Correlation of population SARS-CoV-2 cycle threshold values to local disease dynamics: An exploratory observational study

This article was originally published here

JMIR Public Health Surveill. 2021 Apr 26. doi: 10.2196/28265. Online ahead of print.

ABSTRACT

BACKGROUND: 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.

OBJECTIVE: Conduct an exploratory analysis of potential correlations between the population distribution of cycle threshold (CT) values and COVID-19 disease dynamics, operationalized as percent positivity, transmission rate and COVID-19 hospitalizations.

METHODS: 148,410 specimens collected between September 15th, 2020 and January 11th, 2021 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 33 day time delay), and the daily change in percent positivity among testing samples (p<.001 for all correlations). 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 (p<.001).

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.

PMID:33999831 | DOI:10.2196/28265