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

Nucleus Biotech are proud to cooperate with Paragon Genomics who have developed amplicon panel based NGS kits to support SARS-CoV-2, Influenza and RSV research.

Paragon Genomics released CleanPlex SARS-CoV-2 Research and Surveillance Kit in early 2020 for ultra-sensitive detection and complete genomic sequencing of the SARS-CoV-2 virus responsible for the COVID-19 pandemic. Throughout flu season, there is a need for assaying common respiratory viruses concurrently. The CleanPlex Respiratory Virus Research Kit combines the original SARS-CoV-2 whole-genome sequencing with expertly designed primers specific to influenza A subtypes H1N1, H1N2, H3N2, influenza B, and respiratory syncytial virus (RSV) A&B.

CleanPlex SARS-CoV-2 FLEX Panel

This kit offers sensitive detection and robust characterisation of the whole genome of the SARS-CoV-2 virus for mutation analysis, wastewater surveillance and public health research. SARS-CoV-2 Emerging Variants Add-on operates as an easy spike-in panel to maintain even coverage and confident identification of the defining mutations of variants of Omicron includingBA.2.12.1, BA.3,  BA.4 and BA.5, the Delta variant B.1.617.2, as well as Alpha V1, Beta V2, Gamma V3, and Mu.


  • 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

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.

CleanPlex® Respiratory Virus Research Panel

This kit 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. It detects multiple viral pathogens to not only allow for differentiation of the respiratory tract viruses but also enables sub-typing and strain information for mutation analysis.


  • Strategically Designed Content: RSV and Influenza subtype detection and complete SARS-CoV-2 genome sequencing
  • Ultra-sensitive Detection: Multiplex PCR based amplification for sensitive detection
  • Fast and Streamlined Workflow: Generate sequencing-ready libraries in just 6 hours using a rapid, four-step protocol from extracted RNA to sequence ready libraries

Learn more about how this technology has enabled researchers like Dr. Edwin Oh to discover new vaccine-resistant variants in influenza H3N2 (3C.2a1b.2a.2 subclade) circulating in elementary school wastewater with >80% coverage at 100X depth. The Respiratory Virus Research Panel has aided these early warning wastewater surveillance programs to monitor viruses like SARS-CoV-2, Influenza, MPX, and more. Please see full presentation as showcased at AMP2022.

SARS-CoV-2 related NGS Amplicon Panel
CleanPlex® ACE2 & TMPRSS2 Panel:  Facilitates  investigations of host genome mutations related to the ACE2 binding affinity and the expression level of ACE2 and TMPRSS2.

All respiratory research 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. T


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