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Vaccination reshapes the virus-specific T cell repertoire in unexposed adults

Pan*, Aiamkitsumrit* et al. (BioRxiv) DOI: 10.1101/2020.10.01.322958



  • pre-existing virus-specific memory-phenotype CD4 T cells

  • yellow fever vaccine (YVF-17D)

  • TCR sequencing


Main Findings

Pre-existing/potentially cross-reactive virus-specific memory-phenotype CD4 T cells have been previously described in the T cell repertoire of unexposed individuals, e.g. against HIV (cf. Su, L. F. et al. Immunity 2013;38:373-383) and, more recently, against SARS-CoV-2 (cf. Mateus, J. et al. Science 2020;370:89-94). However, it remains currently unknown how these memory-phenotype CD4 T cells may impact an individual’s immune response to novel foreign antigen in the context of infection or vaccination. 

In this preprint, Pan/Aiamkitsumrit et al. study the virus-specific CD4 T cell response in 7 antigen-naïve individuals before and after live attenuated yellow fever virus (YVF) vaccine (YVF-17D). Employing a pool of 20 class II peptide-MHC tetramers in combination with direct ex vivo magnetic column-based cellular enrichment, the authors report memory-phenotype CD4 T cells present in a substantial number of YVF-specific precursors pre-vaccination, overall ranging from 0.15 to 137 cells per million CD4 T cells. After vaccination, longitudinal blood sampling and analysis of virus-specific populations demonstrated that these CD4 T cells may be classified into (1) abundant pre-vaccine populations with overall limited proliferation post YVF-17D and (2) rare cells with naïve-like responses preferentially contributing to the memory repertoire post vaccination. Furthermore, TCR Vβ sequencing of YFV-specific CD4 T cells sorted pre-vaccination and at >7 months post-YFV indicated that vaccination primarily boosted the representation of rare TCRs, leading to a restructured clonal hierarchy of virus-specific CD4 T cells.  


In general, this is a well-conducted study providing insight into the potential role of pre-existing memory-phenotype CD4 T cells in response to novel foreign antigen. However, some limitations should be addressed/discussed by the authors.

  • Methodological/technical: (1) phenotype/kinetics of YFV-specific CD4 T cells were assessed only in a relatively small number of individuals (n=7 for population-specific dynamics; n=3 for TCR sequencing) and any observations made here therefore need to be confirmed in future larger studies; (2) it remains somewhat unclear whether a combinatorial/dual tetramer staining approach was employed to initially validate specific staining of newly identified YFV epitopes/exclude background staining (this seems particularly relevant in the context of low-frequency pre-vaccination/tetramer enriched samples); (3) likewise, the method section lacks information on how individual MFI values (ICOS, CD38 and tetramer signal) across different sampling/experimental time points were normalized for comparative analysis/statistics.

  • General limitations: Longitudinal analysis of ICOS and CD38 expression on YFV-specific CD4 T cells demonstrated persistent cellular activation (vs. basal levels) for at least one month following vaccination/post-contraction of effector CD4 T cells suggesting the possibility of viral persistence. Importantly, delayed viral clearance may lead not only to phenotypical changes such as prolonged activation/persistent expression of co-inhibitory molecules, but may potentially override initial immunodominance/epitope hierarchies. Thus, an expanded phenotypical analysis of YFV-specific CD4 T cells including additional activation/co-inhibitory markers and determination of TCR affinities as well as assessment of individual/longitudinal viral loads would have been of interest. Of note in this context, Akondy et al. previously demonstrated that viral loads following YVF-17D vaccination vary among individuals leading to differences in the magnitude of effector CD8 T cell responses (cf. Akondy, R.S. et al. PNAS Mar 2015, 112 (10): 3050-3055), which in turn may affect memory development/composition. Finally, since YVF-17D employs a live attenuated YFV strain providing relatively large amounts of primary antigen, it also remains to be confirmed whether the observations made here will be generally transferrable to other kinds of vaccines. 


Previous exposure to non-related antigens may influence the ratio of naïve to memory-phenotype virus-specific precursor CD4 T cells, leading to distinct clonal selection, and may thus determine an individual’s T cell response to a novel pathogen. Approaches to designing vaccines that preferentially recruit relevant rare/naïve-like precursors could therefore be critical.


Reviewed by Verena van Der Heide as part of the cross-institutional journal club of the Immunology Institute of the Icahn School of Medicine, Mount Sinai and the Kennedy Institute of Rheumatology, University of Oxford. Follow her on Twitter.

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