New publications confirm Paragon Genomics CleanPlex SARS-CoV-2 Panel enables accurate identification of variants of concern

Paragon Genomics, Inc., a leader in amplicon-based target enrichment solutions for next-generation sequencing (NGS) and precision medicine, today reported publication of three scientific studies confirming that its CleanPlex^® SARS-CoV-2 Research and Surveillance Panel for viral detection, mutation analysis, variant tracking and epidemiological research accurately identifies important COVID-19 variants, such as the B.1.1.7 Alpha variant and the B.1.617.2 Delta variant, major variants of concern that have been implicated in surges of COVID-19 infections worldwide.

The accuracy of the CleanPlex technology and its utility for variant detection and surveillance, including identification of individual viral mutations, have contributed to its adoption by hundreds of laboratories around the globe in the past 18 months.

A Brazilian study from researchers at the Federal University of Rio Grande do Sul and Hospital de Clínicas de Porto Alegre published in the journal Eurosurveillance examines the association between the emergence of the SARS-CoV-2 P.1 lineage, or Gamma variant, in the northern region of Brazil and subsequent rapid growth in hospitalizations. Whole-genome sequencing of patient specimens was performed using the CleanPlex SARS-CoV-2 Panel. The data revealed that the previously undetected P.1 lineage accounted for 89% of specimens collected from patients at a referral COVID-19 hospital. These findings raised awareness of a possible association between the P.1 lineage and rapid growth in cases and hospitalizations in the region.

A retrospective study from researchers at the University of Sassari and Sassari University Hospital in Italy investigated the spread in northern Italy of B.1.1.7, a SARS–CoV–2 variant of concern originally identified in the UK. They performed whole genome sequencing using the CleanPlex SARS-CoV-2 Panel to confirm inconclusive RT-PCR results. The analyses enabled the researchers to assign the viral genomes to SARS-CoV-2 lineages and confirm the presence of the B.1.1.7 variant. The CleanPlex panel was able to identify the characteristic mutations along the whole SARS-CoV-2 viral genome, including mutations in the S gene encoding for the spike protein.

A third study, from a Paragon Genomics public health laboratory customer, describes how the CleanPlex SARS-CoV-2 Panel enabled the early identification of one of the first confirmed cases of the B.1.617.2 Delta variant in Brazil. The study traced how the Delta variant was brought into the country by sailors on a ship of Asian origin that docked at a Brazilian port, helping to establish the route of transmission into the country. The Delta variant in particular has sparked concern worldwide due to its increased transmissibility and its potential to cause more severe disease, to render some treatments for COVID-19 infections less effective and to reduce the protection provided by some vaccines. It has emerged as the predominant form of COVID-19 infections in many countries, including India, the UK and the US.

Paragon Genomics CEO Tao Chen commented, “These new studies confirm the importance of sequencing for COVID-19 detection and surveillance and reinforce what we have been hearing from our customers—our CleanPlex products for COVID-19 surveillance and research are important contributors to efforts to track and contain the pandemic in countries around the globe. The speed and data-rich output of our targeted amplicon sequencing technology offer unsurpassed accuracy along with ease of use and cost-effectiveness.

Mr. Chen continued, “As the SARS-CoV-2 virus mutates, using sequencing to accurately identify variants is critical for informed monitoring and prevention. The ongoing emergence of new variants of concern and novel escape mutations make accurate genotyping more important than ever, and we are proud of our contribution to these efforts.”

Paragon Genomics’ CleanPlex SARS-CoV-2 technology has powered variant detection and tracking since the virus first appeared. The CleanPlex technology offers unique chemistries that generate top quality libraries for sequencing. The panels offer high genome coverage with high sensitivity, even with degraded or low copy number samples. Their high on-target rate and uniformity of amplification also provide cost-efficient sequencing.

In March 2020, the company launched the CleanPlex SARS-CoV-2 Panel whole-genome SARS-CoV-2 sequencing on Illumina and MGI Tech sequencing platforms. This panel allows for the sequencing of the entire SARS-CoV-2 genome and provides accurate nucleic acid-level information on the virus for strain-typing, mutation monitoring, and epidemiological studies.

The CleanPlex SARS-CoV-2 portfolio also includes the CleanPlex SARS-CoV-2 FLEX Panel, which proactively anticipates increases in SARS-CoV-2 viral mutations and is designed to provide assurance that mutation detection and genome coverage remain optimal as the virus mutates; 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’ 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.

CleanPlex SARS-CoV-2 panels are for Research Use Only. They are not intended for disease diagnosis.

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