Time Series Analysis of Dengue, Zika, and Chikungunya in Ecuador: Emergence Patterns, Epidemiological Interactions, and Climate-Driven Dynamics (1988–2024)

<b>Background:</b> Ecuador presents a unique epidemiological laboratory for studying arboviral dynamics due to its diverse ecological zones and exposure to climatic variability. <b>Methods:</b> We conducted a comprehensive 36-year analysis (1988-2024) of dengue (DENV), Zika (ZIKV), and chikungunya (CHIKV) using national surveillance data from Ecuador's Ministry of Public Health. Statistical analyses included time series decomposition, change-point detection, correlation analysis, and climate association studies. <b>Results:</b> Ecuador reported 387,543 arboviral cases, with dengue comprising 91.3% (353,782 cases). Dengue exhibited endemic-epidemic cycles with major peaks during El Niño events (1994: 10,247 cases; 2000: 22,937 cases; 2015: 42,483 cases; 2024: 23,156 cases through week 26). CHIKV emerged explosively in 2015 (29,124 cases, incidence 181.10 per 100,000), followed by ZIKV in 2016 (2947 cases). Both showed rapid decline post-epidemic. Severe dengue cases paradoxically decreased from 2-4% of total cases in early 2000s to <0.1% post-2016, suggesting immunological modulation. Cross-correlation analysis revealed significant associations between climatic indices and epidemic timing (r=0.67, p<0.001), particularly for the El Niño-Southern Oscillation. <b>Conclusions:</b> Arboviral diseases in Ecuador function as an integrated epidemiological system with evidence of viral interactions, cross-protective immunity, and strong climate forcing. These findings emphasize the need for integrated surveillance and adaptive control strategies.