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Rapid, automated NGS solution to survey the complete SARS-CoV-2 genome for epidemiological investigation

A major challenge for microbiologists and virologists is the prediction of patterns of evolution and emergence of disease agents. RNA viruses like coronaviruses share the biological feature of high genetic variability, which causes them to appear as clouds of mutants. Coronavirus variants also emerge through antigenic shift within animal reservoirs, such as bats, snakes, pangolins.

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Read case study: Children's Hospital Los Angeles goes beyond emergency testing: staying ahead of SARS-CoV-2 with NGS to help disrupt the current trajectory ›

Ion Torrent targeted next-generation sequencing (NGS) enables a streamlined research workflow for complete genome sequencing and epidemiological studies of SARS-CoV-2 (the coronavirus responsible for COVID-19). Through the use of a set of highly specific, universal coronavirus primers in combination with a high-fidelity master mix, all genomic segments are amplified, sequenced, and analyzed in an automated workflow on the Ion Torrent Genexus Integrated Sequencer. This new NGS solution enables you to rapidly go from nucleic acid to variant report in under a single day with minimal hands-on time.

The Ion AmpliSeq SARS-CoV-2 Insight Research Assay consists of two pools with amplicons 125–275 bp in length for complete coverage of over 99% of the viral genome and variants.

Benefits of Ion AmpliSeq SARS-CoV-2 Insight Research Assay for the Genexus Integrated Sequencer include:

  • Rapid turnaround time—our fastest NGS workflow for infectious disease research for critically time sensitive applications
  • Automation—hands-off, setup-and-go workflowenables minimal user touchpoints, lowering user variability and increasing reproducibility of results
  • Accuracy of variants—lower substitution errors for SNVs
  • Higher success rates—analyze samples directly with low viral loads 
  • Higher-resolution and longer-read NGS—accurate and rapid viral typing for viral surveillance and epidemiology investigation

Application note


Workflow and performance of the Ion AmpliSeq SARS-CoV-2 Insight Research Assay on the Genexus Integrated Sequencer

Targeted NGS workflow for Ion AmpliSeq SARS-CoV-2 Insight Research Assay on the Genexus Integrated Sequencer

Figure 1. A typical workflow for analyzing 16 samples using the Ion AmpliSeq SARS-CoV-2 panel on the Genexus Integrated Sequencer, featuring rapid NGS automation.

Ordering information

Ion AmpliSeq SARS-CoV-2 Insight Research Assay - GX

This assay is compatible with the Genexus Integrated Sequencer, which performs library preparation, sequencing, analysis, and reporting in an automated sample-to-result workflow


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The content provided herein may relate to products that have not been fully validated by Thermo Fisher Scientific.

For Research Use Only. Not for use in diagnostic procedures.