CleanPlex SARS-CoV-2 Kit


This amplicon-based SARS-CoV-2 NGS panel is designed for COVID-19 Coronavirus research and surveillance, enabling complete genome sequencing of the new SARS-CoV-2 virus responsible for the COVID-19 pandemic. This panel is specific for Illumina Sequencing platforms. The other version is available for MGI sequencing platforms. For high throughput labs, we now have up to 2,688 dual-indexed PCR primer combinations (56  x 48 indexes) for pooling up to 2,688 samples onto a single Illumina flowcell.

Additional pack sizes may be available. Please contact your local sales representative to learn more about additional pack sizes and bulk pricing.

Product Description

CleanPlex® SARS-CoV-2 Panel for COVID-19 coronavirus detection, tracking, and research via amplicon-based target enrichment for Next Generation Sequencing (NGS) on Illumina sequencing platforms

Paragon Genomics designed a highly multiplexed target enrichment panel covering the entire genome of the SARS-CoV-2 virus (except for 92 bases at the ends). The panel enables complete genome sequencing and epidemiological studies of the new SARS-CoV-2 virus responsible for the COVID-19 pandemic. With our CleanPlex technology, the entire genome of the virus can be amplified from RNA to sequence-ready libraries in 5.5 hours. Two versions of this panel are available for two major sequencing platforms: Illumina and MGI. CleanPlex Technology allows the ease and flexibility to sequence samples for confident infectious disease surveillance and research.

The CleanPlex SARS-CoV-2 FLEX Kit is also available for front-end leading coronavirus research customers and those who may benefit from internal library preparation control.  

The CleanPlex SARS-CoV-2 Kit has repeatedly demonstrated consistently high coverage of multiple variants. Read more about how the panel has been used around the globe for surveillance and research.

To ensure that our customers get the most out of their sequencing runs, we’re proud to offer up to 2688 sample multiplexing capability with our combinatorial dual-indexed primers for Illumina sequencing. Additionally, we provide 384 unique-dual indexes, allowing for low variant calling and other in-depth sequencing applications. These exciting additions allow for cost-effective and high-throughput sequencing with our best-in-class CleanPlex targeted sequencing technologies.


  • Significant Cost Savings
    99% reduction in sequencing cost. Only 50K reads per sample required versus 10M reads required by many shotgun metagenomics sequencing methods.
  • High Coverage of Target Regions
    99% coverage of the entire SARS-CoV-2 genome
  • Sensitive Detection
    Can detect down to 1 copy with high confidence compared 3-5 copies by RT-qPCR (1)
  • Fast, Streamlined Workflow
    Generate sequencing-ready libraries in just 5.5 hours using a rapid, four-step protocol including RT step with minimal hands-on time.
  • Superb Performance
    Prepare high-quality NGS libraries with excellent on-target performance using CleanPlex Technology to enable efficient use of sequencing reads. The CleanPlex panels’ on-target rates are usually much higher than those of hybrid captured-based small target enrichment panels.

The CleanPlex SARS-CoV-2 Kit contains the CleanPlex Multiplex PCR Primers and CleanPlex Targeted Library Kit with RT components. CleanPlex Indexed PCR Primers for sample pooling and CleanMag® Magnetic Beads for bead purification and size selection are ordered separately to complete the workflow from input RNA to sequencing-ready NGS libraries.

For a complete solution, please use the following indexed PCR primers and magnetic beads SKUs.

Pack Size (Reactions)SKUs for Indexed PCR PrimersSKUs for Magnetic Beads
961 x SKU#716006 – CleanPlex® Dual-Indexed PCR Primers for Illumina® Set A (12 x 8 indexes, 96 reactions)4 x SKU#718002 – CleanMag Magnetic Beads (5 mL, ~25 reactions for CleanPlex 2-pool panels)
3841 x SKU#716017 – CleanPlex® Dual-Indexed PCR Primers for Illumina® Set A (12 x 8 indexes, 384 reactions) 1 x SKU#718003 – CleanMag Magnetic Beads (60 mL, ~300 reactions for CleanPlex 2-pool panels)

4 x SKU#718002 – CleanMag Magnetic Beads (5 mL, ~25 reactions for CleanPlex 2-pool panels)

Storage Temperature

Store at -20 °C.

(1) Corman VM et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

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

Paragon Genomics’ CleanPlex SARS-CoV-2 NGS Panel shows exceptional sensitivity on very low virus copy numbers even at a low sequencing depth. Data above are obtained from our hospital collaborators using CleanPlex Panel to sequence patient samples that were tested positive by RT-PCR. With a high-throughput NGS sequencer from Illumina or MGI, you can pool hundreds to thousands of samples onto a single sequencing run.

Down sampling was performed in silico for samples with various viral loads. All sequencing metrics maintains high performance even at 50,000 total paired-end (PE) reads at even down to 20 viral copies/rxn.


(Left) Using plasmids containing the N and S genes of SARS-CoV-2 on with a single pool workflow for detection, the detection rate at low copy numbers are show. The detection rate was shown to be 56% at 1.1 copy and 100% when more than 2 copies were present. With the use of both pools to cover the entire viral genome, the sensitivity is expected to only further increase. (Right) For these detected, the panel was able to on average capture all targets within 10 fold read depth range for 2.8 viral copies, and similarly for all but one target for 1.4 viral copies. All targets were also uniformly distributed across the GC range.

Please see our publication for method and result details.

Additional Information

Pack Size (Reactions)

8, 96, 384

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