TY - JOUR
AU - N. T. Parker
AU - V. Hong
AU - G. S. Davis
AU - M. Pomichowski
AU - I. A. Reyes
AU - F. Xie
AU - N. F. Mueller
AU - I. Rodriguez-Barraquer
AU - S . Y. Tartof
AU - J. A. Lewnard
A1 - 
AB - Mathematical and computational models are often used to forecast respiratory infectious disease burden, including to inform healthcare capacity. We aimed to characterize pathways of clinical progression associated with SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) infections using data from patients aged 0 to >90 years in an integrated healthcare system, whose encounters were monitored across all levels of acuity spanning virtual, ambulatory, and inpatient care settings. Using parametric survival models, we estimated probabilities of progression and distributions of time to progression from each setting to all higher-acuity settings on a cascade encompassing the following classes of events or encounters: symptoms onset; diagnostic testing; telehealth or other virtual care appointment; outpatient physician office visit; urgent care presentation; emergency department presentation; hospital admission; mechanical ventilation; and death. Our analyses included data from 59,668, 22,705, and 1,668 episodes associated with positive SARS-CoV-2, influenza, and RSV tests, respectively, between 1 April 2023 and 31 March 2024. First clinical encounters occurred in inpatient settings for only 4.7%, 3.4%, and 18.7% of SARS-CoV-2, influenza, and RSV episodes, respectively, with median times (interquartile range) of 6.8 (3.6-13.2), 6.6 (3.5-12.1), and 6.4 (3.8-10.6) days from symptoms onset to admission. Overall, 7.9% of SARS-CoV-2 episodes, 5.8% of influenza episodes, and 33.8% of RSV episodes resulted in inpatient admission, ventilation, or death. Between 40.4-62.1%, 71.6-87.3%, and 47.9-58.7% of SARS-CoV-2, influenza, and RSV infections, respectively, had encounters in lower-acuity virtual care, outpatient, or urgent care settings. For all three viruses, the proportions of cases receiving care at each level of acuity increased with older age and greater numbers of comorbid conditions. Median durations of hospital stay were 4.2 (2.6, 7.3), 4.0 (2.3, 6.8), and 4.3 (2.5, 7.4) days for SARS-CoV-2, influenza, and RSV episodes resulting in admission. These estimates provide a basis for modeling real-world clinical care requirements and the progression of respiratory viral infections.
AD - Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America.; School of Public Health, University of California, Berkeley, Berkeley, California, United States of America.; Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California, United States of America.; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, United States of America.; Chan Zuckerberg Biohub, San Francisco, California, United States of America.; Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, California, United States of America.; Center for Computational Biology, College of Data Science and Society, University of California, Berkeley, Berkeley, California, United States of America.
AN - 41259406
BT - PLoS Comput Biol
C5 - HIT & Telehealth
CP - 11
DA - Nov
DO - 10.1371/journal.pcbi.1013723
DP - NLM
ET - 20251119
IS - 11
JF - PLoS Comput Biol
LA - eng
N2 - Mathematical and computational models are often used to forecast respiratory infectious disease burden, including to inform healthcare capacity. We aimed to characterize pathways of clinical progression associated with SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) infections using data from patients aged 0 to >90 years in an integrated healthcare system, whose encounters were monitored across all levels of acuity spanning virtual, ambulatory, and inpatient care settings. Using parametric survival models, we estimated probabilities of progression and distributions of time to progression from each setting to all higher-acuity settings on a cascade encompassing the following classes of events or encounters: symptoms onset; diagnostic testing; telehealth or other virtual care appointment; outpatient physician office visit; urgent care presentation; emergency department presentation; hospital admission; mechanical ventilation; and death. Our analyses included data from 59,668, 22,705, and 1,668 episodes associated with positive SARS-CoV-2, influenza, and RSV tests, respectively, between 1 April 2023 and 31 March 2024. First clinical encounters occurred in inpatient settings for only 4.7%, 3.4%, and 18.7% of SARS-CoV-2, influenza, and RSV episodes, respectively, with median times (interquartile range) of 6.8 (3.6-13.2), 6.6 (3.5-12.1), and 6.4 (3.8-10.6) days from symptoms onset to admission. Overall, 7.9% of SARS-CoV-2 episodes, 5.8% of influenza episodes, and 33.8% of RSV episodes resulted in inpatient admission, ventilation, or death. Between 40.4-62.1%, 71.6-87.3%, and 47.9-58.7% of SARS-CoV-2, influenza, and RSV infections, respectively, had encounters in lower-acuity virtual care, outpatient, or urgent care settings. For all three viruses, the proportions of cases receiving care at each level of acuity increased with older age and greater numbers of comorbid conditions. Median durations of hospital stay were 4.2 (2.6, 7.3), 4.0 (2.3, 6.8), and 4.3 (2.5, 7.4) days for SARS-CoV-2, influenza, and RSV episodes resulting in admission. These estimates provide a basis for modeling real-world clinical care requirements and the progression of respiratory viral infections.
PY - 2025
SN - 1553-734X (Print); 1553-734x
SP - e1013723
ST - Clinical progression parameters associated with SARS-CoV-2, influenza, and respiratory syncytial virus infections in a large US integrated healthcare population
T1 - Clinical progression parameters associated with SARS-CoV-2, influenza, and respiratory syncytial virus infections in a large US integrated healthcare population
T2 - PLoS Comput Biol
TI - Clinical progression parameters associated with SARS-CoV-2, influenza, and respiratory syncytial virus infections in a large US integrated healthcare population
U1 - HIT & Telehealth
U3 - 10.1371/journal.pcbi.1013723
VL - 21
VO - 1553-734X (Print); 1553-734x
Y1 - 2025
ER -