Analytical Sensitivity of the SalivaDirect™ Assay on the Liberty16 for detecting SARS-CoV-2 B.1.1.529 (“Omicron”)

The newly emerged Omicron variant of SARS-CoV-2 has numerous mutations that are not found in other variants of concern (VOCs). Despite acquiring extended functions in adapting to the host-cell environment, the viral genetic variation exerts a potential negative impact on a molecular test, which in turn, compromises public health and safety. The Liberty16 has been clinically validated as a flexible and accessible device system for running the affordable SalivaDirect™ real time PCR detection assay for SARS-CoV-2 especially in low resource settings. Preliminary, based on in-silico sequence analysis, we found that Omicron’s mutation at position 28,311 overlaps with the CDC 2019-nCoV_N1 probe binding region. In order to verify the performance of CDC 2019-nCoV-N1 primers-probe set in detecting the Omicron variant of SARS-CoV-2, plasmids containing Wuhan/WH01/2019 (wild-type) and B.1.1.529 (Omicron) sequences were serially diluted and subsequently directed for SalivaDirect™ RT-qPCR detection on Liberty16 using commercially procured reagents. Our findings provide analytical support for reports that the mutations in the Omicron variant have little or no impact on SalivaDirect™ assay in terms of amplification efficiency and detection sensitivity using either standard and the recently reported fast Liberty16 SalivaDirect™ thermal cycling protocols.