Considering challenges for fast and accurate diagnosis of infectious diseases, this study presents a novel electrochemical biosensor that employs a refined aptamer (C9t) for the detection of spike (S) protein SARS-CoV-2 variants in a flexible multielectrode aptasensor array with PoC capabilities. Two aptamer modifications were employed: the removal of the primer binding sites and the inclu-sion of two dithiol phosphoramidite anchor molecules. Thus, reducing fabrication time from 24 to 3 hours for multi-thiol aptasensors compared to a standard aptasensor using single thiols, without reduction in aptamer density. The biosensor fabrication, optimization, and detection were verified in detail by electrochemistry, QCM-D, SPR, and XPS. The analyte-receptor binding was further confirmed spectroscopically at the level of individual molecules by AFM-IR. The aptasensor pos-sesses a low limit of detection (8.0 fg/mL), the highest sensitivity reported for S protein (209.5 sig-nal per concentration decade), and a wide dynamic detection range (8.0 fg/mL - 38 ng/mL) in na-sopharyngeal samples, covering the clinically relevant range. Furthermore, the C9t aptasensor showed high selectivity for SARS-CoV-2 S proteins over biomarkers for MERS-CoV, RSV, and In-fluenza. Even more, it showed a 3 times higher sensitivity for the Omicron in comparison to the Wuhan strain (wild type), alpha, and beta variants of the SARS-CoV-2 virus. Those results demonstrated an affordable and variant-selective refined C9t aptasensor that outperformed cur-rent rapid diagnosis tests.