Correlation of Population SARS-CoV-2 Cycle Threshold Values to Local Disease Dynamics: Exploratory Observational Study

Chak Foon Tso,Ritankar Das,Qingqing Mao,Anurag Garikipati,Abigail Green-Saxena

doi:10.2196/28265

Abstract

BackgroundDespite the limitations in the use of cycle threshold (CT) values for individual patient care, population distributions of CT values may be useful indicators of local outbreaks.ObjectiveWe aimed to conduct an exploratory analysis of potential correlations between the population distribution of cycle threshold (CT) values and COVID-19 dynamics, which were operationalized as percent positivity, transmission rate (Rt), and COVID-19 hospitalization count.MethodsIn total, 148,410 specimens collected between September 15, 2020, and January 11, 2021, from the greater El Paso area were processed in the Dascena COVID-19 Laboratory. The daily median CT value, daily Rt, 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 were used to evaluate possible associations between daily median CT values and outbreak measures. Cross-correlation plots were used to determine whether a time delay existed between changes in daily median CT values and measures of community disease dynamics.ResultsDaily median CT values negatively correlated with the daily Rt values (P<.001), the daily COVID-19 hospitalization counts (with a 33-day time delay; P<.001), and the daily changes in percent positivity among testing samples (P<.001). Despite visual trends suggesting time delays in the plots for median CT values and outbreak measures, a statistically significant delay was only detected between changes in median CT values and COVID-19 hospitalization counts (P<.001).ConclusionsThis 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.

Highlights

As of February 16, 2021, the SARS-CoV-2 virus has infected more than 109 million people around the world and has been implicated in 2.41 million deaths [1]
This study describes an exploratory analysis of potential correlations between median cycle threshold (CT) values and COVID-19 dynamics, which were operationalized as percent positivity, transmission rate (Rt), and COVID-19 hospitalization count
Variability over time was observed in the median CT values and measures of COVID-19 dynamics in El Paso (Figure 1)

Summary

Introduction

As of February 16, 2021, the SARS-CoV-2 virus has infected more than 109 million people around the world and has been implicated in 2.41 million deaths [1]. In the United States alone, more than 486,500 deaths have been attributed to COVID-19 [1]. RT-PCR tests detect viral genetic material in biological samples [4]. The cycle threshold (CT) value represents the number of polymerase chain reaction cycles that are required to detect a positive signal [5]. The CT value is inversely related to the viral load; a 3.3 increase in CT value indicates an approximately 10-fold decrease in the amount of viral genetic material present in a sample [5]. COVID-19 RT-PCR tests are generally considered positive only if they generate a result with a CT value that is lower than the recommended cutoff. Despite the limitations in the use of cycle threshold (CT) values for individual patient care, population distributions of CT values may be useful indicators of local outbreaks

Methods

Results

Discussion

Conclusion