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. Nucleus Biotech are proud to cooperate with Paragon Genomics who have developed amplicon panel based NGS kits for high throughput SARS-CoV-2 genomic surveillance, covering emerging variants such as the Omicron variant B.1.1.529 including its sublineages BA.1, BA.2, and BA.3, the Delta variant B.1.617.2, as well as Alpha V1, Beta V2, Gamma V3, and Mu.


CleanPlex SARS-CoV-2 FLEX Panel

  • Whole SARS-CoV-2 Genome Sequencing from RNA samples of Covid-19 positive patients even with very low viral loads
  • Degenerated PCR Primers, strategically designed for detection of new mutations incl. N501Y, del 69H/V70, L452R, P681R etc.
  • CleanPlex Technology– advanced PCR primer and background cleaning chemistry for extremely accurate variant calling at less sequencing costs
  • In Process Control: Human mRNA primers are included as library preparation control
  • New: SARS-CoV-2 Emerging Variant Panel Add-On V2: For enhanced coverage of newly discovered variants and their sub-lineages such as Omicron, Delta, Mu, Beta, and Alpha

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 even 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.

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. The technology inherits major advantages associated with traditional multiplex PCR-based methods while overcoming shortcomings such as PCR background noise, scalability (panel size), uniformity and limitation on detecting novel fusion genes. The schematic below shows the CleanPlex Technology workflow for SARS-CoV-2 samples:

SARS-CoV-2 related NGS Amplicon Panels

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.

CleanPlex® ACE2 & TMPRSS2 Panel:  Facilitates  investigations of host genome mutations related to the ACE2 binding affinity and the expression level of ACE2 and TMPRSS2.


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