Fast, automated, and accurate targeted NGS workflow for SARS-CoV-2 research

Where did the SARS-CoV-2 virus come from?
How does the virus work?
How is it potentially being transmitted?

These are common questions in epidemiology and virology research. In the race against time, a complete, accurate, and easy-to-use solution is necessary to quickly get you to the answers you need.

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Ion Torrent targeted next-generation sequencing (NGS) technology enables a streamlined research workflow for complete viral genome sequencing and variant detection for epidemiological studies of SARS-CoV-2.

The Ion AmpliSeq SARS-CoV-2 Research Panel consists of two pools with amplicons ranging from 125 bp to 275 bp in length and covers >99% of the SARS-CoV-2 genome, including all serotypes. The assay is part of a fast, automated, and accurate targeted NGS workflow that enables coronavirus typing in under a day. This end-to-end solution includes the assay and plug-in suite that was developed in collaboration with researchers at the forefront of the SARS-CoV-2 crisis. Our complementary targeted NGS systems makes SARS-COV-2 epidemiology research accessible to any lab, regardless of your team’s current level of NGS expertise.

Learn about importance of targeted NGS for emerging research applications in SARS-CoV-2 epidemiology and transmission studies

Benefits of using Ion Torrent NGS for SARS-CoV-2 research:

  • Rapid turnaround time
  • Highly automated NGS workflow—for easier adoption, lower user intervention, and improved lab efficiency
  • Accuracy of variants—lower substitution errors for SNVs
  • Higher success rates—analyze samples directly with lower viral loads (as low as 20 copies)

The panel can be used for the following types of research applications:

  • Viral identification and lifecycle
  • Viral genome sequencing
  • Viral surveillance and epidemiology research

Webinar: SARS-CoV-2 Research: Implications of Viral Sequencing—The Children's Hospital Los Angeles Experience


In this webinar, Dr. Timothy J. Triche MD, PhD, Co-Director of Center for Personalized Medicine at Children’s Hospital Los Angeles​ (CHLA), shares how he and his team used sequencing data generated from the Ion AmpliSeq SARS-CoV-2 Research Panel to analyze phylogenetic relationships among a cluster of six SARS-CoV-2-positive samples. By identifying two distinct lineages between the two sets, the team was able to conclude that the source of transmission wasn’t shared. Comparative analysis showed that, not unexpectedly, the mother and son had nearly identical strains of the virus that originated in Utah, with links to Europe, while the four health care workers had strains only distantly related to each other and to the family. This confirmed that there was no transmission between the patient family and the health care workers. Further, the health care workers acquired the virus from community spread and not from the patient and family member. "The NGS sequence data permitted Children's Hospital Los Angeles to draw conclusions within 48 hours of sample procurement from the six individuals. This information gave leaders at our institution greater confidence in our ability to provide a safe environment for our patients and our team members."

Additional topics include: Ion AmpliSeq panel workflow, uniformity and coverage performance, limit of detection and sensitivity metrics, and integrated analysis pipelines.

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Read the case study: Beyond emergency testing: staying ahead of SARS-CoV-2 with NGS to help disrupt the current trajectory ›

Targeted NGS workflow for the Ion AmpliSeq SARS-CoV-2 Research Panel


Complementary Ion Torrent NGS systems for SARS-CoV-2 research


Ion GeneStudio S5 Series

 Scalable, targeted NGS workhorse with wide application breadth and throughput capability 

Learn more about SARS-CoV-2 research using the GeneStudio S5 Series System ›

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Ion Torrent Genexus Integrated Sequencer

Go from nucleic acid to report in a single day with a hands-off, automated workflow*

Learn more about SARS-CoV-2 research using the Genexus System ›

Request project costs