An exploratory study on the correlation of population SARS-CoV-2 cycle threshold values to local disease dynamics

Tso, C. F.; Garikipati, A.; Green-Saxena, A.; Mao, Q.; Das, R.

Introduction: Despite limitations on the use of cycle threshold (CT) values for individual patient care, population distributions of CT values may be useful indicators of local outbreaks. Methods: Specimens from the greater El Paso area were processed in the Dascena COVID-19 Laboratory. Daily median CT value, daily transmission rate R(t), daily count of COVID-19 hospitalizations, daily change in percent positivity, and rolling averages of these features were plotted over time. Two-way scatterplots and linear regression evaluated possible associations between daily median CT and outbreak measures. Cross-correlation plots determined whether a time delay existed between changes in the daily median CT value and measure of community disease dynamics. Results: Daily median CT was negatively correlated with the daily R(t), the daily COVID-19 hospitalization count (with a time delay), and the daily change in percent positivity among testing samples. Despite visual trends suggesting time delays in the plots for median CT and outbreak measures, a statistically significant delay was only detected between changes in median CT and COVID-19 hospitalization count. Conclusions: This study adds to the literature by analyzing samples collected from an entire geographical area, and contextualizing the results with other research investigating population CT values.