Applied DNA Launches Linea 2.0 COVID-19 Assay Kit, As A Part Of Strategy Against Omicron SARS-CoV-2 Variant

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Linea COVID-19 Assay Kit Likely Subject to Unique Double S-Gene Target Drop, Allows Rapid Reflex Testing of Positive Samples without Sequencing to Confirm Probable Presence of Omicron

In response to the emergence of Omicron , a newly identified SARS-CoV-2 variant of concern, Applied DNA Sciences, Inc., a leader in Polymerase Chain Reaction (PCR)-based DNA manufacturing and nucleic acid-based technologies, today announced its COVID-19 diagnostic strategy. After submitting its validation data to the New York State Department of Health in the coming days, the Company plans to launch its LineaTM 2.0 COVID-19 Assay , a new RT-PCR assay for the SARS-CoV-2 E and N genes that builds on the Company’s established COVID-19 line of diagnostics.

The company also revealed that their EUA-approved LineaTM COVID-19 Assay Kit is anticipated to show a unique double S-gene target failure peculiar to the Omicron form. While the presence of the 69-70 mutation found in Omicron has been used to demonstrate the presence of SGTF in other assays, this mutation is seen in numerous SARS-CoV-2 lineages and is not unique to the novel variation. Based on preliminary study, Omicron believes that the mutations that generate the unique double SGTF in the Linea 1.0 Assay are unique to the company. When using the Linea 1.0 Assay as a primary diagnostic, this unusual double SGTF may result in false negative results in patients infected with the Omicron strain.

“Viruses evolve; it is in their nature. The potential need to evolve the Linea Assay 1.0 assay was anticipated and spurred the side-by-side development of our Linea SARS-CoV-2 Mutation Panel and the Linea 2.0 Assay to utilize the same testing workflows established for the Linea 1.0 Assay that brought high specificity, high sensitivity, and rapid time to results for population-scale testing. We continue to service our safeCircle clients with the Linea 1.0 Assay unless or until health officials indicate the presence of Omicron in our operating area, at which point we will transition to the Linea 2.0 Assay to provide seamless testing services to our customers. While viruses may evolve, ours is an unwavering commitment to providing gold-standard PCR-testing to meet the need for COVID-19 testing.” 

Dr. James A. Hayward, president and CEO of Applied DNA, stated.

However, because of this distinct pattern, the Linea 1.0 Assay may be able to give a high-specificity reflex test for the Omicron type. More specifically, because of the unique double SGTF, the Linea 1.0 Assay could be used as a reflex test to indicate the presence of Omicron in samples that have tested positive for COVID-19 via third-party assays that cannot discriminate for the new variant, the Linea 1.0 Assay could be used as a reflex test to indicate the presence of Omicron in samples that have tested positive for COVID-19 via third-party assays that cannot discriminate for the new variant.

In silico analysis of the mutations reflected in the Omicron variant’s genome sequences publicly available in GISAID (the online SARS-CoV-2 genome sequence database) reveals that the variant’s mutations have no effect on either of the Linea 2.0 Assay targets. Validation testing for the Linea 2.0 Assay has already been completed for both single sample and pooled testing. In the next few days, the company plans to submit its validation data to the NYSDOH as a Laboratory Developed Test (LDT). The validation data for the Linea 2.0 Assay reveal that the new assay’s performance is comparable to or better than that of the Linea 1.0 Assay.

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