High-surety isothermal amplification and detection of SARS-CoV-2, including with crude enzymes

Sanchita Bhadra; Timothy E Riedel; Simren Lakhotia; Nicholas D Tran; Andrew D Ellington

In summary, we have demonstrated a facile way to rapidly configure LAMP assays for accurate probe-based readout of SARS-CoV-2 by integrating OSD probes into individual and multiplex assays. The SARS-CoV-2 LAMP-OSD assays can be executed in one-pot reactions assembled using individual reverse transcription LAMP reagents, including with trivially produced cellular reagents. Moreover, these assays can be used to directly analyze crude human samples, such as saliva, to detect SARS-CoV-2 without interference from spurious signal. A few hundreds to a few tens of virion genomic RNA can be identified using individual or multiplex LAMP-OSD assays, respectively. We suggest that while LAMP-OSD may not have the same sensitivity as 'gold standard' RT-qPCR assays, that the versatility of LAMP-OSD, especially for resource poor settings with limited infrastructure, might prove useful for screening for positives, which could then be followed up with more limited or difficult to execute RT-qPCR tests.