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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.

4-hour
enrichment and library prep workflow that can be automated, allowing you to go from purified RNA to sequence – no need for fragmentation, tagmentation or ligation steps.
~250 bp
amplicons generated for superior uniformity and better coverage across the SARS-CoV-2 genome and better sequencing performance compared with the most widely-used amplicon-based options.
Up to 768
samples can be multiplexed to improve scalability and efficiency.
50%
reduction in plasticware usage.
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.

QIAseq SARS-CoV-2 Primer Panel
QIAseq SARS-CoV-2 Primer Panel
Targeted whole genome library preparation of SARS-CoV-2 for genomic surveillance and variant detection
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QIAseq FX DNA Library UDI Kit
QIAseq FX DNA Library UDI Kit
All-enzymatic whole genome and hybrid capture library preparation for Illumina instruments with minimal bias
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Get started with a trial kit

QIAseq SARS-CoV-2 Primer Panel Kit

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QIAseq FX DNA Library UDI Kit

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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.

Publications

Acute SARS-CoV-2 alpha variant infection leading to placental insufficiency and fetal distress

Explore how SARS-CoV-2 whole genome sequencing using the QIAseq Direct SARS-CoV-2 Kit helped identify a mutated strain of the SARS-CoV-2 alpha variant in a study on the links between acute SARS-CoV-2 alpha variant infection and placental insufficiency and fetal distress.

Reference: Dumont, S., Balduyck, J., Reynders, M., Vanwalleghem, L. and Lebbe, B. (2021) Acute SARS-CoV-2 alpha variant infection leading to placental insufficiency and fetal distress.

QIAseq technology shown to be among the most effective for SARS-CoV-2 whole genome sequencing

A recent study evaluating different SARS-CoV-2 whole genome sequencing methods revealed that the QIAseq SARS-CoV-2 Primer Panel enabled preferential amplification of the SARS-CoV-2 genome by up to 100-fold and ensured high coverage.

Reference: Liu et al. (2020) A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples.

Tracking mutations in SARS-CoV-2 RNA using QIAseq technology

Discover how the QIAseq SARS-CoV-2 Primer Panel helped reveal a bird’s eye view on the accumulation of mutations in the SARS-CoV-2 genome in this study from Eastern India.

Reference: Maitra, A. et al. (2020) Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility

Altered microRNA expression in COVID-19 patients enables identification of SARS-CoV-2 infection

Read about how the QIAseq miRNA Library Kit and QIAseq miRNA NGS 48 Index IL helped determine altered miRNA expression in COVID-19 patients leading to the development of a development of a robust miRNA biomarker signature of COVID-19.

Reference: Farr, R. et al. (2021) Altered microRNA expression in COVID-19 patients enables identification of SARS-CoV-2 infection

icon_0059_quote_bubble-s
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

Moving beyond SARS-CoV-2 surveillance: How can next-generation sequencing support wastewater-based epidemiology?
Moving beyond SARS-CoV-2 surveillance: How can next-generation sequencing support wastewater-based epidemiology?
Speaker: Davida Smyth, Ph.D., Associate Professor of Microbiology Texas A&M University San Antonio, Texas
Register now
Accelerating SARS-CoV-2 genomic surveillance with a new high-throughput NGS solution
Accelerating SARS-CoV-2 genomic surveillance with a new high-throughput NGS solution
Speakers: Brian Dugan, M.S., Associate Director, Global Product Management, Genomics, QIAGEN and Fernando Spilki, Ph.D., Feevale University, Novo Hamburgo, Brazil
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Enabling high-throughput genomic surveillance of emerging SARS-CoV-2 strains B.1.1.7 and B.1.351
Enabling high-throughput genomic surveillance of emerging SARS-CoV-2 strains B.1.1.7 and B.1.351
Speakers: Brian Dugan, M.S., Associate Director, Global Product Management, Genomics, QIAGEN and Shawn Prince, B.S., Senior Field Application Scientist, Bioinformatics, QIAGEN
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Expand insights into SARS-CoV-2 metatranscriptomics
Explore how our innovative NGS solutions can enhance RNA-seq sensitivity in SARS-CoV-2 metatranscriptomics research.

Dive deeper

SARS-CoV-2 Whole Genome Sequencing Services
SARS-CoV-2 Whole Genome Sequencing Services
Ramp up SARS-CoV-2 genomic surveillance efforts by taking advantage of our comprehensive SARS-CoV-2 Whole Genome Sequencing Services. Extend your in-house resources with the expertise and custom services that you expect from QIAGEN.
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Analyze SARS-CoV-2 sequence data with ease
Analyze SARS-CoV-2 sequence data with ease
Make sense of your SARS-CoV-2 sequencing data with integrated bioinformatics. Intuitive and easy-to-use QIAGEN CLC Genomics Workbench enables visualization and comparison of multiple reads and variants simultaneously. The new QIAGEN CoV-2 Insights Service now offers a low-cost, highly-scalable cloud infrastructure for distributed processing, analysis and reporting of SARS-CoV-2 variants and lineages. From phylogenetic to metagenomic analyses, accelerate impactful insights with our integrated bioinformatics solutions for SARS-CoV-2 genomic surveillance.
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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.