AmpliSeq for Illumina SARS-CoV-2 Research Panel

This sequencing panel offers a quick, accurate, and cost-effective method to research the SARS-CoV-2 virus.Read More...
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AmpliSeq™ SARS-CoV-2 Research Panel for Illumina®



Product Highlights

This research panel contains 247 amplicons in 2 pools targeting the SARS-CoV-2 genome. The panel includes >99% coverage of the Coronavirus genome (~30kb) and covers all potential serotypes.

Community Panel Features

AmpliSeq for Illumina Community Panels are made-to-order. We provide the designs for your convenience; however, they do not have associated performance metrics. For predesigned and tested content, view AmpliSeq for Illumina Ready-to-Use Panels.

AmpliSeq for Illumina Community Panels contain content selected and designed with input from leading disease researchers. You can order this community panel as is, or customize the panel to meet your needs, using Illumina Concierge to add or remove genes and amplicons.

Other Required Products

In addition to the community panel, you will also need an AmpliSeq Library PLUS kit and index adapters.

Additional Information

Frequently Asked Questions

Panel Type and Usage

The AmpliSeq for Illumina SARS-CoV-2 Community Panel, in combination with AmpliSeq for Illumina library prep, index, and accessories, is a targeted RNA/cDNA amplicon assay for epidemiological research of the SARS-CoV-2 virus (Research Use Only). The panel is a 2-pool design, containing 247 amplicons/primer pairs (242 unique amplicons (Pool 1: 125 amplicon, Pool 2: 122 amplicons): 237 viral specific SARS-CoV-2 targets and 5 human gene expression controls) ranging from 125-275 bps in length that covers >99% of the viral genome and all potential serotypes of the virus.

The panel is intended for research use only (RUO) applications, and not for use in diagnostic procedures. No claim or representation is intended to provide information to indicate the panel may be used in diagnosis, prevention, or management of an infection.


We recommend customers evaluate commercially available extraction kits capable of isolating viral RNA. The QIAGEN QIAmp Viral RNA Mini Kit (PN 52904) has been demonstrated to be compatible for use in next-generation sequencing library preparation and other testing methods internally. In the event of a back order, any commercially available extraction kit from other companies should be compatible as well.

See the following resources for additional information:

Library preparation for the AmpliSeq for Illumina SARS-CoV-2 Community Panel follows the AmpliSeq for Illumina Custom and Community Panels Reference Guide: Chapter 3 Protocol for RNA Panels (

In “Amplify cDNA Targets”, proceed with the following:

  • 2 primer pools for the AMP_RNA program
  • Table 7: 97–192 primer pairs per pool at 18 cycles and 4 minutes
    • Pool 1: 125 amplicons/primer pairs, Pool 2: 122 amplicons/primer pairs
  • Table 8: Adjustments can be made based on sample quality and sample input

Library preparation using the AmpliSeq Library PLUS for Illumina is compatible with all AmpliSeq CD or UD Index Sets for Illumina.

Read depth: 250,000 reads per sample.

Read length: 2 x 151 bp.

Platforms: AmpliSeq for Illumina libraries are compatible with iSeq 100, MiSeq, MiniSeq, and NextSeq systems.

Ordering Information

After adding the panel to your MyIllumina cart and checking out, you will receive your panel order. The panel should state the solution ID: IAACY126664577_100.

1 order = $2223 USD is sufficient for preparing 2250 samples (~$9/amplicon). This does not include AmpliSeq Library PLUS for Illumina, Ampliseq cDNA Synthesis for Illumina, or AmpliSeq CD or UD Indexes for Illumina.


DNA Amplicon BaseSpace Sequence Hub app or DRAGEN Metagenomics app can be used for data analysis.

Resources and Contact Information

For additional questions please contact

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