NEXTFLEX® Variant-Seq SARS-CoV-2 Kit

  • Complete solution –Reagents, barcodes, beads, and analysis software included
  • Pressure tested – Developed and optimized using real samples
  • Robust – Same input volume regardless of Ct value
  • Minimal sample prep – No new extraction or normalization prior to library prep
  • High-throughput – Up to 1,536 indexes available
  • Automated – Automation available in Sciclone® G3 NGS/NGSx, Sciclone® G3 NGSx iQ and JANUS® G3 liquid handlers
  • Fast sequencing – 1 x 36 nt sequencing possible, for quick turnaround time
  • No minimum purchase requirements
  • Compatible with all Illumina® sequencing platforms
Detect SARS-CoV-2 variants quickly
Download Manual
For research use only. Not for use in diagnostic procedures.

  • NOVA-5349-096


    96 RXNS | BARCODES 1-96

  • NOVA-5349-384A


    384 RXNS | BARCODES 1-384

  • NOVA-5349-384B


    384 RXNS | BARCODES 385-768

  • NOVA-5349-384C


    384 RXNS | BARCODES 769-1152

  • NOVA-5349-384D


    384 RXNS | BARCODES 1153-1536

Whole Genome Sequencing of the SARS-CoV-2 Genome

As of March 2021, SARS-CoV-2 has infected 115 million people and caused over 2.56 million deaths.1 The discovery of particularly aggressive variants such as B.1.1.7 and B.1.351 has shown that  monitoring for mutations associated with changes to infection outcome and transmission of SARS-CoV-2 is critical to ensure the success of vaccination programs and establish robust public health responses2. Once a sample is detected as positive for COVID-19 using an RT-PCR assay, the next question that needs to be answered is, does the sample contain a SARS-CoV-2 Variant of Concern (VOC). NGS is ideal for this as its high resolution enables it to identify all mutations, known and unknown, providing insights to SARS-CoV-2 infection and transmission.

The NEXTFLEX® Variant-Seq SARS-CoV-2 workflow is optimized to quickly, easily, and affordably identify all mutations in a SARS-CoV-2 PCR-positive sample. It utilizes an amplicon-based target enrichment workflow which offers many advantages over hybridization capture-based protocols, most notably speed, scalability, and cost.

Track & Identify SARS-CoV-2 Variants

The NEXTFLEX® Variant-Seq SARS-CoV-2 Kit has optimized the identification and tracking of SARS-CoV-2 variants. Sample preparation has been simplified, throughput has been increased, and multiple automation solutions offer flexibility based on your lab’s needs. Along with a complete, sample-to-answer workflow, PerkinElmer is here to help labs meet their SARS-CoV-2 variant detection challenges.

The NEXTFLEX® Variant-Seq™ SARS-CoV-2 Kit is powered by COSMOSID® software, converting sequencing data into a concise sample report within minutes. These reports are compliant with the CDC requirements for tracking variants. The Pangolin lineage, used by the CDC to track variants, is included in the reports. Additionally, the SARS-CoV-2 consensus created using the report can be easily submitted to NCBI and GISAID.

SARS-CoV-2 WGS Simplified

The NEXTFLEX® Variant-Seq SARS-CoV-2 kit simplifies the identification of existing and new variants of the SARS-CoV-2 virus by greatly reducing the sample preparation needed prior to sequencing. The NEXTFLEX® Variant-Seq SARS-CoV-2 workflow begins with synthesizing cDNA from previously extracted nucleic acids from a sample already identified as containing SARS-CoV-2 using RT-PCR. A single universal volume of the extracted nucleic acids is used as template, with no prior dilution step. The viral genome is then amplified using the ARTIC v3 primer pools, provided in the kit. The PCR product is purified and without quantification or normalization goes directly through a fast library preparation protocol to generate libraries that are compatible with Illumina® sequencing.

By eliminating the need for a repeat nucleic acid extraction and complicated sample preparation required by most other NGS-based protocols, the entire procedure from sample to finalized library ready for sequencing only takes 7 hours.

NEXTFLEX Variant-Seq SARS-CoV-2 workflow

Maximize Your Variant Detection Throughput While Reducing Your Sequencing Costs

The NEXTFLEX® Variant-Seq SARS-CoV-2 kit includes up to 1,536 unique dual index barcodes, supplied in four sets of 384 barcodes each, for ultra high-throughput multiplexing on the Illumina® NovaSeq® sequencer or other Illumina® platform. The 1,536 NEXTFLEX® UDIs maximize your sequencing throughput and increase your workflow efficiencies. By multiplexing 1,536 samples per run, you can:

  • Sequence 4x as many samples per run
  • Get answers faster by reducing the numbers of runs needed
  • Reduce sequencing reagent costs by up to 4x

Automate Your Variant Detection

Easy-to-use protocols have been developed for automating the NEXTFLEX® Variant-Seq SARS-CoV-2 kit on the Sciclone® G3 NGSx, Sciclone® G3 NGSx iQ and JANUS® G3 liquid handlers. These multiple automation options offer labs the flexibility to meet their specific throughput and hands-on time needs.


  • NEXTFLEX® Reverse RT
  • NEXTFLEX® Amplicon PCR Mix
  • NEXTFLEX® Primer Pool 1
  • NEXTFLEX® Primer Pool 2
  • NEXTFLEX® Fragmentation Buffer
  • NEXTFLEX® Fragmentation Enzyme Mix
  • NEXTFLEX® Ligation Master Mix
  • NEXTFLEX® PCR Master Mix
  • NEXTFLEX® Primer Mix
  • Nuclease-free Water
  • Resuspension Buffer
  • NEXTFLEX® Cleanup Beads XP
  • NEXTFLEX® Unique Dual Index Barcodes
    (12 μM, 5 μL per well)


  • 8 μL of nucleic acids extracted from COVID-19 test sample.
  • Ethanol 80% (room temperature)
  • 96 well PCR Plate Non-skirted (Phenix Research, Cat # MPS-499) or similar
  • Adhesive PCR Plate Seal (BioRad, Cat # MSB1001)
  • Magnetic Stand -96 (Thermo Fisher Scientific, Cat # AM10027) or similar
  • Thermal Cycler
  • 2, 10, 20, 200 and 1000 μL pipettes / multichannel pipettes
  • Nuclease-free barrier pipette tips
  • Vortex


  • Sequences of NEXTFLEX® Unique Dual-Indexed Barcode (1-1,536) Indexes – Excel


  • NEXTFLEX® Variant-Seq SARS-CoV-2 Kit-PDF


  • NEXTFLEX® Variant-Seq SARS-CoV-2 Software from CosmosID – PDF


  • NEXTFLEX® Variant-Seq SARS-CoV-2 – PDF

The NEXTFLEX® Variant-Seq™ SARS-CoV-2 kit contains enough material to prepare 96 or 384 samples for Illumina® sequencing. The Nuclease-free Water and Resuspension Buffer can be stored at room temperature. The NEXTFLEX® Cleanup Beads XP should be stored at 4°C, and all other components should be stored at -20°C.

Contact Us to Track and Identify SARS-CoV-2 Variants
For research use only. Not for use in diagnostic procedures.