A novel G-quadruplex aptamer-based spike trimeric antigen test for the detection of SARS-CoV-2

The recent SARS-CoV-2 outbreak has been declared a global health emergency. It will take years to vaccinate the whole population to protect them from this deadly virus, hence the management of SARS-CoV-2 largely depends on the widespread availability of an accurate diagnostic test. Toward addressing the unmet need of a reliable diagnostic test in the current work by utilizing the power of Systematic Evolution of Ligands by EXponential enrichment, a 44-mer G-quadruplex-forming DNA aptamer against spike trimer antigen of SARS-CoV-2 was identified. The lead aptamer candidate (S14) was characterized thoroughly for its binding, selectivity, affinity, structure, and batch-to-batch variability by utilizing various biochemical, biophysical, and in silico techniques. S14 has demonstrated a low nanomolar KD, confirming its tight binding to a spike antigen of SARS-CoV-2. S14 can detect as low as 2 nM of antigen. The clinical evaluation of S14 aptamer on nasopharyngeal swab specimens (n = 232) has displayed a highly discriminatory response between SARS-CoV-2 infected individuals from the non-infected one with a sensitivity and specificity of -91% and 98%, respectively. Importantly, S14 aptamer-based test has evinced a comparable performance with that of RT-PCRbased assay. Altogether, this study established the utility of aptamer technology for the detection of SARS-CoV-2.

Automated summary

The study identified a DNA aptamer with strong binding ability to the spike trimer antigen of SARS-CoV-2 using Systematic Evolution of Ligands by EXponential enrichment. The aptamer, named S14, showed high affinity and structure, capable of detecting antigens as low as 2 nM. Clinical evaluation demonstrated its highly discriminatory performance in differentiating between SARS-CoV-2 infected and non-infected individuals.