Single‐cell transcriptomic analysis of the immune response to CHIKV infection

Background The Chikungunya virus (CHIKV), a re-emerging mosquito-borne alphavirus, is responsible for acute febrile illness and severe polyarthralgia. Although both innate and adaptive immune responses influence the disease outcomes, the detailed cellular immunopathogenesis of CHIKV in peripheral blood is not yet fully elucidated. Methods We profiled PBMCs from 29 patients with acute CHIKV infection and 10 controls via single-cell RNA sequencing. Between-group analyses treated donors as biological replicates, incorporating pseudobulk differential expression analysis as well as donor-level comparisons of pathway scores and cell proportions. Orthogonal validation was performed using qPCR and ELISA, and an exploratory analysis was conducted on a publicly available DENV dataset. Results Interferon-response signatures were upregulated across the majority of PBMC populations, with particularly prominent signals observed in monocytes and NK cells. Differences in relative cell composition were detected in descriptive statistics, but did not retain statistical significance after donor-level multiple testing correction. B-cell immunoglobulin isotypes varied across cell subsets, and their transcripts did not allow determination of antigen specificity. Cross-study analysis of DENV did not support the quantitative conclusion that the CHIKV-induced immune response is stronger. Conclusions Acute CHIKV infection is associated with a broad interferon-stimulated transcriptional program in PBMCs. Conclusions drawn from cross-sectional and cross-study comparisons require cautious interpretation.