Paragon Genomics NGS Panel Captures New SARS-CoV-2 Mutations

Paragon Genomics, Inc., a leader in amplicon-based target enrichment solutions for next-generation sequencing (NGS) and precision medicine, today announced a solution for capturing the new mutations of the SARS-CoV-2 variants that have been sweeping across the United Kingdom and South Africa, and already finding its way in various countries worldwide.

The new UK (20B/501Y.V1, VOC 202012/01, or B.1.1.7 lineage) and South African (20C/501Y.V2, or B.1.351 lineage) SARS-CoV-2 variants contain mutations in the receptor binding domain (RBD) of the spike protein, leading to concern and alarm worldwide. Several EU countries have issued travel bans within the UK in an effort to stop the new variant from spreading further. Officials in both the UK and South Africa have said that these mutations are driving the countries’ resurgence of the disease, with higher numbers of confirmed cases, hospitalizations and deaths.

These mutations in the spike protein have been shown to significantly increase infection rates, and may have further implications for the efficiency of the new vaccines and current test methods, confirming that a robust detection method and continued screening and surveillance are more critical than ever in our continued global efforts to control this pandemic.

The CleanPlex® SARS-CoV-2 FLEX Panel for full viral genome sequencing has been updated to specifically and confidently capture these new emerging mutations of this ever-evolving virus. The FLEX panel assay design covers the critical N501Y mutation and 69/70 deletion along with other mutations specific to these new variants. The FLEX panel is designed with the intention of evolving alongside the virus to support the front-end researchers and scientists in surveillance and monitoring efforts.

These new SARS-CoV-2 variants contain multiple spike protein mutations, including the N501Y mutation, one of six key contact residues within the Receptor-Binding Domain (RBD). This mutation has been shown to increase binding affinity of the virus to ACE2, the entry receptor for SARS-CoV-2 into human cells. Other mutations (especially the HV 69-70 deletion) have been shown to impact the efficacy of qPCR-based assays that specifically target the S protein. This inability to positively detect the virus leads to what is known as S-gene target failure (SGTF). This further confirms that qPCR-based assays, usually based on very few specific targets, can lead to false negative calls with the accumulation of SARS-CoV-2 mutations.

The FDA has identified the Mesa Biotech Accula SARS-CoV-2 Test, the Thermo Fisher Scientific TaqPath COVID-19 Combo Kit, and the Applied DNA Sciences Linea COVID-19 Assay Kit whose performance could be negatively affected by SARS-CoV-2 genetic variants. The agency put out a statement saying that local or state clinical laboratories with access to quick-turnaround whole-genome sequencing services should consider further characterizing the specimen with genetic sequencing when S gene dropout patterns appear.

A multi-target approach (such as Paragon’s CleanPlex multiplex PCR-based targeted amplification approach) ensures much more confident detection of viral infection.

“Sequencing and monitoring of new mutations are critical, as there could be important implications on not only detection accuracy, but also on vaccine efficacy,” said Paragon Genomics CEO, Tao Chen.

“The SARS-CoV-2 FLEX panel is built upon the original SARS-CoV-2 panel and contains additional critical design elements for detecting new mutations and variants over time. Specifically, this new panel contains degenerate primer designs of polymorphic regions of the SARS-CoV-2 genome to allow for more robust amplification of variable regions , thus improving coverage robustness for emerging variants.”

Paragon’s CleanPlex technology offers a variety of products for additional COVID-19 research such as in COVID-19 susceptibility through human ACE2 and TMPRSS2 complete sequencing, and common respiratory virus sequencing with the Respiratory Virus Research Panel that concurrently targets SARS-CoV-2, influenza A/B, and respiratory syncytial virus (RSV). The portfolio offers comprehensive solutions for confident SARS-CoV-2 detection, surveillance, and related research.

The team at Paragon Genomics has been vigilantly monitoring SARS-CoV-2 mutations since the initial emergence of this virus in late 2019 and will continue to stay on top of SARS-CoV-2 research progress to ensure that the best detection and surveillance solutions with robust coverage are provided to the scientific community worldwide.

For more information on Paragon Genomics’ CleanPlex SARS-CoV-2 Flex panel and other COVID-19 related products, check out

CleanPlex NGS panels are for Research Use Only. They are not intended for disease diagnosis.

About Paragon Genomics

Paragon Genomics ( is a leader in amplicon-based target enrichment and library preparation solutions to accelerate the development of next-generation sequencing (NGS)-based assays for research and clinical testing. The company designs and manufactures high performance and ultra-multiplexed amplicon NGS library preparation products for analyzing difficult, clinically relevant samples. It strives to be the NGS assay partner of choice for research and clinical NGS labs and to make custom NGS assays easily available to a broad range of users. Privately held Paragon Genomics is located in Hayward, California.

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