of EBV infection was performed and over 600 TCR sequences targeting an EBV-immunodominant epitope were analyzed. Although some repertoire evolution occurred during the year, in general, the degree of repertoire drift was small. TCR repertoire analysis for an HIV-immunodominant epitope revealed a highly conserved amino acid motif in the Dbeta region of TCR that recognizes the epitope and suggested that T cell precursor frequency influences which epitopes are targeted early in HIV infection. This methodology, which allows one to sort antigen-specific T cells based on different functional assays and to obtain a snapshot of their TCR repertoire with relative ease, should lead to a richer understanding of the rules underlying antigen recognition and T cell evolution during viral infection.
authors.affiliation: Partners AIDS Research Center and Infectious Disease Unit, Massachusetts General Hospital and Harvard Medical School, Boston 02129, USA. gcohen@hms.harvard.edu
authors.forename: George B
authors.initials: GB
authors.lastname: Cohen
authors.forename: Sabina A
authors.initials: SA
authors.lastname: Islam
authors.forename: Miriam S
authors.initials: MS
authors.lastname: Noble
authors.forename: Christina
authors.initials: C
authors.lastname: Lau
authors.forename: Christian
authors.initials: C
authors.lastname: Brander
authors.forename: Marcus A
authors.initials: MA
authors.lastname: Altfeld
authors.forename: Eric S
authors.initials: ES
authors.lastname: Rosenberg
authors.forename: Jörn E
authors.initials: JE
authors.lastname: Schmitz
authors.forename: Thomas O
authors.initials: TO
authors.lastname: Cameron
authors.forename: Spyros A
authors.initials: SA
authors.lastname: Kalams
mesh_terms: D018414:CD8-Positive T-Lymphocytes / Q000276:immunology; D002460:Cell Line; D002908:Chronic Disease; D020031:Epstein-Barr Virus Infections / Q000276:immunology*; D015658:HIV Infections / Q000276:immunology*; D004854:Herpesvirus 4, Human / Q000276:immunology; D006801:Humans; D016056:Immunodominant Epitopes; D007371:Interferon-gamma / Q000096:biosynthesis; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000737:chemistry / Q000235:genetics / Q000276:immunology*
chemical_list: D016056:Immunodominant Epitopes; D016693:Receptors, Antigen, T-Cell, alpha-beta; D007371:Interferon-gamma