JMIR Publications

ABSTRACT

Background:

Previous studies highlight viral shedding using cycle threshold (Ct) with the RT-PCT for epidemic trajectories of SARS-CoV-2 infection, but assessing Ct values transition kinetics before recovery for surveillance using individual repeated Ct values data is rare.

Objective:

We propose a new Ct-enshrined compartment model for understanding viral shedding kinetics in susceptible, pre-symptomatic, and symptomatic compartments before recovery or death.

Methods:

A series of useful recovery indices are developed to quantify the kinetic movement of Ct-up-down viral shedding toward recovery and are demonstrated with two scenarios, one is small-scale community-acquired Alpha VOC infection under the “zero-COVID-19” policy without available vaccine in May 2021, and the other is large-scale community-acquired Omicron infection with high booster vaccination but lifting the “zero-COVID-19” policy in April 2022 in Taiwan.

Results:

Kinetic indicators revealed Alpha's increased Ct-up transitions, indicative of reduced viral loads, especially among asymptomatic infections. In contrast, Omicron displayed swifter viral shedding and a higher asymptomatic recovery rate. Vaccination showed discernible effects; non-boosted individuals had a 19% higher pre-symptomatic incidence. Sensitivity analysis affirmed the chosen Ct values of 18 and 25, ensuring robust results across recovery phases.

Conclusions:

The study provides a new insight into the dynamic CT transitions with the notable finding that Ct-up transitions toward recovery outpace Ct-down and symptom-surfacing transitions during the pre-symptomatic phase. The Ct-up against Ct-down transition varies with variants and vaccination status. The proposed Ct-enshrined compartment model is useful for the surveillance of emerging infectious diseases in the future to prevent community-acquired outbreaks.