To unravel the heterogeneity and molecular signature of effector memory Th2 cells (Tem2), we analyzed 23 individuals’ PBMCs of filaria-infected (Filaria
+
) and 24 healthy volunteers (Filaria
–
), with or without coincident house dust mite (HDM) allergic sensitization. Flow cytometry revealed 3 CD4
+
Tem subsets — CCR4
+
CCR6
+
CRTH2
–
Tem17, CCR4
+
CCR6
-
CRTH2
+
Tem2, and CCR6
+
CCR4
+
CRTH2
+
Tem17.2 — markedly enriched in Filaria
+
individuals. These subsets were sorted and analyzed by multiomic single-cell RNA immunoprofiling. SingleR-annotated Th2 cells from Tem2 and Tem17.2 cell subsets had features of pathogenic Th2 effector cells based on their transcriptional signatures, with downregulated
CD27
and elevated expression levels of
ITGA4
,
IL17RB
,
HPGDS
,
KLRB1
,
PTGDR2
,
IL9R
,
IL4
,
IL5
, and
IL13
genes. When the Filaria
+
individuals were subdivided based on their allergic status, Tem2 cells in HDM
+
Filaria
+
individuals showed an overall reduction in TCR diversity, suggesting the occurrence of antigen-driven clonal expansion. Moreover, HDM
+
Filaria
+
individuals showed not only an expansion in the frequency of both Tem2 and Tem17.2 cell subsets, but also a change in their molecular program by overexpressing
GATA3
,
IL17RB
,
CLRF2
, and
KLRB1
, as well as increased antigen-induced IL-4, IL-5, and IL-13 production, suggesting that aeroallergens reshape the transcriptional and functional programming of Th2 cell subsets in human filarial infection toward a pathogenic immunophenotype.