bioRxiv (Cold Spring Harbor Laboratory)
Prediction of SARS-CoV-2 transmission dynamics based on population-level cycle threshold values: A Machine Learning and mechanistic modeling study
March 2023 • Afraz A. Khan, Hind Sbihi, Michael A. Irvine, Agatha N. Jassem, Yayuk Joffres, Braeden Klaver, Naveed Z. Janjua, Aamir Bharmal, Carmen Ng, Amanda Wil…
Abstract Background Polymerase chain reaction (PCR) cycle threshold (Ct) values can be used to estimate the viral burden of Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2) and predict population-level epidemic trends. We investigated the use of machine learning (ML) and epidemic transmission modeling based on Ct value distribution for SARS-CoV-2 incidence prediction during an Omicron-predominant period. Methods Using simulated data, we developed a ML model to predict the reproductive number based…