A framework for the development and validation of an aptamer-based assay for pathogen detection using SARS-CoV-2 as a model

The COVID-19 pandemic exposed major disparities in global diagnostic capacity, particularly in low- and middle-income countries (LMICs) where reliance on conventional assays and external technologies hindered rapid response. Aptamers offer a promising alternative; however, practical and experimentally validated frameworks that connect aptamer discovery to assay development and evaluation in LMIC settings remain limited. Here, we present an integrated and stepwise framework and its feasibility for developing and validating aptamer-based testing tools using SARS-CoV-2 as a model. Native viral particles served as targets in a nine-round systematic evolution of ligands by exponential enrichment (SELEX) protocol optimized for low- to medium-complexity laboratories. High-throughput sequencing and bioinformatic analyses identified candidate sequences, which were then experimentally assessed under defined experimental conditions. The top-performing aptamer, APT-35b, was incorporated into a DNA aptamer-based qPCR assay (Apta-qPCR). When evaluated using 475 clinical samples, the Apta-qPCR achieved 80.8% sensitivity and 95.3% specificity for Omicron BA.1/BA.1.1, with no cross-reactivity to other human coronaviruses. However, performance decreased for more evolved Omicron subvariants (n = 68). This framework offers a practical and adaptable roadmap that links aptamer discovery with functional assay development and can be applied to diverse pathogens, ultimately supporting enhanced diagnostic preparedness and response capacity.