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Omicron

A lot is still unknown about the Omicron variant - how transmissible it is, what level of disease severity it causes, and how much protection previous infection of COVID-19 or vaccination offer. This uncertainty reaffirms the importance of testing as a means to control the spread of SARS-CoV-2 and prevent future variants from emerging.
Will the SalivaDirect™ test detect Omicron?
The mutation seen in Omicron, which falls in the region targeted by the N1 probe, is the mutation seen in the earlier Lambda variant that is successfully identified using the CDC’s N1 assay. Nevertheless, we are staying on top of all the latest developments. This includes working with the FDA and our suppliers as well as closely monitoring sequences shared on GISAID and Rosalind. Should there be a need to expand the test, we have an updated protocol waiting in the wings that can be quickly implemented.

We would like to thank NEB for testing the SalivaDirect™ assay on synthetic RNA of the Omicron variant, as well as in comparison to detection with N2 and demonstrating no loss in assay sensitivity. More information about NEB’s findings can in this MedRxiv publication.

To ensure all tests for SARS-CoV-2 remain effective in detecting Omicron, the FDA required EUA holders that utilize a single target, including SalivaDirect™, to confirm their test efficacy through in-vitro verification. In response, the SalivaDirect™ lab team evaluated the detection of SARS-CoV-2 RNA from Omicron-confirmed samples as targeted using N1, N2, and E primers and probes. Through this validation we found comparable detection of all targets, indicating that despite this mutation, detection with N1 remains unaffected. Subsequently, to confirm the continued sensitivity of SalivaDirect™, we tested Omicron-confirmed samples spiked into negative saliva and performed an LOD range finding study, with spiked samples tested through the full SalivaDirect™ protocol. Using 20 replicates at the preliminary LOD, we confirmed that SalivaDirect™ detects the Omicron variant with the same sensitivity as previous variants.
What target does the SalivaDirect™ test look for?
When developing SalivaDirect™, we chose the CDC's N1 target due to how widely used it is in SARS-CoV-2 detection assays. During development, we found that through targeting only one gene this allowed us to achieve a higher level of sensitivity of detection as compared to when assays add multiple gene targets. With development starting early in the pandemic, we wanted to insure there were as few false-negative results as possible so sensitivity was important to us. From the start, we have been aware of the risk that comes from targeting one gene so we keep a close eye on emerging variants and any mutations that may affect the SalivaDirect™ assay. Moreover, through the course of the pandemic we have worked to develop a multiplex SalivaDirect™ assay, should there arise a need to expand beyond the single N1 gene, we will deploy the multiplex test that is currently on standby.
Looking for more information about Omicron?
Visit the CDC’s Omicron Variant page for the latest updates.
Interested in asking a specific question?
Contact us at info@salivadirect.org

Important Regulatory Information about SalivaDirect™

SalivaDirect™has not been FDA cleared or approved. It has been authorized by the FDA under an emergency use authorization for use by authorized laboratories. The test has been authorized only for the detection of nucleic acid from SARS-CoV-2, not for any other viruses or pathogens. This test is only authorized for the duration of the declaration that circumstances exist justifying the authorization of emergency use of in vitro diagnostic tests for detection and/or diagnosis of COVID-19 under Section 564(b)(1) of the Act, 21 U.S.C. § 360bbb-3(b)(1), unless the authorization is terminated or revoked sooner.