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Next-Generation Sequencing

NGS solutions for genomic surveillance of SARS-CoV-2

In the race against new viral variants, hours and minutes matter

The latest twist in the COVID-19 pandemic is the alarming emergence of new SARS-CoV-2 Variants of Concern (VOC), such as lineages Alpha, Beta, Gamma, Delta, Mu and Omicron. The potential for new variants to evade the immune response, lowering the efficacy of vaccines remains a threat. Labs are therefore under pressure to sequence samples as quickly as possible to identify new and catalog existing SARS-CoV-2 variants circulating in the population. To help you accelerate your SARS-CoV-2 genomic surveillance efforts, we’ve developed two tailored solutions for viral amplification and NGS library preparation.

NGS solutions for Omicron bubble

Get the right genomic surveillance solution for your needs

The faster you can sequence samples, the quicker you can develop a comprehensive picture of circulating variants, allowing you to stay one step ahead. Explore how our genomic surveillance solutions can help.

Product Kitbox
QIAseq DIRECT SARS-CoV-2 Kit works with all known Variants of Concern, including Omicron

Accelerate SARS-CoV-2 variant sequencing with a 50% faster, high-throughput NGS solution. The QIAseq DIRECT SARS-CoV-2 Kit provides superior viral genome coverage using a 4-hour, automatable workflow, with a 50% reduction in plasticware use, and support for up to 768-sample multiplexing in a single flow cell lane. The higher-density amplicon tiling of the QIAseq DIRECT SARS-CoV-2 Kit ensures robust performance across all VOCs, including detection of the Omicron and Delta variants, without the need for primer redesign strategies or primer booster kits.

New! QIAseq DIRECT SARS-CoV-2 Enhancer Kit

The QIAseq DIRECT SARS-CoV-2 Enhancer Kit works to further increase genomic coverage while simplifying your workflow when combined with the QIAseq DIRECT SARS-CoV-2 Kit.

Benefit from:

  • A streamlined workflow: No need for normalization/quantification prior to library amplification
  • Boosted genome coverage and uniformity: >95% coverage even at extremely low viral genome copy numbers
  • A lower read requirement: 4X reduction in recommended clusters per sample, saving on sequencing costs and allowing greater multiplexing

Get the QIAseq DIRECT SARS-CoV-2 Enhancer Kit at no additional charge when you buy the QIAseq DIRECT SARS-CoV-2 Kit. Terms and conditions apply.


Davida Dmyth working in lab
Flushing out SARS-CoV-2 variants from wastewater using NGS

Dr. Davida Smyth discusses how whole genome NGS helped her detect circulating SARS-CoV-2 variants and even reveal new mutations from wastewater samples.

White paper: Identifying VOCs from real-world COVID samples

Learn how Nicolò Musso and his team at the University of Catania analyzed 250 COVID-positive samples of varying RNA quality using the QIAseq DIRECT SARS-CoV-2 Kit and detected many of the VOCs circulating in the local population at the time, including Alpha, Gamma and Delta variants.

Coronavirus poster
Corona virus, COVID-19, virus with antibodies
Variants, surveillance and vaccine efficacy: Twists in the COVID-19 pandemic
As the COVID-19 pandemic continues to evolve with the emergence of the Omicron variant, explore how NGS, in particular whole genome sequencing, is being used to determine the prevalence of circulating variants. Our blog post dives into SARS-CoV-2 variant detection, wastewater testing, vaccine escape mutants and more.
Why choose the QIAseq DIRECT SARS-CoV-2 Kit?

Use our ultrafast, high-throughput, single-box NGS solution if you want to maximize efficiency, ramp up your sequencing capability and ensure superior coverage to accelerate variant detection. You can now take advantage of the QIAseq DIRECT SARS-CoV-2 Enhancer Kit, a new addition that – when used in combination with the QIAseq DIRECT SARS-CoV-2 Kit – further streamlines the workflow and boosts coverage while requiring fewer reads per sample.

QIAseq SARS-CoV-2 Primer Panel

Expedite SARS-CoV-2 variant detection and real-time genomic surveillance with our scalable, single-day workflow, which is faster and has lower-input requirements than hybrid capture solutions. Based on optimized publicly available ARTIC V3 designs, the QIAseq SARS-CoV-2 Primer Panel provides targeted enrichment of the complete viral genome, allowing you to:

  • Achieve high coverage, even at low copy number due to reduced primer dropouts and primer-dimer effects
  • Multiplex up to 384 samples in a single run on high-throughput Illumina platforms
  • Track and visualize phylogenetic divergence with integrated bioinformatics analysis pipelines
A winning combination for improved scalability

Combine the QIAseq SARS-CoV-2 Primer Panel with the QIAseq FX DNA Library UDI Kit to multiplex up to 384 samples in a single run.

Get started with a trial kit
Automate and accelerate your library prep
How can automating your NGS library prep benefit your lab?
Genomics, QIAseq NGS Solutions, Dr. Mette Christiansen, Aarhus University hospital, COVID-1
Sequencing COVID-19 mutations after jumping species

By November 2020, more than 200 people in Denmark were believed to have caught COVID-19 from mink. Meanwhile, the virus had been mutating within the animals, resulting in a handful of variants. Dr. Mette Christiansen, Head of the Diagnostic NGS Core Facility, Molecular Medicine (MOMA) at Aarhus University Hospital, discusses the how sequencing all positive cases helped achieve a clear picture of circulating variants. Explore how QIAGEN NGS technologies facilitated this effort.


We call to increase the sequencing of the virus, to supplement ongoing surveillance, monitoring and test efforts
Director-General, World Health Organization

Check out our webinars

Expand insights into SARS-CoV-2 metatranscriptomics
Explore how our innovative NGS solutions can enhance RNA-seq sensitivity in SARS-CoV-2 metatranscriptomics research.

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All photos taken prior to COVID-19
The offer is based on list price. Offer void where prohibited and not to be used in combination with other promotions. Offer not valid in all countries. Freight and delivery costs are not included. The offer is limited in time and subject to certain restrictions set forth herein. It is the customer's responsibility to ensure that acceptance of this offer will not violate any internal policies of the customer's organization and applicable laws and regulations.