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This three-year longitudinal study analyzed data from 93 adults (mean age of 48.9\u2009\u00b1\u200914.0, 60 female) after confirmed SARS-CoV-2 infection. Every follow-up visit included clinical, neuropsychological, and laboratory assessments, capturing multidimensional indicators of patient health. A machine learning framework was implemented to classify temporal stage of patient health status, identify visit-specific predictive markers, and manage incomplete data using both native handling in tree-based models and explicit imputation techniques. Gradient boosting methods consistently achieved the best performance across all visit comparisons, achieving F1-scores close to or above 90%. Classification performance improved with greater time intervals between visits, suggesting progressive divergence in patient phenotypes over time. 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