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SARS-CoV-2 Viral Genome NGS Testing

A highly sensitive targeted amplicon NGS solution facilitating comprehensive profiling of the SARS-CoV-2 genome

Complete genome characterization of SARS-CoV-2 is instrumental in the understanding of the COVID-19 pandemic. The emergence of variants of concern has placed a greater importance in monitoring changes to the SARS-CoV-2 genome through NGS. Gain a deeper understanding of underlying influences affecting vaccine and therapeutic efficacy by monitoring changes in the viral genome over time with our SARS-CoV-2 viral genome assay. We utilize the Ion Ampliseq SARS-CoV-2 Research Panel, a targeted amplicon sequencing chemistry, to provide complete genome coverage and accurate variant calling at low viral loads allowing for flexibility to a range of sample types. This panel consists of 2 primer pools providing redundant coverage minimizing any potential coverage dropout as a result of mutational changes in the viral genome. Using a comprehensive data analysis solution, we are able to deliver a complete SARS-CoV-2 viral genome sequence with accurate variant calling and informed annotation.


NGS Workflow


  Nasopharyngeal Swab
  • NGS assay designed to test wide range of viral loads
  • On-going development expanding acceptable sample types
  Viral Load Quantitation
  • Quantitative SARS-CoV-2 Viral Load Assay
  • NGS Library optimized based on viral load  
  Viral RNA Isolation
  • High-Throughput Automated Isolation
  • Magnetic bead based viral RNA isolation protocol
  Ion Genestudio S5 Sequencing
  • High-Throughput Ion AmpliSeq Technology
  • Complete viral genome coverage with great sensitivity



Thermo Fisher Ion Ampliseq SARS-CoV-2 Research Panel

Reference sequence: MN908947.3

Covers >99% of the SARS-CoV-2 genome, all serotypes included

100% Accuracy and Sensitivity for SNVs and Indels above LoD

Data Deliverables:

  • Assembled SAR-CoV-2 Viral Genome (FASTA)
  • Variant Calls against viral reference genome (VCF)
  • Annotated Variants (TSV)

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