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

• Main Authors: Ankit Gupta, Anjali Anand, Neha Jain, Sandeep Goswami, Anbalagan Anantharaj, Sharanabasava Patil, Rahul Singh, Amit Kumar, Tripti Shrivastava, Shinjini Bhatnagar, Guruprasad R. Medigeshi, Tarun Kumar Sharma
• Format: Article
• Language: English
• Published: Elsevier 2021-12-01
• Series: Molecular Therapy: Nucleic Acids
• Subjects: aptamer; SARS-CoV-2; diagnostics; ALISA; spike trimer; batch-to-batch variation
• Online Access: http://www.sciencedirect.com/science/article/pii/S2162253121001554

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-PCR-based assay. Altogether, this study established the utility of aptamer technology for the detection of SARS-CoV-2.