High-Throughput Engineering of SARS-CoV-2 Aptamers for Adaptation to Rapid Viral Evolution

Rapid pathogen evolution, exemplified by the recent SARS-CoV-2, complicates diagnostic development. Aptamers are attractive recognition elements due to low cost, chemical stability, and programmability, yet quickly generating binders with the right combination of sensitivity and specificity remains challenging for both targeting particular variants and maintaining detection performance as new variants of concern (VOCs) emerge. We here present SELEX-CHAMP (systematic evolution of ligands by exponential enrichment–chip-based hybridization-associated mapping platform), which couples rational diversification with high-throughput, on-chip profiling to identify aptamers tailored to evolving targets. Starting from a wild-type (WT) SARS-CoV-2 spike binder (Apt2 by Zu, et al.), we designed a library and mapped the binding across variants. This yielded: (1) a promoted Delta binder with a ~5-fold lower kd than Apt2 against Delta, (2) a WT-selective binder with Delta signal completely suppressed, and (3) an OmicronXBB-preferring binder with a distinct binding profile relative to earlier strains with the kd for OmicronXBB switched from >677 nM to ~6.6 nM. Using the WT- and OmicronXBB-selective binders, we built a dual-color sensor that differentiates WT from OmicronXBB samples, supporting variant-aware diagnostics that preserves strain resolution. Further exploration for the OmicronXBB binder implicated a potential G-quadruplex contribution to distinct binding profile, and molecular modeling suggests modes of interaction between spike and both the seeding and evolved aptamers. Together, these results demonstrate that SELEX-CHAMP rapidly delivers aptamers optimized either for stronger binding (sensitivity) or sharper discrimination (specificity), which would potentially offer a flexible path to diagnostics that keep pace with fast-evolving pathogens for both the on-going and future pandemics.