Fig. 3.

Upregulation of several tissue-homing genes in natural DENV-infected patients observed in clonally expanded plasma cells and plasmablasts.

(A). UMAP plot of the integrated 5′ scRNA-seq and scBCR-seq datasets from six DENV-infected patients, colored by B cell subsets in the left panel and colored by expanded clones in the right panel. At least three B cells that expressed identical BCR clonotypes are indicated by “ ≥ 3” and at least two B cells are indicated by “2”. Only one B cell that expresses a specific BCR clonotype is indicated by “1”.

(B). Numbers (upper panel) and proportions (lower panel) of clonally expanded groups in each B cell subset in DENV-infected patients.

(C). Relative abundances of B cell subsets (upper panel) and relative abundances of expanded clones (lower panel) in primary acute (one day before defervescence), primary early convalescent (Days 1–3 after defervescence and Day 5 after defervescence), secondary acute (one day before defervescence and defervescence), and secondary early convalescent (Days 1–3 after defervescence, Day 5 after defervescence and Day 7 after defervescence).

(D). Stacked violin plot of tissue-homing genes in clonal expansion groups (top panel), B cell subsets (second panel), primary or secondary infection and clinical phases (third panel), and antibody isotypes (bottom panel). Color intensity represents the median expression level in the group. PCs = plasma cells, PBs = plasmablasts, Early con = early convalescent phase. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)