Population-Level SARS-CoV-2 RT–PCR Cycle Threshold Values and Their Relationships with COVID-19 Transmission and Outcome Metrics: A Time Series Analysis Across Pandemic Years
This study investigates the relationship between SARS-CoV-2 RT–PCR cycle threshold (Ct) values and key COVID-19 transmission and outcome metrics across five years of the pandemic in Jalisco, Mexico. Utilizing a comprehensive time-series analysis, we evaluated weekly median Ct values as proxies for v...
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| Format: | Article |
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2025-01-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/17/1/103 |
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| author | Judith Carolina De Arcos-Jiménez Ernestina Quintero-Salgado Pedro Martínez-Ayala Gustavo Rosales-Chávez Roberto Miguel Damian-Negrete Oscar Francisco Fernández-Diaz Mariana del Rocio Ruiz-Briseño Rosendo López-Romo Patricia Noemi Vargas-Becerra Ruth Rodríguez-Montaño Ana María López-Yáñez Jaime Briseno-Ramirez |
| author_facet | Judith Carolina De Arcos-Jiménez Ernestina Quintero-Salgado Pedro Martínez-Ayala Gustavo Rosales-Chávez Roberto Miguel Damian-Negrete Oscar Francisco Fernández-Diaz Mariana del Rocio Ruiz-Briseño Rosendo López-Romo Patricia Noemi Vargas-Becerra Ruth Rodríguez-Montaño Ana María López-Yáñez Jaime Briseno-Ramirez |
| author_sort | Judith Carolina De Arcos-Jiménez |
| collection | DOAJ |
| description | This study investigates the relationship between SARS-CoV-2 RT–PCR cycle threshold (Ct) values and key COVID-19 transmission and outcome metrics across five years of the pandemic in Jalisco, Mexico. Utilizing a comprehensive time-series analysis, we evaluated weekly median Ct values as proxies for viral load and their temporal associations with positivity rates, reproduction numbers (Rt), hospitalizations, and mortality. Cross-correlation and lagged regression analyses revealed significant lead–lag relationships, with declining Ct values consistently preceding surges in positivity rates and hospitalizations, particularly during the early phases of the pandemic. Granger causality tests and vector autoregressive modeling confirmed the predictive utility of Ct values, highlighting their potential as early warning indicators. The study further observed a weakening association in later pandemic stages, likely influenced by the emergence of new variants, hybrid immunity, changes in human behavior, and diagnostic shifts. These findings underscore the value of Ct values as scalable tools for public health surveillance and highlight the importance of contextualizing their analysis within specific epidemiological and temporal frameworks. Integrating Ct monitoring into surveillance systems could enhance pandemic preparedness, improve outbreak forecasting, and strengthen epidemiological modeling. |
| format | Article |
| id | doaj-art-47b487cf40b44b0ebbb60d7a749bccfa |
| institution | Kabale University |
| issn | 1999-4915 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj-art-47b487cf40b44b0ebbb60d7a749bccfa2025-01-24T13:52:36ZengMDPI AGViruses1999-49152025-01-0117110310.3390/v17010103Population-Level SARS-CoV-2 RT–PCR Cycle Threshold Values and Their Relationships with COVID-19 Transmission and Outcome Metrics: A Time Series Analysis Across Pandemic YearsJudith Carolina De Arcos-Jiménez0Ernestina Quintero-Salgado1Pedro Martínez-Ayala2Gustavo Rosales-Chávez3Roberto Miguel Damian-Negrete4Oscar Francisco Fernández-Diaz5Mariana del Rocio Ruiz-Briseño6Rosendo López-Romo7Patricia Noemi Vargas-Becerra8Ruth Rodríguez-Montaño9Ana María López-Yáñez10Jaime Briseno-Ramirez11State Public Health Laboratory, Zapopan 45170, MexicoState Public Health Laboratory, Zapopan 45170, MexicoAntiguo Hospital Civil de Guadalajara, “Fray Antonio Alcalde”, Guadalajara 44280, MexicoNuevo Hospital Civil de Guadalajara, “Dr. Juan I. Menchaca”, Guadalajara 44340, MexicoAntiguo Hospital Civil de Guadalajara, “Fray Antonio Alcalde”, Guadalajara 44280, MexicoHealth Division, Tlajomulco University Center, University of Guadalajara, Tlajomulco de Zuñiga 45641, MexicoHealth Division, Tlajomulco University Center, University of Guadalajara, Tlajomulco de Zuñiga 45641, MexicoState Public Health Laboratory, Zapopan 45170, MexicoLaboratory of Microbiological, Molecular, and Biochemical Diagnostics (LaDiMMB), Tlajomulco University Center, University of Guadalajara, Tlajomulco de Zuñiga 45641, MexicoHealth Division, Tlajomulco University Center, University of Guadalajara, Tlajomulco de Zuñiga 45641, MexicoHealth Division, Tlajomulco University Center, University of Guadalajara, Tlajomulco de Zuñiga 45641, MexicoAntiguo Hospital Civil de Guadalajara, “Fray Antonio Alcalde”, Guadalajara 44280, MexicoThis study investigates the relationship between SARS-CoV-2 RT–PCR cycle threshold (Ct) values and key COVID-19 transmission and outcome metrics across five years of the pandemic in Jalisco, Mexico. Utilizing a comprehensive time-series analysis, we evaluated weekly median Ct values as proxies for viral load and their temporal associations with positivity rates, reproduction numbers (Rt), hospitalizations, and mortality. Cross-correlation and lagged regression analyses revealed significant lead–lag relationships, with declining Ct values consistently preceding surges in positivity rates and hospitalizations, particularly during the early phases of the pandemic. Granger causality tests and vector autoregressive modeling confirmed the predictive utility of Ct values, highlighting their potential as early warning indicators. The study further observed a weakening association in later pandemic stages, likely influenced by the emergence of new variants, hybrid immunity, changes in human behavior, and diagnostic shifts. These findings underscore the value of Ct values as scalable tools for public health surveillance and highlight the importance of contextualizing their analysis within specific epidemiological and temporal frameworks. Integrating Ct monitoring into surveillance systems could enhance pandemic preparedness, improve outbreak forecasting, and strengthen epidemiological modeling.https://www.mdpi.com/1999-4915/17/1/103SARS-CoV-2 cycle threshold (Ct)COVID-19 transmission dynamicstime series analysisrespiratory viral trendsepidemiological predictorscycle threshold (Ct) predictive value |
| spellingShingle | Judith Carolina De Arcos-Jiménez Ernestina Quintero-Salgado Pedro Martínez-Ayala Gustavo Rosales-Chávez Roberto Miguel Damian-Negrete Oscar Francisco Fernández-Diaz Mariana del Rocio Ruiz-Briseño Rosendo López-Romo Patricia Noemi Vargas-Becerra Ruth Rodríguez-Montaño Ana María López-Yáñez Jaime Briseno-Ramirez Population-Level SARS-CoV-2 RT–PCR Cycle Threshold Values and Their Relationships with COVID-19 Transmission and Outcome Metrics: A Time Series Analysis Across Pandemic Years Viruses SARS-CoV-2 cycle threshold (Ct) COVID-19 transmission dynamics time series analysis respiratory viral trends epidemiological predictors cycle threshold (Ct) predictive value |
| title | Population-Level SARS-CoV-2 RT–PCR Cycle Threshold Values and Their Relationships with COVID-19 Transmission and Outcome Metrics: A Time Series Analysis Across Pandemic Years |
| title_full | Population-Level SARS-CoV-2 RT–PCR Cycle Threshold Values and Their Relationships with COVID-19 Transmission and Outcome Metrics: A Time Series Analysis Across Pandemic Years |
| title_fullStr | Population-Level SARS-CoV-2 RT–PCR Cycle Threshold Values and Their Relationships with COVID-19 Transmission and Outcome Metrics: A Time Series Analysis Across Pandemic Years |
| title_full_unstemmed | Population-Level SARS-CoV-2 RT–PCR Cycle Threshold Values and Their Relationships with COVID-19 Transmission and Outcome Metrics: A Time Series Analysis Across Pandemic Years |
| title_short | Population-Level SARS-CoV-2 RT–PCR Cycle Threshold Values and Their Relationships with COVID-19 Transmission and Outcome Metrics: A Time Series Analysis Across Pandemic Years |
| title_sort | population level sars cov 2 rt pcr cycle threshold values and their relationships with covid 19 transmission and outcome metrics a time series analysis across pandemic years |
| topic | SARS-CoV-2 cycle threshold (Ct) COVID-19 transmission dynamics time series analysis respiratory viral trends epidemiological predictors cycle threshold (Ct) predictive value |
| url | https://www.mdpi.com/1999-4915/17/1/103 |
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