NGS solutions for genomic surveillance of SARS-CoV-2

High-throughput NGS solutions for reliable detection of emerging SARS-CoV-2 variants

The emergence of new SARS-CoV-2 variants such as B.1.1.7 and B.1.351 is changing the trajectory of the pandemic. Cataloging these variants and evaluating the impact of mutations is critical for effective vaccine development and the implementation of a robust public health response. Partner with QIAGEN to expedite SARS-CoV-2 variant detection and phylogeographic tracking using reliable, high-throughput NGS technologies and integrated bioinformatics pipelines. From genomic surveillance to metatranscriptomics – uncover the multiple facets of SARS-CoV-2 biology with precision.

New benchmark study evaluates SARS-CoV-2 whole genome sequencing protocols for variant detection

A recent study by Liu et al. revealed that the QIAseq SARS-CoV-2 Primer Panel enabled preferential amplification of the SARS-CoV-2 genome by up to 100-fold in human samples, compared to human or bacterial genomes. In comparison with RNA-seq metagenomics-based technologies, it also achieved >100-fold higher coverage of the SARS-CoV-2 genome, depending on viral load and sequencing depth.

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Genomic surveillance

SARS-CoV-2 genomic surveillance

With SARS-CoV-2 rapidly mutating, there is an increased need for high-throughput whole viral genome sequencing to accelerate genomic surveillance for deeper phylogenetic and phylogeographic insights. Detect new SARS-CoV-2 variants with precision using high-throughput QIAseq NGS technology. Based on optimized publicly-available ARTIC V3 designs, the QIAseq SARS-CoV-2 Primer Panel provides targeted enrichment of the complete viral genome. By minimizing primer dropouts and primer-dimer effects, the panel ensures high coverage even at low copy number. Combine with the QIAseq FX DNA Library UDI Kit to multiplex up to 384 samples in a single run on high-throughput Illumina platforms. Track and visualize phylogenetic divergence with our integrated bioinformatics analysis pipelines. Expedite 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.

Metatranscriptomics

SARS-CoV-2 metatranscriptomics

Deciphering the complex interplay between the host and its microbiota can unlock detailed insights into host, microbiome, virus and pathway responses. Highly abundant host and bacterial rRNA can be problematic in coronavirus metatranscriptomics studies, leading to wasted RNA-seq reads. To maximize unique gene expression reads, remove >95% of both host and bacterial rRNA in just 1 hour, while still retaining viral RNAs by using QIAseq FastSelect –rRNA HMR Kits and QIAseq FastSelect –5S/16S/23S Kits either separately or in combination. Then move on to stranded, high-quality library prep using the QIAseq Stranded Total RNA Lib Kit for sensitive detection of low-expression RNA molecules with increased complexity and transcript coverage. Benefit from the specificity and efficiency of the complete QIAseq workflow to expedite SARS-CoV-2 metatranscriptomics research.

Trial kits

Evaluate QIAseq SARS-CoV-2 NGS technologies in your lab – request a trial kit

Genomic surveillance trial kits
- QIAseq SARS-CoV-2 Primer Panel
- QIAseq FX DNA Library UDI Kit
Metatranscriptomics trial kits

Bioinformatics

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. From phylogenetic to metagenomic analyses, accelerate impactful insights with our integrated bioinformatics solutions for SARS-CoV-2 genomic surveillance.

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Resources

Coronavirus research publications using QIAGEN technologies

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

Uncovering the SARS-CoV-2 mutational landscape with QIAseq technology
Explore how combining QIAseq FastSelect and QIAseq FX technologies to generate NGS libraries free from human rRNA facilitated deeper insights in this SARS-CoV-2 phylogenetics study.
Reference: Hartley et al. (2020) Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene

Is reinfection with SARS-CoV-2 possible?
Explore how this study used QIAseq FastSelect for rRNA removal and QIAseq FX for viral genome amplification and sequencing to uncover genetic discordance between SARS-CoV-2 isolates.
Reference: Tillett et al. (2020) Genomic evidence for a case of reinfection with SARS-CoV-2

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

The crucial role of QIAseq FX technology in SARS-CoV-2 sequencing
This publication by Itokawa et al. cites the use of QIAGEN’s QIAseq FX technology for converting amplicons into high-quality NGS-ready libraries ready for sequencing.
Reference: Itokawa, K., Sekizuka, T., Hashino, M., Tanaka, R., and Kuroda, M. (2020) Disentangling primer interactions improves SARS-CoV-2 genome sequencing by the ARTIC Network’s multiplex PCR

High-quality library prep for SARS-CoV-2 sequencing using QIAseq FX
This study by Itokawa et al. illustrates the use of QIAGEN’s QIAseq FX technology for high-quality library prep for sequencing the SARS-CoV-2 genome.
Reference: Itokawa, K., Sekizuka, T., Hashino, M., Tanaka, R., and Kuroda, M. (2020) A proposal of an alternative primer for the ARTIC Network’s multiplex PCR to improve coverage of SARS-CoV-2 genome sequencing

Coronavirus webinars

Sign up for our informative live webinars exploring different themes in coronavirus research.

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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rRNA removal for RNA-seq applications involving viruses, host responses and metatranscriptomics
Speaker: Samuel Rulli, Ph.D., Associate Director, RNA-seq profiling, NGS assay technologies, QIAGEN

On-demand recorded webinar
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Targeted RNA panels to identify SARS-CoV-2 and study host gene expression
Speaker: Samuel Rulli, Ph.D., Associate Director, RNA-seq profiling, NGS assay technologies, QIAGEN

On-demand recorded webinar
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Services

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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.