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.
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.
Authors: Yun Lin; Bingyi Yang; Sarah Cobey; Eric H Y Lau; Dillon C Adam; Jessica Y Wong; Helen S Bond; Justin K Cheung; Faith Ho; Huizhi Gao; Sheikh Taslim Ali; Nancy H L Leung; Tim K Tsang; Peng Wu; Gabriel M Leung; Benjamin J Cowling Journal: Nat Commun Date: 2022-03-03 Impact factor: 14.919
Authors: Matthew C Phillips; David Quintero; Noah Wald-Dickler; Paul Holtom; Susan M Butler-Wu Journal: J Clin Virol Date: 2022-04-08 Impact factor: 14.481
Authors: Jeremy Ratcliff; Farah Al-Beidh; Sagida Bibi; David Bonsall; Sue Ann Costa Clemens; Lise Estcourt; Amy Evans; Matthew Fish; Pedro M Folegatti; Anthony C Gordon; Cecilia Jay; Aislinn Jennings; Emma Laing; Teresa Lambe; George MacIntyre-Cockett; David Menon; Paul R Mouncey; Dung Nguyen; Andrew J Pollard; Maheshi N Ramasamy; David J Roberts; Kathryn M Rowan; Jennifer Rynne; Manu Shankar-Hari; Sarah Williams; Heli Harvala; Tanya Golubchik; Peter Simmonds Journal: J Clin Microbiol Date: 2022-03-24 Impact factor: 11.677