SARS-CoV-2 Emerging Variants Panel Add-on

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. 

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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 UK (B.1.1.7) and South Africa (B.1.351) lineages, 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.

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

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