Benzinga | May 26, 2021 08:07AM EDT

Applied DNA Sciences Reports Completion Of Technical Validation Of PCR-Based SARS-CoV-2 Mutation-Detection Panel

- Linea(tm) COVID-19 SGS(tm) Mutation Panel Can Identify 'Mutations of Therapeutic Concern' that May Lessen Response to Certain Therapies -

- As the Prelude to Whole Viral Genome Sequencing, Mutation Panel Empowers Pursuit of Specific Variant Lineages and Can Minimize Sequencing of Wild Type Virus -

- Company Initiates Development of New Assay to Characterize B.1.617 (Indian) Variant and Sub-Variants -

STONY BROOK, N.Y.--(BUSINESS WIRE)-- Applied DNA Sciences, Inc. (NASDAQ:APDN) (Applied DNA or the "Company"), a leader in Polymerase Chain Reaction (PCR)-based DNA manufacturing, today announced that it has competed technical validation of all seven Research Use Only (RUO) mutation detection assays contained in its Linea(tm) COVID-19 Selective Genomic Surveillance(tm) (SGS) Mutation Panel (the "SGS Panel") across 125 COVID-19 positive clinical samples known to include COVID-19 variants. The results showed 100% concordance when compared to the results of Whole Genome Sequencing (WGS) of the same samples (see table below for a listing of all mutation detection assays and currently associated Variants of Concern (VoC) or Variants of Interest (VoI)). The SGS Panel can be run in hours and can utilize the same extracted viral RNA that was used to obtain the original COVID-19 diagnosis. The SGS Panel will be available on a RUO basis and cannot be used for diagnostic purposes. Based on its successful technical validation, the Company plans to seek EUA-authorization for its SGS Panel.

The SGS Panel contains assays targeting seven different mutations, including the L452R and E484K mutations that have been designated by the Centers for Disease Control and Prevention (CDC) as 'Substitutions (mutations) of Therapeutic Concern' due to potential impacts on the efficacy of certain EUA-authorized antibody treatments1. One or both mutations are found in all current CDC-designated VoCs and VoIs, except the B.1.17 (UK variant) VoC. The inclusion of the L452R and E484K assays, together with the Company's WGS concordance data, validates the SGS Panel's ability to characterize all current CDC-designated VoCs and VoIs, excluding the B.1.1.7 VoC that can be detected via S-gene dropout by the Company's Linea COVID-19 Assay Kit.

In mutation surveillance studies utilizing 924 COVID-19 positive samples conducted by the Company with the SGS Panel, a combined L452R and E484K mutation frequency of 38% (12% and 26%, respectively) was found. These identified samples containing mutations of therapeutic concern should be subjected to WGS, as they have a higher probability of being a VoC or VoI as compared to samples that do not contain these mutations. The Company believes this rational selection of samples for WGS via the SGS Panel can be used to optimize the use of constrained Next Generation Sequencing (NGS) assets nationality, which currently do not provide capacity for widescale genomic surveillance via WGS. For context, for the 30 and 180 days ended May 24, 2021, the U.S. has sequenced and shared only 3.06%2 and 1.91%2 of all reported COVID-19 cases, respectively.

The Company is also undertaking the development of an assay to detect the E484Q mutation that, together with L452R, specifically characterize B.1.617, the Indian variant that was first detected in the U.S. in April 2021 and theorized to have increased transmissibility3 (up to 50%) over that of the UK variant, which itself is up to 45%3 more transmissible than SARS-CoV-2 Wild Type. The E484Q assay will be added to the SGS Panel upon validation.

"With fully half of the U.S. population yet to be vaccinated and the arrival of a potentially more transmissible SARS-CoV-2 Indian variant, this calls for more and not less surveillance and coordination of efforts to identify and characterize variants. We believe our SGS Panel gives Federal- and State-level public health officials the accurate, high-throughput mutational-surveillance tool they need to identify and act on variants quickly. Further, we believe it is a tool that allows for the rapid and inexpensive identification of the L452R and E484K mutations currently worrying the clinical community," said Dr. James A. Hayward, president and CEO of Applied DNA. "We are working diligently to seek EUA-authorization and elevate the capabilities and value proposition of our SGS Panel to federal and state public health authorities as an essential tool to stay ahead of the curve on all current and emerging variants."

The SGS Panel

The SGS Panel is a research use only (RUO) mutation-detection panel comprised of multiple qPCR assays that target the salient SARS-CoV-2 mutations known to characterize certain virus mutations. It was developed to detect specific mutations as a fast, cost-effective screening tool to focus the U.S. NGS capacity on the most impactful SARS-CoV-2 variants. The SGS Panel will be available on a RUO basis and cannot be used for diagnostic purposes.

Click here to learn more about the SGS Panel.

Mutations Identified by Linea COVID-19 Assay Kit and SGS Panel

MutationVariant 69-70del E484K N501Y P681H S477N L452R K417N

B.1.1.7 (UK) ? ? ?

B.1.617* (India) ?

B1.351 (S. Africa) ? ? ?

P.1 (Brazil) ? ?

P.2 (Brazil) ?

B.1.526 (NY) ? ?

B.1.526.1 (NY) ?

B.1.427/B.1.429 (CA) ?

* Includes all sub-variants