CleanPlex SARS-CoV-2 NGS Panels Have Enabled Early Identification of New COVID Variants, including Delta and Omicron, in Patient Samples and Wastewater
New CleanPlex Emerging Variants Panel Add-on V2 Provides Additional Assurance of Accurate Variant Surveillance and Tracking. Covers All Characteristic Mutations in Omicron and Can Identify All Three Omicron Sub-lineages: BA.1, BA.2, and BA.3
Paragon Genomics, Inc., a leader in amplicon-based target enrichment solutions for next-generation sequencing (NGS) and precision medicine, today reported that its CleanPlex® SARS-CoV-2 Research and Surveillance Panels for viral detection, mutation analysis, variant tracking and epidemiological research have continued to play an important role in accurately identifying COVID-19 variants of interest and concern, including early identification of the Delta and Omicron variants in patient samples and in wastewater. The company also announced the release of its Emerging Variant Add-on V2 (EVAv2), an easy-to-use addition to its SARS-CoV-2 panels that provides optimized SARS-CoV-2 coverage for new and emerging variants. With its exceptional coverage and highest confidence variant calling, EVAv2 is designed to further enhance the already high performance of the CleanPlex SARS-CoV-2 panels.
“We are proud that from the early days of the pandemic two years ago Paragon Genomics has been a leader in enabling NGS-based identification of SARS-CoV-2 and its growing repertoire of variants,” noted Tao Chen, Chief Executive Officer of Paragon Genomics. “Our sequencing panels are designed to provide researchers with the ability to confidently detect and identify all major variants of interest and concern, and their utility has been confirmed both in silico and in clinical samples from our customers. The CleanPlex panels have been used by hundreds of laboratories around the world to track the virus and provide early warning of the presence of new variants.”
Mr. Chen continued, “We are pleased now to launch our Emerging Variant Add-on V2, which is optimized to ensure that recent variants are identified even under the most challenging conditions. Our CleanPlex panels have played an important role in the early community identification of variants, including one of the first confirmations of the Delta variant in Brazil, the first case of the Omicron variant in Italy, and in the pioneering wastewater analysis work of Dr. Edwin Oh at the University of Nevada Las Vegas, who first called out the presence of the Omicron variant in the Las Vegas region in early December. With the release of EVAv2, we are continuing to empower researchers to stay ahead of this rapidly evolving pandemic.”
The Emerging Variant Add-on V2 is an update and expansion of Paragon Genomics’ initial Emerging Variant Add-on Panel. It provides additional confidence in variant calling and includes added primers for enhanced coverage of critical variants, such as Alpha, Beta, Delta, Mu and Omicron. EVAv2 has been confirmed in silico to cover all defining and characteristic mutations of the sub-lineages of Omicron: BA.1, BA.2, and BA.3. It is optimized for identifying existing and new mutations for surveillance and tracking, maintaining even uniformity, confident calling of the defining mutations for each variant, and robust coverage even in the presence of mutations. EVAv2 has been designed for ease of use with existing CleanPlex SARS-CoV-2 whole genome sequencing panels and can be directly added to existing CleanPlex workflows with minimal additional time and effort required.
Paragon Genomics offers a number of SARS-CoV-2 NGS sequencing options: CleanPlex SARS-CoV-2 Original, FLEX, and EVAv2 panel designs. The CleanPlex Original and FLEX panels are both top performing panels designed for high coverage of the whole SARS-CoV-2 genome.
- CleanPlex SARS-CoV-2 Original Panel allows for the sequencing of the entire SARS-CoV-2 genome on Illumina, Ion Torrent, and MGI Tech sequencing platforms, and provides accurate nucleic acid-level information on the virus for strain-typing, mutation monitoring and epidemiological studies. It utilizes a tiled 2-pool design, with significant overlap built-in to allow for redundancy and to maintain robust coverage even if a few primers have been affected as the virus evolved.
- CleanPlex FLEX Panel contains additional proactive design elements added to the original panel for robust coverage as the virus mutates. The panel includes degeneracies in primers at highly polymorphic regions for additional confidence. The FLEX panel also includes a pair of Human RNA primers that serves as an internal library preparation quality control with negative samples.
- CleanPlex Emerging Variant Add-on V2 includes primers designed to supplement the CleanPlex SARS-CoV-2 panels to specifically address newly discovered mutations of interest that could benefit from additional coverage.
The CleanPlex SARS-CoV-2 portfolio also includes the CleanPlex Respiratory Virus Research Panel, combining assays for SARS-CoV-2, key influenza A subtypes, influenza B, and RSV A and B subtypes; and the CleanPlex ACE2 & TMPRSS2 Panel, a multiplex PCR-based targeted sequencing assay that assesses key human genetic factors affecting patient susceptibility to COVID-19 infection and the likely severity of illness.
CleanPlex SARS-CoV-2 Panels are powered by Paragon Genomics’ NGS Amplicon CleanPlex Technology, which uses a proprietary multiplex PCR background cleaning chemistry to effectively remove non-specific PCR products, resulting in best-in-class target enrichment performance and efficient use of sequencing reads.
For more information on Paragon Genomics’ coronavirus (SARS-CoV-2) whole genome sequencing via NGS for viral detection, tracking and surveillance, click here.
Paragon Genomics also offers CleanPlex® Custom NGS Panels that make it easy for researchers to build customized NGS assays addressing their specific needs. The ParagonDesigner™ online primer design portal features a streamlined, user-friendly interface that simplifies the assay design process. ParagonDesigner allows customers to build CleanPlex Custom NGS assays with just a few clicks of the mouse, and Paragon Genomics design experts are available to provide hands-on personalized support to ParagonDesigner customers. The company delivers custom NGS panels in about 4 weeks. The custom panels are powered by Paragon Genomics’ unique CleanPlex technology, an ultra-high multiplexed PCR-based target enrichment chemistry that makes it possible to include a large number of genomic targets in a single assay. In the past few years, Paragon Genomics has produced more than 700 custom NGS panels for more than 300 customers worldwide for research and testing applications ranging from tumor profiling, cancer liquid biopsy, pharmacogenomics, neurology, cardiology, infectious disease testing to food safety and agrigenomics.
CleanPlex SARS-CoV-2 panels are for Research Use Only. They are not intended for disease diagnosis.
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