An on-going challenge with COVID-19, which has huge implications for future pandemics, is the rapid emergence of viral variants that makes diagnostic tools less accurate, calling for rapid identifications of recognition elements for detecting new variants caused by mutations.
We hypothesize that we can fight mutations of the viruses with mutations of existing recognition elements. We demonstrate this concept via rapidly evolving an existing DNA aptamer originally selected with the spike protein (S-protein) of wildtype SARS-CoV-2 for enhanced recognition of the same protein of the Omicron variants.
The new aptamer has acquired 22 mutations within its 40-nucleotide core sequence and improved its binding affinity for the S-proteins of diverse Omicron subvariants by > 100-fold compared to its parental aptamer.
The aptamer was implemented into an enzyme-linked aptamer binding assay (ELABA), which was applied for detecting Omicron variants in the saliva of infected patients. The assay produced a sensitivity of 86.5% and a specificity of 100%, which was established with 83 clinical samples
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