Bayesian sequential approach to monitor COVID-19 variants through test positivity rate from wastewater

• Published in: mSystems Vol. 8; no. 4; p. e0001823
• Main Authors: Montesinos-López, J Cricelio, Daza-Torres, Maria L, García, Yury E, Herrera, César, Bess, C Winston, Bischel, Heather N, Nuño, Miriam
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 31.08.2023
• Subjects: Bayes Theorem; Bayesian analysis; Bayesian sequential data assimilation; Coronaviruses; COVID-19; COVID-19 - diagnosis; COVID-19 Testing; COVID-19 vaccines; Decision making; Disease transmission; effective reproductive number; Epidemiology; Humans; Mathematical models; Pandemics; Pandemics - prevention & control; Public health; Research Article; RNA, Viral - genetics; SARS-CoV-2; SARS-CoV-2 - genetics; Severe acute respiratory syndrome coronavirus 2; test positivity rate (TPR); Trends; United States; Wastewater; wastewater-based epidemiology (WBE); United States; COVID-19; SARS-CoV-2; wastewater-based epidemiology (WBE); Bayesian sequential data assimilation; test positivity rate (TPR); effective reproductive number
• ISSN: 2379-5077; 2379-5077
• DOI: 10.1128/msystems.00018-23

Deployment of clinical testing on a massive scale was an essential control measure for curtailing the burden of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and the magnitude of the COVID-19 (coronavirus disease 2019) pandemic during its waves. As the pandemic progressed, new preventive and surveillance mechanisms emerged. Implementation of vaccine programs, wastewater (WW) surveillance, and at-home COVID-19 antigen tests reduced the demand for mass SARS-CoV-2 testing. Unfortunately, reductions in testing and test reporting rates also reduced the availability of public health data to support decision-making. This paper proposes a sequential Bayesian approach to estimate the COVID-19 test positivity rate (TPR) using SARS-CoV-2 RNA concentrations measured in WW through an adaptive scheme incorporating changes in virus dynamics. The proposed modeling framework was applied to WW surveillance data from two WW treatment plants in California; the City of Davis and the University of California, Davis campus. TPR estimates are used to compute thresholds for WW data using the Centers for Disease Control and Prevention thresholds for low (<5% TPR), moderate (5%-8% TPR), substantial (8%-10% TPR), and high (>10% TPR) transmission. The effective reproductive number estimates are calculated using TPR estimates from the WW data. This approach provides insights into the dynamics of the virus evolution and an analytical framework that combines different data sources to continue monitoring COVID-19 trends. These results can provide public health guidance to reduce the burden of future outbreaks as new variants continue to emerge. IMPORTANCE We propose a statistical model to correlate WW with TPR to monitor COVID-19 trends and to help overcome the limitations of relying only on clinical case detection. We pose an adaptive scheme to model the nonautonomous nature of the prolonged COVID-19 pandemic. The TPR is modeled through a Bayesian sequential approach with a beta regression model using SARS-CoV-2 RNA concentrations measured in WW as a covariable. The resulting model allows us to compute TPR based on WW measurements and incorporates changes in viral transmission dynamics through an adaptive scheme.