Fig 2: HIV Env-Specific CD4+ T Cells and Env-Specific CD8+ T Cells at Week 0 Are Not Associated with the Observed Protection from Infection(A–C) Representative flow plots of Env-specific CD4+ T cells from week 0 PBMCs: using an OX40/4-1BB AIM assay (Reiss et al., 2017) (A), intracellular staining (ICS) assay for IFN-γ (B), and ICS assay for TNF/CD40L (C) when not stimulated (NS) versus stimulated with antigen (Env).(D) Representative flow plot of IFN-γ and TNF expression in CD8+ T cells by ICS when not stimulated (NS) versus stimulated with antigen (Env).(E–G) Quantification of the percent of CD4+ T cells that are Env-specific based on: OX40/4-1BB (E), IFN-γ (F), or CD40L/TNF (G) expression.(H) Quantification of the percent of CD8+ T cells that are Env-specific based on IFN-γ and TNF expression. Signal from the unstimulated condition was subtracted from the antigen-specific signal for each sample. Each dot represents an individual animal. Shown are high and low nAb titer, as well as control group animals.See also Figure S6.

Fig 3: Single-cell BCR clonotype expansion analysis across COVID-19 severity.a, UMAP visualisation of B cell lineage and coloured by clonotype size in the V(D)J data. Only expanded clonotypes are coloured (clonotype size > 2). b, Single-cell BCR network plots for each severity status coloured by assigned cell type. c, Single-cell BCR network plots for each severity status coloured by heavy chain isotype subclass (IgM, IgD, IgA1, IgA2, IgE, IgG1, IgG2, IgG3 or IgG4). Each circle/node corresponds to a single B cell with a corresponding set of BCR(s). Each clonotype is presented as a minimally connected graph with edge widths scaled to 1/d + 1 for edge weight d where d corresponds to the total (Levenshtein) edit distance of BCRs between two cells. Size of nodes is scaled according to increasing node closeness centrality scores that is nodes that are highly central to a clonotype network will be larger.

Fig 4: Single-cell BCR networks across COVID-19 severity.Single-cell BCR network plots for each severity status coloured by heavy chain isotype class (IgM, IgD, IgA, IgE, or IgG). Each circle/node corresponds to a single B cell with a corresponding set of BCR(s). Each clonotype is presented as a minimally connected graph with edge widths scaled to 1/d + 1 for edge weight d where d corresponds to the total (Levenshtein) edit distance of BCRs between two cells. Size of nodes is scaled according to increasing node closeness centrality scores that is nodes that are highly central to a clonotype network will be larger.