We also compared the transcriptome profile of individuals with and without brain fog in our cohort with long COVID. Upregulated genes were enriched in pathways related to T cell differentiation and activation (for example, RUNX3, IFNG, TNFSF9), negative regulation of the immune response (for example, WASL, ID2, TNFAIP3) and circa- dian regulation of gene expression (for example, RORA, PER1, NRIP1) (Fig. 6f,j–l). Pathways related to immunoglobulin, production, defense responses and B cell activation were among those downregulated, including immunoglobulin production (IGKV1–12, IGKV1–17), adaptive immune response (for example, CX3CR1, FCGR1BP) and B cell activa- tion (HDAC9, CD180, MNDA) (Extended Data Fig. 7 and Supplemen- tary Tables 4 and 5–12). In agreement with previous studies, several factors involved in the coagulation pathway were downregulated specifically in the cohort with brain fog, including PF4, PF4V1 and SELP (Fig. 6g–i)32.