NEXTFLEX® Variant-Seq SARS-CoV-2 V2 Kit

Now available with normalization beads

The  NEXTFLEX® Variant-Seq™ SARS-CoV-2 kit is a complete kit and software solution

  • Developed and optimized using real samples
  • No new extraction needed
  • Robust protocol using the same extracted nucleic acid input volume regardless of Ct value
  • Normalization beads that remove the need for sample quantification at all steps prior to the final library pool, regardless of viral load
  • Improved manual and automation workflow with a streamlined protocol that uses consistent input volumes at all sample preparation steps
  • High throughput with 1,536 indexes available
  • Fast sequencing using 1 x 36 nt, for quick turnaround time
  • With Artic v4.1 pool of primers
  • Compatible with all Illumina® sequencers

Automation available in Sciclone® G3 NGSx, Sciclone® G3 NGSx iQ and JANUS® G3 liquid handlers

The NEXTFLEX® Variant-Seq™ SARS-CoV-2 Kit v2 has been designed to detect all mutations associated with SARS-CoV-2, including those specific to the omicron variant, in a PCR-positive sample. With the incorporation of normalization beads, the NEXTFLEX® Variant-Seq™ SARS-CoV-2 v3 kit reduces turn-around time by up to three hours mostly due to eliminating the need for individual library quantification prior to the pooling step. Additionally, our 1,536 UDIs used in the NEXTFLEX® Variant-Seq™ SARS-CoV-2 Kit v2 enables the sequencing of 6,000 SARS-CoV-2 libraries in one flow cell, providing extremely high throughput.

Detect SARS-CoV-2 variants quickly
For research use only. Not for use in diagnostic procedures.

The new NEXTFLEX® Variant-Seq™ SARS-CoV-2 Kit v2 introduces proprietary NEXTFLEX® normalization beads, which provide a consistent mass and sequencing cluster density for all samples in a library pool, regardless of their viral load. This shortens the time needed for quantification and pooling preparation for sequencing in a high throughput lab by 3 hours.


  • NOVA-5350-096

    96 RXNS | BARCODES 1-96

  • NOVA-5350-384A

    384 RXNS | BARCODES 1-384

  • NOVA-5350-384B

    384 RXNS | BARCODES 385-768

  • NOVA-5350-384C

    384 RXNS | BARCODES 769-1152

  • NOVA-5350-384D

    384 RXNS | BARCODES 1153-1536

Whole Genome Sequencing of the SARS-CoV-2 Genome

As of December 2021, SARS-CoV-2 has infected over 260 million people and caused more than 5.2 million deaths1. 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 SARS-CoV-2 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 its use 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. They utilize an amplicon-based target enrichment workflow delivering speed, scalability, and cost.

Track & Identify SARS-CoV-2 Variants

The NEXTFLEX® Variant-Seq SARS-CoV-2 Kit v2 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, we are here to help labs meet their SARS-CoV-2 variant detection challenges.

The NEXTFLEX® Variant-Seq™ SARS-CoV-2 Kit v2 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 v2 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 kit v2 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 v4.1 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® sequencers.

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.

The introduction of NEXTFLEX® Normalization Beads in the NEXTFLEX® Variant-Seq SARS-CoV-2 v2 kit further reduces sample preparation time by removing the need to quantify samples prior to pooling and simplifies the workflow because the same volume of each prepared library is added to the final pool, regardless of their initial Ct values.

Maximize Your Variant Detection Throughput While Reducing Your Sequencing Costs

The NEXTFLEX® Variant-Seq SARS-CoV-2 kit v2 includes up to 1,536 unique dual index barcodes, supplied in four sets of 384 barcodes each, ideally suited to ultra high-throughput multiplexing on the Illumina® NovaSeq® sequencer or other Illumina® platform. The 1,536 NEXTFLEX® UDIs maximize your sequencing throughput, minimize sequencing costs 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 sequencing 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 v2 on the Sciclone® G3 NGSxSciclone® G3 NGSx iQ and JANUS® G3 liquid handlers. These multiple automation options offer labs the flexibility to meet throughput, resourcing and hands-on time needs.

For research use only. Not for use in diagnostic procedures.