Fig. 2

Envelope clones cluster into two groups according to inflammatory immune response. a Unsupervised hierarchical clustering (in R) was used to visualize all 9 differentially released cytokine concentrations secreted in response to pseudovirus (PSV) stimulation of MDDCs, and to cluster different Envelope (Env) clones according to similarity of their cytokine expression profiles irrespective of their sequence and cytokine function. Cytokine concentrations are indicated using a colour scale, ranging from blue (low), through white, to red (high). The dendrogram above the heat map illustrates degrees of relatedness between cytokines, while the dendrogram on the left illustrates Env clusters according to their capacity to induce cytokine secretion. The identity of the Env clones are indicated on the right of the heat map with transmitted founder (TF) and chronic infection (CI) clones indicated by black and white keys, respectively. Cytokines were grouped according to whether they were b pro-inflammatory (IL-1β, TNF-α, IL-6) or c chemokines (MIP-1α, MIP-1β and IL-8) and inflammatory cytokine component scores were generated using principal component analysis and plotted as bar graphs. The pro-inflammatory I) and chemotactic II) component scores of TF clones and CI clones are indicated as pink and blue bars, respectively, with boxes representing the interquartile ranges, lines within boxes represent medians and whiskers represent minimum and maximum values