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Analysis of SARS-CoV-2 data

QIAGEN Digital Insights resources for SARS-CoV-2 and COVID-19 research and analysis

QIAGEN CoV-2 Insights Service for genomic surveillance

QIAGEN CoV-2 Insights Service is an automated, high-throughput solution designed for genomic surveillance of SARS-CoV-2 from next-generation sequencing data. It offers a low-cost, highly-scalable cloud infrastructure for distributed processing, analysis and reporting of SARS-CoV-2 variants and lineages from targeted whole genome sequencing data obtained from a variety of technologies.

This solution enables efficient scaling of any lab’s data analysis, without the need for significant investment in IT infrastructure, expert resources or additional staff.

With our robust analytics pipelines, complete automation and concise reporting, our QIAGEN CoV-2 Insights Service can help transform any sequencing lab into a SARS-CoV-2 genomic surveillance powerhouse.

Characterizing SARS-CoV-2 with QIAGEN CLC Genomics

QIAGEN CLC Genomics Workbench bioinformatics software is used by hundreds of microbiology and virology labs around the world for basic research and infectious disease epidemiology. QIAGEN CLC Genomics Workbench has also been critical for many labs on the front lines of the COVID-19 pandemic involved in sequencing the SARS-CoV-2 virus.

NGS panel support using QIAGEN CLC Genomics

Two workflows are available for analyzing SARS-CoV-2 data. One workflow is customized for use with QIAseq SARS-CoV-2 Primer Panel data and the other is customized for use with Ion AmpliSeq SARS-CoV-2 Research Panel data. Both workflows can take one or multiple samples as input, which allows for analysis of either a single sample or comparison of multiple samples, based on a single workflow run.

The general approach of both workflows involves mapping the reads to a reference, generating a consensus sequence from the mapping, calling variants and generating outputs that allow for efficient review of results, including cross-sample comparison.

A detailed description is found in the manual.

The workflows are available in the workbench by installing the Biomedical Genomics Analysis plugin.

Linking 3D structure to variants is done first by downloading the SARS-CoV-2 structure database and then linking the variants to the 3D structures.

The workflow outputs can be used with the tools in QIAGEN CLC Microbial Genomics Module. Examples include:

  • Understanding sample contamination through taxonomic profiling of unmapped reads
  • Functional analysis with BLAST and DIAMOND
  • Tree construction from consensus sequences or variant calls to trace the evolution of the virus

For further details, see the sections in the manual on taxonomic analysis, functional analysis, phylogenetic trees using SNPs and k-mers, and large MLST scheme tools.

Understanding SARS-CoV-2 with QIAGEN IPA

QIAGEN Ingenuity Pathway Analysis (IPA) is used by thousands of researchers and virology labs worldwide and cited extensively in studies of the host response to viruses. This valuable tool accelerates the understanding of ‘omics data from organisms and viruses to help assess interactions between the two, and reveal where therapeutics could potentially come into play to help modulate host response.

Read our brochure about IPA for viral research.

Coronavirus Network Explorer

Check out our Coronavirus Network Explorer, available at no cost. Our data scientists have expanded upon recent peer-reviewed research to generate relevant SARS-CoV-2 protein networks using the QIAGEN Knowledge Base as well as artificial intelligence. This freely available tool helps you visualize how SARS-CoV-2 proteins interact with human host proteins to disable protective responses and pathways, and explore hypotheses around how to fight coronavirus. The Coronavirus Network Explorer supports and accelerates your research by helping you gain a deeper understanding of how SARS-CoV-2 affects the host and behaves biologically.

Read our recent publication on Coronavirus Network Explorer.

Explore viral ‘omics data with QIAGEN Viral Land

Accelerate your antiviral host response research with QIAGEN Viral Land, a gene expression database on viral studies delivered in a simple-to-use web portal known as QIAGEN OmicSoft Land Explorer. Viral land is a highly curated and re-processed collection of high-value human viral host and viral vaccine RNA-seq and microarray expression data, harmonized into a single platform. 

This specialized collection of viral ‘omics data is available through QIAGEN Discovery Bioinformatics Services.

“During the first appearance of the COVID-19 pandemic, we were invited to use the QIAGEN CLC tools for free. This opportunity allowed us to study the co-infection rate seen in COVID-patients which we published here: https://pubmed.ncbi.nlm.nih.gov/33033248/ ”

-Ronny Nienhold, Lab Director, Kantonsspital Baseland

QIAGEN CLC Genomics resources and tutorials for SARS-CoV-2

QIAGEN resources for microbial and viral genomics

Other resources/external tools

Select publications using QIAGEN IPA and/or QIAGEN CLC Genomics to study COVID-19