SARS-CoV-2 and Influenza/RSV NGS Amplicon Panels

Full-genome sequencing is a critical tool in understanding the emerging SARS-CoV-2 virus. Next-Generation Sequencing (NGS) enables to track COVID-19 transmission and viral mutations, inform testing protocols and infection control measures, and guide vaccine and therapeutics development.

SARS-CoV-2 related NGS Amplicon Panels

Paragon Genomics developed the CleanPlex SARS-CoV-2 FLEX Panel containing strategically designed degenerate primers as a preemptive effort to ensure confident mutation detection and genome coverage even as the virus mutates. The Flex panel already covers the critical N501Y mutation along with other novel mutations being discovered. These mutations in the spike protein have shown significant higher infection rates, and have further implications for the efficacy of the new vaccines, confirming that continued surveillance is ever more critical in our continued global efforts to control this pandemic.

The FLEX Panel is based on the original CleanPlex SARS-CoV-2 Panel developed for sequencing the whole genome of SARS-CoV-2 from samples with very low SARS-CoV-2 viral content. Panel design is based on the SARS-CoV-2 sequence NC_045512.2.  Primers were optimized to preferentially amplify the SARS-CoV-2 cDNA versus the background human cDNA or DNA. They were also optimized to uniformly amplify the covered genome. This expertly designed panel allows for the interrogation of the entire viral sequence with as little as 200,000 sequencing reads per samples.

Especially in the flu season, there is a need for assaying common respiratory viruses concurrently. The CleanPlex® Respiratory Virus Research Panel combines the SARS-CoV-2 whole-genome sequencing panel with expertly selected primers specific to influenza A subtypes H1N1, H1N2, H3N2, influenza B, and respiratory syncytial virus (RSV) A&B.

Research has shown that SARS-CoV-2 virus is internalized by the binding of its S protein to the host ACE2 receptor with the help of TMPRSS2 cell surface protein. The binding affinity of ACE2, along with ACE2 and TMPRSS2 expression levels, are major determinants of SARS-CoV-2 replication rate and disease severity. Due to this, Paragon Genomics launched CleanPlex® ACE2 & TMPRSS2 Panel to facilitate further investigations in host genome mutations related to the ACE2 binding affinity and expression of ACE2 and TMPRSS2.


All SARS-CoV-2 related panels from Paragon Genomics are based on their proprietary CleanPlex technology which is superior to other amplicon panels or approaches such as hybridization capture based enrichment or metagenomic sequencing.


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