SARS-CoV-2 Emerging Variants Panel Add-on

NOTICE: Emerging Variants Add-on Panel v2 is now available: please refer to this product page to see the updated v2 panel that serves as a replacement for this product. 

CleanPlex amplicon-based SARS-CoV-2 NGS panels are designed for Coronavirus research and surveillance, enabling complete genome sequencing of the SARS-CoV-2 virus responsible for the COVID-19 pandemic. The Add-on primers are used in conjunction with the original SARS-CoV-2 Panel or FLEX Panel and contain additional primers for more robust coverage of Emerging Variants for confident variant calling even as the virus mutates. 


Product Description

CleanPlex® SARS-CoV-2 Emerging Variants Panel Add-on for robust whole-genome coverage

The SARS-CoV-2 Emerging Variant Panel Add-on is designed to be used with the existing CleanPlex SARS-CoV-2 products to maintain high coverage for variant calling and identification as the virus evolves. Follow the links here to learn more about the Original CleanPlex SARS-CoV-2 and FLEX Panels.

The new variants of concern, such as the Alpha variant from UK (B.1.1.7), Beta variant from South Africa (B.1.351) lineages, and Delta variant from India contain mutations in the receptor-binding domain (RBD) of the spike protein, which have been shown to significantly increase infection rates and can negatively impact the efficacy of the recently developed vaccines and current COVID-19 qPCR mass testing methods. Thus, a robust detection method and continued screening and surveillance are more critical than ever in our continued global efforts to control this pandemic.

The Add-on primers were generated by cross-referencing the FLEX panel design with selected emerging SARS-CoV-2 variants for uniform coverage and confident identification of their defining mutations.

The CleanPlex SARS-CoV-2 Panel 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.

Highlights of the FLEX panel

    • Robust Coverage
      Added primers for enhanced coverage of newly discovered UK and South African variants.
    • Additional Confidence in Variant Calling
      Optimized for identifying existing and new mutations for surveillance and tracking.
    • Easy Spike-in Workflow
      Directly add to existing CleanPlex SARS-CoV-2 and FLEX panels for ease of use and flexible future updates.

The CleanPlex SARS-CoV-2 Panels 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)Main Panel & Kits Required with Add-on PrimersSKUs
96/384CleanPlex® SARS-CoV-2 FLEX Panel918014/ 918015
96/384CleanPlex® SARS-CoV-2 Panel918011/ 918012
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)1 x SKU#718002 – CleanMag Magnetic Beads (20 mL, ~100 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)

1 x SKU#718002 – CleanMag Magnetic Beads (20 mL, ~100 reactions for CleanPlex 2-pool panels)

4 X 961 x Each of SKU#716037 to 716040  – CleanPlex® Unique Dual-Indexed PCR Primers for Illumina® Set C, D, E, F 96-well Plated (96 reactions)

*Note: Use 8 sets of 384 on NovaSeq dual S4 flow cell sequencing for maximum 3072 sample multiplexing.

1 x SKU#718003 – CleanMag Magnetic Beads (60 mL, ~300 reactions for CleanPlex 2-pool panels)

1 x SKU#718002 – CleanMag Magnetic Beads (20 mL, ~100 reactions for CleanPlex 2-pool panels)

Storage Temperature

Store at -20 °C.

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

The Original, FLEX, and FLEX with Add-on Panels were run in triplicates using a synthetic control (B.1.1.7). Variants were called against the reference genome NC_045512.2. All 36 expected mutations were covered and accurately called in each panel conditions tested. Improvements of coverage in FLEX and with Add-on Primers are highlighted above.

Additional Information

Weight10 g
Pack Size (Reactions)

8, 96, 384

Related Products…