One assay surveying 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 SARS-CoV-2 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 and snakes.

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Ion Torrent targeted next-generation sequencing (NGS) enables a streamlined research workflow for complete genome sequencing and epidemiological studies of SARS-CoV-2. 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 and the DNA amplicons are sequenced on any Ion Torrent system to deliver highly accurate coronavirus typing in under a day.

The Ion AmpliSeq SARS-CoV-2 Insight Research Assay consists of 2 pools with amplicons ranging from 125–275 bp in length for complete coverage of over 99% of the viral genome and variants. This assay is part of an end-to-end solution, including a plug-in suite developed in collaboration with scientists at the forefront of the SARS-CoV-2 crisis.

Benefits of using Ion Torrent NGS include:

  • Fast turnaround time—get sequencing data in as little as 2.5 hours
  • Fewer operator introduced errors with automated workflow—~45 minutes of hands on time
  • Accuracy of variants—lower substitution errors for SNVs
  • Higher success rates—analyze samples directlywith viral loads as low as 20 copies

White paper


White Paper: SARS-CoV-2 research applications using the Ion GeneStudio S5 system

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."

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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 Ion AmpliSeq SARS-CoV-2 Insight Research Assay

Targeted next-generation sequencing (NGS) workflow for Ion AmpliSeq™ Coronavirus Research Panel
Figure 1. Ion AmpliSeq workflow. Ion AmpliSeq libraries are prepared manually or with the Ion Chef System. Libraries are then placed in the Ion Chef System for emulsion PCR, enrichment, and loading onto Ion S5 chips.

In addition to targeted sequencing, which covers >99% of the viral genome and variants, Ion Torrent systems can be used for de novo (whole genome) sequencing of SARS-CoV-2 by NGS .

Selecting the right chip

Up to 80 samples can be multiplexed on a single Ion 540 Chip:

Number of samples
(1M reads per sample)


2–3 samples
Ion 510 Chip
4–6 samples
Ion 520 Chip
15–20 samples
Ion 530 Chip
60–80 samples
Ion 540 Chip

Ion SARS-CoV-2 Research Plug-in Package

Annotate variants, build consensus sequences, and construct de novo sequences for SARS-CoV-2 samples

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Torrent Suite Software

Perform basecalling and alignment for single samples, run plugins for secondary analysis and easily manage your NGS data

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Ion AmpliSeq Designer

Design on demand with ease and order Ion AmpliSeq research panels focused on your genes and organisms of interest

Visit Ion AmpliSeq Designer ›

For assay ordering information, select from the table below.

Ion AmpliSeq SARS-CoV-2 Insight Research Assay GS, manual

Consists of the Ion AmpliSeq SARS-CoV-2 Insight Research Panel and  Ion AmpliSeq Library Kit Plus reagents for those performing manual library preparation


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Ion AmpliSeq SARS-CoV-2 Insight Research Assay GS, Chef-ready

Consists of the Ion AmpliSeq SARS-CoV-2 Insight Research Panel and the Ion AmpliSeq Kit for Chef DL8 for those utilizing the Ion Chef System for library preparation


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