Extended Data Fig. 9: Generation probabilities (Pgen) of BAL CD4+ TCRs is lower in SARS-CoV-2-P than in OVP, OP, and NPC. | Nature Immunology

Extended Data Fig. 9: Generation probabilities (Pgen) of BAL CD4+ TCRs is lower in SARS-CoV-2-P than in OVP, OP, and NPC.

From: Distinctive evolution of alveolar T cell responses is associated with clinical outcomes in unvaccinated patients with SARS-CoV-2 pneumonia

Extended Data Fig. 9

(a) Logarithmic distribution of Pgen for post-GLIPH2-enriched CDR3β amino acid sequences across diagnoses (q < 0.05, pairwise Wilcoxon rank-sum tests with FDR correction). Each dot corresponds to a TCRβ chain. (b) Probability density of the data in a. (c) Logarithmic distribution of Pgen for post-GLIPH2-enriched and cross-referenced CDR3β amino acid sequences to MIRA MHCII dataset in SARS-CoV-2-P and OP. Each dot corresponds to a TCRβ chain. Nonsignificant after Wilcoxon rank-sum test. (d) Probability density of the data in c. (e) Similarity network analysis of BAL CD4+ TCR sequences cross-referenced to MIRA MHCII dataset epitope pools. Nodes represent unique TCR (CDR3β) sequences and are color-coded by diagnosis status (non-SARS-CoV-2-P [NPC, OP, and OVP], SARS-CoV-2, or shared). Edges connect TCR sequences belonging to the same patterns or specificity groups identified through the GLIPH2 algorithm. Dot size represents calculated generation probability (Pgen) of individual TCRβ sequences. Left: Representative TCR sequences from prominent clusters are annotated.

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