We discovered that the higher FOXP4 levels in nonacute COVID-19 samples were associated with increased risk of long COVID (OR = 2.31 per 1 s.d. increase in FOXP4 expression, 95% CI = 1.27–4.22, P = 0.0063; Supplementary Fig. 9), while FOXP4 levels in acute COVID-19 samples were not associated with long COVID (P = 0.62). This evidence concerns the gene FOXP4 and COVID-19.