Adapting KS-Detect technology to high-throughput COVID-19 screening

Abstract: The COVID-19 pandemic represents a worldwide infectious disease challenge that disrupted our economic,educational, and social norms in a way that was largely unimaginable just months ago. At present the mostefficacious method of limiting the spread of the disease has been to test those that exhibit symptoms - typicallyby nucleic acid based viral identification methods - and isolate those that are positive. Even at this early stagethis approach has put significant strain on the diagnostic infrastructure of advanced countries, let alone thosewith fewer resources. As we move beyond symptom-initiated confirmation diagnoses to the larger scalescreening that may be required to identify asymptomatic carriers and to restart sections of our economy, muchmore rapid and higher throughput techniques will be required.Under ongoing NIH/NCI UH2/UH3 (UH3CA202723) funding we have been developing TINY (Tiny IsothermalNucleic acid quantification sYstem). The TINY system is a self-contained, portable device for the detection andLAMP-based quantification of viral nucleic acids designed for use in settings with limited resources. Through thatprogram, the system is currently deployed within Uganda for identifying Kaposi's Sarcoma Herpes Virus (KSHV)in human biopsies as a novel diagnostic technique for Kaposi's Sarcoma. The system has been validated onover 500 samples showing sensitivity and specificity of 93% and 95%.Through this supplement request, we propose to upscale the TINY system to enable much high-throughputscreening - from 6 parallel samples to 96 - and adapt it to a run a recently developed LAMP assay for SARS-CoV-2 detection which has already been validated on 182 patients in New York City. We believe that this willsimultaneously contribute to the need for higher throughout COVID-19 diagnostics and advance the NCIs desirefor platforms that can enable broader screening for viruses which are known to cause cancers (e.g. HPV in thecase of cervical cancer).