Research & Development
Applied DNA Forms Strategy to Address Omicron SARS-CoV-2 Variant, Introduces Linea 2.0 COVID-19 Assay Kit
29 November 2021 - - US-based DNA manufacturing and nucleic acid-based technologies provider Applied DNA Sciences, Inc. (NASDAQ: APDN) has 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 said it plans to introduce its Linea 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, 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 likely exhibits a unique double S-gene target failure 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 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.

The Linea COVID-19 Assay Kit is a real-time RT-PCR test intended for the qualitative detection of nucleic acid from SARS-CoV-2 in respiratory specimens, including anterior nasal swabs, self-collected at a healthcare location or collected by a healthcare worker, and nasopharyngeal and oropharyngeal swabs, mid-turbinate nasal swabs, nasopharyngeal washes/aspirates or nasal aspirates, and bronchoalveolar lavage specimens collected by a healthcare worker from individuals who are suspected of COVID-19 by their healthcare provider.

The test is also intended for use with anterior nasal swab specimens that are self-collected in the presence of an HCP from individuals without symptoms or other reasons to suspect COVID-19 when tested at least weekly and with no more than 168 hours between serially collected specimens.

The scope of the Linea COVID-19 Assay Kit EUA, as amended, is expressly limited to use consistent with the Instructions for Use by authorized laboratories, certified under the Clinical Laboratory Improvement Amendments of 1988 to perform high complexity tests.

The EUA will be effective until the declaration that circumstances exist justifying the authorization of the emergency use of in vitro diagnostics for detection and/or diagnosis of COVID-19 is terminated or until the EUA's prior termination or revocation.

The diagnostic kit has not been FDA cleared or approved, and the EUA's limited authorization is only for the detection of nucleic acid from SARS-CoV-2, not for any other viruses or pathogens.

Applied DNA is commercializing LinearDNA, its proprietary, large-scale polymerase chain reaction-based manufacturing platform that allows for the large-scale production of specific DNA sequences.

The LinearDNA platform has utility in the nucleic acid-based in vitro diagnostics and preclinical nucleic acid-based drug development and manufacturing market.

The platform is used to manufacture DNA for customers as components of in vitro diagnostic tests and for preclinical nucleic acid-based drug development in the fields of adoptive cell therapies (CAR T and TCR therapies), DNA vaccines (anti-viral and cancer), RNA therapies, clustered regularly interspaced short palindromic repeats (CRISPR) based therapies, and gene therapies.

Applied DNA has also established a COVID-19 diagnostic and testing offering that is grounded in the company's expertise in DNA.

The LinearDNA platform also has non-biologic applications, such as supply chain security, anti-counterfeiting, and anti-theft technology. Key end-markets include Gov/Mil, textiles, pharmaceuticals and nutraceuticals, and cannabis, among others.
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