Development of Q-LAAD, an allonamer-based antigen test for the rapid detection of SARS-CoV-2

The SARS-CoV-2 virus has spread globally causing coronavirus disease 2019 (COVID-19). Rapidly and accurately identifying viral infections is an ongoing necessity. We used the systematic evolution of ligands by exponential enrichment (SELEX) technique to produce a DNA allonamer with two distinct binding domains made allosteric through a linker section; one domain binds SARS-CoV-2 spike (S) protein, inducing a conformational change that allows the reporter domain to bind a fluorescent reporter molecule. We used bead-based fluorescence and immunofluorescence assays to confirm the allonamer’s affinity and specificity for S-protein and confirmed that the allonamer can bind to S-proteins with mutations corresponding to those of the alpha, beta, gamma, and delta variants. We then developed the allonamer-based Quantum-Logic Aptamer Analyte Detection (Q-LAAD) test, a rapid, high-throughput antigen test for qualitative detection of SARS-CoV-2 in clinical settings. We validated Q-LAAD against retrospective and prospective clinical anterior nasal swab samples collected from symptomatic patients suspected of having COVID-19. Q-LAAD showed 97% sensitivity and 100% specificity compared to the RT-qPCR assay. Q-LAAD has a limit of detection (LOD) of 1.88 TCID50/mL, is cost-effective and convenient, and requires only a common fluorescence plate reader. Q-LAAD may be a useful clinical diagnostic tool in the fight against SARS-CoV-2. ![Figure][1] HIGHLIGHTS ### Competing Interest Statement Elise Overgaard declares no conflicts of interest. Shiwei Li was employed by Facible Diagnostics, LLC while data was being generated and is an inventor on International Patent Application No. PCT/US21/41883. Hunter J. Covert shares ownership in Facible Diagnostics, LLC, is currently employed by Facible Diagnostics, LLC, and is an inventor on International Patent Application No. PCT/US21/41883. Ken Tawara is currently employed by Facible Diagnostics, LLC. Aidan M. Poe was employed by Facible Diagnostics, LLC while data was being generated and is an inventor on International Patent Application No. PCT/US21/41883. N. Hagan Shults was employed by Facible Diagnostics, LLC while data was being generated and is an inventor on International Patent Application No. PCT/US21/41883. Aliona A. Chernish was employed by Facible Diagnostics, LLC while data was being generated. Brandi Sweet was employed by Facible Diagnostics, LLC while data was being generated. Cara R. Gonzales was employed by Facible Diagnostics, LLC while data was being generated. Clémentine F.N. Gibard shares ownership in Facible Diagnostics, LLC, is currently employed by Facible Diagnostics, LLC, and is an inventor on International Patent Application No. PCT/US21/41883. Steven Burden shares ownership in Facible Diagnostics, LLC, is currently employed by Facible Diagnostics, LLC, and is an inventor on International Patent Application No. PCT/US21/41883. ### Funding Statement This study was funded by Facible BioDiagnostics. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Pearl IRB on behalf of Facible BioDiagnostics LLC gave ethical work approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors. [1]: pending:yes