In Silico Design and ELONA Validation of an Aptamer for SARS- CoV-2 Omicron RBD Detection

Abstract

COVID-19, caused by the SARS-CoV-2 virus, has resulted in a pandemic with 6.8 million confirmed cases in Indonesia as of December 2023. The high number of cases has necessitated the need for robust and specific diagnostic tools. Despite its effectiveness, the qRT-PCR suggested by the World Health Organization has a number of drawbacks, such as expensive costs, the need for trained personnel and equipment, and longer processing times. To address these issues, this study explores the development of aptamer-based diagnostic tools. An aptamer was designed to specifically bind to the SARS-CoV-2 Omicron receptor binding domain (RBD) using in silico methods and subsequently validated through ELONA (Enzyme-Linked Oligonucleotide Assay). apt41 was found to have a strong bind to the target RBD, and also showed less cross-reactivity to other related RBDs. The binding efficiency of apt41 was tested using ELONA at various concentrations (1, 1.5, and 2.5 μM). Results indicated that the minimum concentration required for effective binding was around 1.5 μM. For diagnostic applications, higher concentrations are recommended to avoid false negative results and ensure reliable detection. This study highlights the potential of aptamer-based diagnostics as an alternative to traditional methods.