This repository contains the clinical, viral, T cell and proteomics data reported in the manuscript ‘Early immune response have long-term associations with clinical, virologic, and immunologic outcomes in patients with COVID-19’. We also provide the random forest models for predicting the clinical, virologic, and immunologic outcomes as an R data file. A tutorial for using the predictive models were included in the "ML models" folder. For the RNA-sequencing data, please visit: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178967.