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Vortex-induced vibration (VIV) of deck girders frequently drives the wind-resistant design of wind-sensitive bridges from the preliminary to final design stages. Shaping bridge decks is a proven strategy to mitigate VIV. While significant shape modifications are commonly restricted to preliminary design stages, only minor medications are possible at advanced design stages, typically involving adding flow modifiers or changing the shape and location of existing appendages. These mitigation strategies have been implemented in the last decades by carrying out expensive wind tunnel campaigns and following heuristic design rules. This paper proposes an experimental data-driven adaptive surrogate-based optimization approach to systematically identify optimum deck shapes that minimizes the economic cost of the bridge while fulfilling the VIV project specifications. The methodology is conceived to carry out simultaneously the general and detailed shape design of the final deck configuration by harnessing a sequential sampling plan aiming at reducing the sectional model construction costs. The proposed holistic design framework is successfully applied to a real application case involving 26 wind tunnel tests of 1.8-meter wide sectional models to figure out the optimal gap distance and location of maintenance tracks of a twin-box deck equipped with all the appendages included in the final deck design.