Using natural language processing on free-text clinical notes to identify patients with long-term COVID effects

As of May 15th, 2022, the novel coronavirus SARS-COV-2 has infected 517 million people and resulted in more than 6.2 million deaths around the world. About 40% to 87% of patients suffer from persistent symptoms weeks or months after their original infection. Despite remarkable progress in preventing and treating acute COVID-19 conditions, the clinical diagnosis of long-term COVID remains difficult. In this work, we use free-text clinical notes and natural language processing (NLP) techniques to explore long-term COVID effects. We first obtain free-text clinical notes from 719 outpatient encounters representing patients treated by physicians at Emory Clinic to detect patterns in patients with long-term COVID symptoms. We apply state-of-the-art NLP frameworks to automatically identify patients with long-term COVID effects, achieving 0.881 recall (sensitivity) score for note-level prediction. We further interpret the prediction outcomes and discuss potential phenotypes. Our work aims to provide a data-driven solution to identify patients who have developed persistent symptoms after acute COVID infection. With this work, clinicians may be able to identify patients who have long-term COVID symptoms to optimize treatment.