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

Gupta, Ankit; Anand, Anjali; Jain, Neha; Goswami, Sandeep; Ananthraj, Anbalagan; Patil, Sharanabasava; Singh, Rahul; Kumar, Amit; Shrivastava, Tripti; Bhatnagar, Shinjini; Medigeshi, Guruprasad R.; Sharma, Tarun Kumar

Recent SARS-CoV-2 outbreak has been declared as a global health emergency. It takes 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. Towards 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 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.