Applied DNA Announces Strategy to Address Omicron SARS-CoV-2 Variant, Introduces Linea 2.0 COVID-19 Assay Kit

Applied DNA Sciences, Inc. (NASDAQ: APDN) (Applied DNA or the “Company”), a leader in Polymerase Chain Reaction (PCR)-based DNA manufacturing and nucleic acid-based technologies, today announced its COVID-19 diagnostic strategy in response to the emergence of Omicron (B.1.1.529), a newly identified SARS-CoV-2 variant of concern. The Company plans to introduce its Linea 2.0 COVID-19 Assay (“Linea 2.0”), 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, after submission of its validation data to the New York State Department of Health (NYSDOH) in the next few days.

The Company also announced that its EUA-authorized Linea COVID-19 Assay Kit (the “Linea 1.0 Assay”) likely exhibits a unique double S-gene target failure (or “drop”) (SGTF) specific to the Omicron variant. While other assays have been shown to have SGTF based on the presence of the Δ69-70 mutation contained in Omicron, this specific mutation is shared across several SARS-CoV-2 lineages and is not specific to the new variant. Based on the Company’s initial analysis, the Company believes that the combination of mutations that cause the unique double SGTF in the Linea 1.0 Assay is unique to Omicron. This unique double SGTF may result in false negative results in patients infected with the Omicron variant when tested with the Linea 1.0 Assay as a primary diagnostic. This unique pattern may, however, allow the Linea 1.0 Assay to provide a high-specificity reflex test for the Omicron variant. More specifically, the Linea 1.0 Assay may be potentially 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 because these same samples will test negative on the Linea 1.0 Assay due to the unique double SGTF.

Analysis in silico of the mutations represented in the Omicron variant’s genome sequences publicly available in GISAID (the online SARS-CoV-2 genome sequence database) shows that neither of the Linea 2.0 Assay targets are affected by the variant’s mutations. Validation testing for the Linea 2.0 Assay for both single sample and pooled testing is already complete. The Company intends to submit its validation data as a Laboratory Developed Test (LDT) to the NYSDOH in the next few days. The validation data for the Linea 2.0 Assay show the performance of the new assay meets or exceeds the performance of the Linea 1.0 Assay.