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 (the coronavirus that causes COVID-19) 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 Research Panel 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 pandemic.

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 directly with viral loads as low as 20 copies

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

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

Learn more ›

Ion AmpliSeq Designer

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

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Ordering information

Product How to order
Ion AmpliSeq SARS-CoV-2 Research Panel 

1. Visit Ion AmpliSeq Designer at and sign in. If you do not have an account, follow the registration process to create a new account.

2. After signing in, go to Fixed Panels > Community Panels located in the top navigation to find the Ion AmpliSeq SARS-CoV-2 Research Panel and place your order.

3. Fill out the project cost request form to inquire about ordering an Ion GeneStudio S5 series system.