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 pandemic phases. Granger causality tests and vector autoregressive modeling confirmed the predictive value of Ct values, highlighting their potential as early warning indicators. Demographic stratification showed lower Ct values in older adults and males, indicative of higher viral loads in these subgroups. The study further observed a weakening association in later pandemic stages, likely due to vaccination campaigns, natural immunity, and diagnostic shifts. These findings underscore the utility of Ct values as scalable tools for public health surveillance, offering actionable insights for resource allocation and outbreak mitigation. Integrating Ct monitoring into surveillance systems could enhance preparedness for respiratory viral pandemics and improve epidemiological modeling frameworks.