Paragon Genomics expands portfolio of CleanPlex SARS-CoV-2-related NGS tests

Paragon Genomics, Inc., a leader in amplicon-based target enrichment solutions for next-generation sequencing (NGS) and precision medicine, has announced the introduction of new coronavirus related CleanPlex^® NGS tests. They include the new 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. The new CleanPlex SARS-CoV-2 FLEX Research Panel provides extra assurance of accurate mutation detection and genome coverage as the SARS-CoV-2 virus continues to mutate. These new panels expand on the capabilities of the CleanPlex SARS-CoV-2 Research and Surveillance Panel, which has achieved broad global use since its introduction earlier this year. This panel allows for the sequencing of the entire SARS-CoV-2 genome and enables researchers to obtain accurate nucleic acid-level information on the virus for strain-typing, mutation monitoring and other epidemiological studies.

The CleanPlex ACE2 & TMPRSS2 Panel focuses on identifying genetic mutations in patients that are related to disease susceptibility and severity. It targets genes affecting the binding affinity and expression of angiotensin-converting enzyme 2 (ACE2) and Transmembrane Serine Protease 2 (TMPRSS2), which play critical roles in helping the COVID-19 virus enter into patients’ cells and thereby affect susceptibility to infection and likely disease severity. The CleanPlex ACE2 & TMPRSS2 Panel interrogates the entire coding region of ACE2 and TMPRSS2, along with more than 70 curated unique quantitative trait loci (eQTL) shown to regulate their expression. It uses CleanPlex technology’s simple, 3-step, 3-hour workflow to generate high-quality, enriched NGS libraries for sequencing on all major platforms. High uniformity and on-target rates allow confident variant calling for genotyping with minimum reads.

The CleanPlex SARS-CoV-2 FLEX Research Panel proactively anticipates increases in SARS-CoV-2 viral mutations and is designed to provide extra assurance that mutation detection and genome coverage remain optimal. The core CleanPlex SARS-CoV-2 Research and Surveillance Panel’s high coverage of target regions is explicitly intended to ensure sensitive detection in the presence of mutations, but the new FLEX panel goes even further, specifically focusing on variant analysis and tracking of mutations over time. It includes strategically designed degenerate primers and human RNA primer controls for more confident negative sample calling, especially when viral copies are not present or are at extremely low counts. Together, the additional components of the FLEX panel give coronavirus researchers added confidence in the accuracy of their results as viral mutations increase.

Paragon Genomics also announced that in anticipation of the upcoming flu season, next week it will release an early access edition of the CleanPlex Respiratory Research Panel combining assays for SARS-CoV-2, influenza A subtypes H1N1, H1N2, H3N2, and influenza B. Compared to other flu panels, the CleanPlex panel contains significantly more targets, strategically selected to cover characteristic regions of each viral segment for highly confident viral RNA detection and identification. This combination panel allows concurrent influenza detection along with detection or whole genome sequencing of SARS-CoV-2. The extra sensitivity and additional coverage of this multiplex-PCR based method is also suitable for high throughput sample pooling and screening strategies. The company expects to expand the panel to include respiratory syncytial virus and potentially other respiratory viruses going forward.

Lastly, Paragon Genomics is introducing new plated 384 Unique Dual-Indexed (UDI) PCR Primers for Illumina sequencing of CleanPlex SARS-CoV-2 NGS panels. These will allow additional multiplexing capability enabling researchers to run up to 3072 CleanPlex sequencing samples simultaneously on Illumina NovaSeq instruments, enabling higher throughput workflows.

Dr. Xiaowu Gai, Director of Bioinformatics at the Center for Personalized Medicine in the Department of Pathology and Laboratory Medicine at Children's Hospital Los Angeles, and Associate Professor of Clinical Pathology at the Keck School of Medicine at the University of Southern California, said, “I was very impressed by how well the CleanPlex SARS-CoV-2 panel worked when we evaluated it back in March. Working with Paragon Genomics, we were able to leverage the panel to quickly launch a SARS-CoV-2 whole-genome sequencing assay and used it effectively for a number of genomic epidemiology studies.”

Dr. Gai continued, “As a human geneticist and informaticist, I am also excited about the availability of the CleanPlex ACE2/TMPRSS2 germline + eQTL panel. We have sequenced thousands of positive COVID 19 samples, which revealed a tremendous amount of viral genetic diversity. It is therefore most interesting now to study the host genetic variants, especially in the ACE2 and TMPRSS2 genes that are the two most essential genes for SARS-CoV-2 infection. The interplay of human host genetic variants in these genes, along with the SARS-CoV-2 mutations and haplotypes, may well determine how severe the infection is and the resulting clinical phenotypes.”

Paragon Genomics CEO Tao Chen commented, “Building on the global success of our core CleanPlex SARS-CoV-2 research and surveillance panel, we are pleased to introduce important new panels for patient susceptibility assessments, for ensuring coverage of new viral mutations, and for simultaneous testing for SARS-CoV-2 and influenza. The speed, accuracy and data-rich output of our targeted amplicon sequencing technology have proven to be very valuable for researchers, who also appreciate its ease of use and cost effectiveness of the CleanPlex panels. We applaud the innovative spirit and hard work of the entire Paragon Genomics team that is enabling us to deliver a growing portfolio of advanced research tools to combat the worldwide threat posed by COVID-19.”

The CleanPlex RNA four-step workflow converts viral RNA into sequencing-ready libraries in just five hours. It is powered by Paragon Genomics’ proprietary, ultra-high multiplexed NGS target enrichment technology featuring an innovative PCR background cleaning chemistry that allows tens of thousands of amplicons to be multiplexed in a single reaction pool, allowing a large number of targets to be interrogated in a single assay and resulting in best-in-class target enrichment performance and efficient use of sequencing reads.

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