Applied DNA Completes Technical Validation of PCR-based SARS-CoV-2 Mutation-Detection Panel, Highlights Ability to Rapidly Identify Mutations and Probable VariantsPosted by On


STONY BROOK, N.Y.–()–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™ COVID-19 Selective Genomic Surveillance™ (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










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






About the Linea™ COVID-19 Assay Kit and the Linea™ COVID-19 Selective Genomic Surveillance™ (SGS) Mutation Panel

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 (BAL) specimens collected by a healthcare worker from individuals who are suspected of COVID-19 by their healthcare provider (HCP). 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 (CLIA) 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.

The Linea™ COVID-19 Selective Genomic Surveillance™ (SGS) Mutation Panel (the “SGS Panel”) is for Research Use Only (RUO) and shall not be used for clinical diagnostic purposes. The SGS Panel has not been approved or authorized to diagnose, ameliorate and/or detect any disease by any U.S. or international regulatory authority.

About Applied DNA Sciences

Applied DNA is commercializing LinearDNA™, its proprietary, large-scale polymerase chain reaction (“PCR”)-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 in the early stages of commercialization and is grounded in the Company’s deep 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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The Company’s common stock is listed on NASDAQ under ticker symbol ‘APDN,’ and its publicly traded warrants are listed on OTC under ticker symbol ‘APPDW.’

Applied DNA is a member of the Russell Microcap® Index.

Forward-Looking Statements

The statements made by Applied DNA in this press release may be “forward-looking” in nature within the meaning of Section 27A of the Securities Act of 1933, Section 21E of the Securities Exchange Act of 1934 and the Private Securities Litigation Reform Act of 1995. Forward-looking statements describe Applied DNA’s future plans, projections, strategies, and expectations, and are based on assumptions and involve a number of risks and uncertainties, many of which are beyond the control of Applied DNA. Actual results could differ materially from those projected due to its history of net losses, limited financial resources, limited market acceptance, the possibility that the assay kits could become obsolete or have its utility diminished, the possibility that the SGS Panel will never receive Emergency Use Authorization (EUA) approval from U.S. FDA, be commercialized or results in any revenues to Applied DNA, the uncertainties inherent in research and development, future clinical data and analysis, including whether any of Applied DNA’s or its partner’s diagnostic candidates will advance further in the preclinical research or clinical trial process, including receiving clearance from the U.S. Food and Drug Administration (U.S. FDA) or equivalent foreign regulatory agencies to conduct clinical trials and whether and when, if at all, they will receive final approval or authorization from the U.S. FDA or equivalent foreign regulatory agencies, the unknown outcome of any applications or requests to U.S. FDA, equivalent foreign regulatory agencies and/or the New York State Department of Health, the unknown limited duration of any Emergency Use Authorization (EUA) approval from U.S. FDA, changes in guidance promulgated by the CDC, U.S. FDA and/or CMS relating to COVID-19 surveillance and diagnostic testing, disruptions in the supply of raw materials and supplies, and various other factors detailed from time to time in Applied DNA’s SEC reports and filings, including our Annual Report on Form 10-K filed on December 17, 2020, and Quarterly Reports on Form 10-Q filed on February 11, 2021 and May 13, 2021, and other reports we file with the SEC, which are available at Applied DNA undertakes no obligation to update publicly any forward-looking statements to reflect new information, events or circumstances after the date hereof or to reflect the occurrence of unanticipated events, unless otherwise required by law.


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