Accuracy of COVID-19-Like Illness Diagnoses in Electronic Health Record Data: Retrospective Cohort Study

BACKGROUND

Electronic health record (EHR) data provide a unique opportunity to study the epidemiology of COVID-19, clinical outcomes of the infection, comparative effectiveness of therapies, and vaccine effectiveness but require a well-defined computable phenotype of COVID-19-like illness (CLI).

OBJECTIVE

The objective of this study was to evaluate the performance of pathogen-specific and other acute respiratory illness (ARI) International Statistical Classification of Diseases-9 and -10 codes in identifying COVID-19 cases in emergency department (ED) or urgent care (UC) and inpatient settings.

METHODS

We conducted a retrospective observational cohort study using EHR, claims, and laboratory information system data of ED or UC and inpatient encounters from 4 health systems in the United States. Patients who were aged ≥18 years, had an ED or UC or inpatient encounter for an ARI, and underwent a SARS-CoV-2 polymerase chain reaction test between March 1, 2020, and March 31, 2021, were included. We evaluated various CLI definitions using combinations of International Statistical Classification of Diseases-10 codes as follows: COVID-19-specific codes; CLI definition used in VISION network studies; ARI signs, symptoms, and diagnosis codes only; signs and symptoms of ARI only; and random forest model definitions. We evaluated the sensitivity, specificity, positive predictive value, and negative predictive value of each CLI definition using a positive SARS-CoV-2 polymerase chain reaction test as the reference standard. We evaluated the performance of each CLI definition for distinct hospitalization and ED or UC cohorts.

RESULTS

Among 90,952 hospitalizations and 137,067 ED or UC visits, 5627 (6.19%) and 9866 (7.20%) were positive for SARS-CoV-2, respectively. COVID-19-specific codes had high sensitivity (91.6%) and specificity (99.6%) in identifying patients with SARS-CoV-2 positivity among hospitalized patients. The VISION CLI definition maintained high sensitivity (95.8%) but lowered specificity (45.5%). By contrast, signs and symptoms of ARI had low sensitivity and positive predictive value (28.9% and 11.8%, respectively) but higher specificity and negative predictive value (85.3% and 94.7%, respectively). ARI diagnoses, signs, and symptoms alone had low predictive performance. All CLI definitions had lower sensitivity for ED or UC encounters. Random forest approaches identified distinct CLI definitions with high performance for hospital encounters and moderate performance for ED or UC encounters.

CONCLUSIONS

COVID-19-specific codes have high sensitivity and specificity in identifying adults with positive SARS-CoV-2 test results. Separate combinations of COVID-19-specific codes and ARI codes enhance the utility of CLI definitions in studies using EHR data in hospital and ED or UC settings.

SARS-CoV-2 Infection among Pregnant and Postpartum Women, Kenya, 2020-2021

We determined incidence of severe acute respiratory syndrome coronavirus 2 and influenza virus infections among pregnant and postpartum women and their infants in Kenya during 2020–2021. Incidence of severe acute respiratory syndrome coronavirus 2 was highest among pregnant women, followed by postpartum women and infants. No influenza virus infections were identified.