Statistical modeling of outcomes based on a patient's presenting symptoms (symptomatology) can help deliver high quality care and allocate essential resources, which is especially important during the COVID-19 pandemic. Patient symptoms are typically found in unstructured notes, and thus not readily available for clinical decision making. In an attempt to fill this gap, this study compared two methods for symptom extraction from Emergency Department (ED) admission notes. Both methods utilized a lexicon derived by expanding The Center for Disease Control and Prevention's (CDC) Symptoms of Coronavirus list. The first method utilized a word2vec model to expand the lexicon using a dictionary mapping to the Uni ed Medical Language System (UMLS). The second method utilized the expanded lexicon as a rule-based gazetteer and the UMLS. These methods were evaluated against a manually annotated reference (f1-score of 0.87 for UMLS-based ensemble; and 0.85 for rule-based gazetteer with UMLS). Through analyses of associations of extracted symptoms used as features against various outcomes, salient risks among the population of COVID-19 patients, including increased risk of in-hospital mortality (OR 1.85, p-value < 0.001), were identified for patients presenting with dyspnea. Disparities between English and non-English speaking patients were also identified, the most salient being a concerning finding of opposing risk signals between fatigue and in-hospital mortality (non-English: OR 1.95, p-value = 0.02; English: OR 0.63, p-value = 0.01). While use of symptomatology for modeling of outcomes is not unique, unlike previous studies this study showed that models built using symptoms with the outcome of in-hospital mortality were not significantly different from models using data collected during an in-patient encounter (AUC of 0.9 with 95% CI of [0.88, 0.91] using only vital signs; AUC of 0.87 with 95% CI of [0.85, 0.88] using only symptoms). These findings indicate that prognostic models based on symptomatology could aid in extending COVID-19 patient care through telemedicine, replacing the need for in-person options. The methods presented in this study have potential for use in development of symptomatology-based models for other diseases, including for the study of Post-Acute Sequelae of COVID-19 (PASC).

Objective With COVID-19 there was a need for rapidly scalable annotation system that facilitated real-time integration with clinical decision support systems (CDS). Current annotation systems suffer from high resource utilization and poor scalability limiting real-world integration with CDS. A potential solution to mitigate these issues is to use the rule-based gazetteer developed at our institution. Materials and Methods Performance, resource utilization and runtime of the rule-based gazetteer was compared with five annotation systems: BioMedICUS, cTAKES, MetaMap, CLAMP and MedTagger. Results This rule-based gazetteer was fastest, had low resource footprint and similar performance for weighted micro-average and macro-average measures of precision, recall and f1-score compared to other annotation systems. Discussion Opportunities to increase its performance include fine-tuning lexical rules for symptom identification. Additionally, it could run on multiple compute nodes for faster runtime. Conclusion This rule-based gazetteer overcame key technical limitations facilitating real-time symptomatology identification for COVID-19 and integration of unstructured data elements into our CDS. It is ideal for large-scale deployment across a wide variety of health care settings for surveillance of acute COVID-19 symptoms for integration into prognostic modeling. Such a system is currently being leveraged for monitoring of post-acute sequelae of COVID-19 (PASC) progression in COVID-19 survivors. This study conducted the first in-depth analysis and developed a rule-based gazetteer for COVID-19 symptom extraction with the following key features: low processor and memory utilization, faster runtime and similar weighted micro-average and macro-average measures for precision, recall and f1-score compared to industry standard annotation systems. Lay Summary With COVID-19 came an unprecedented need to identify symptoms of COVID-19 patients under investigation (PUIs) in a time sensitive, resource-efficient and accurate manner. While available annotation systems perform well for smaller healthcare settings, they fail to scale in larger healthcare systems where 10,000+ clinical notes are generated a day. This study covers 3 improvements addressing key limitations of current annotation systems. (1) High resource utilization and poor scalability of existing annotation systems. The presented rule-based gazetteer is a high-throughput annotation system for processing high volume of notes, thus, providing opportunity for clinicians to make more informed time-sensitive decisions around patient care. (2) Equally important is our developed rule-based gazetteer performs similar or better than current annotation systems for symptom identification. (3) Due to minimal resource needs of the rule-based gazetteer, it could be deployed at healthcare sites lacking a robust infrastructure where industry standard annotation systems cannot be deployed because of low resource availability.

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