SARS-CoV-2 data analysis
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 SARS-CoV-2 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
Three workflows are available for SARS-CoV-2 data analysis. One workflow is a generic workflow for use with ARTIC V3 SARS-CoV-2 primers designs; another workflow is customized for use with QIAseq DIRECT SARS-CoV-2 Panel data or QIAseq SARS-CoV-2 Primer Panel data. The third workflow is customized for use with Ion AmpliSeq SARS-CoV-2 Research Panel data. These workflows use one or multiple samples as input, which allows for analysis of either a single sample or the comparison of multiple samples based on a single workflow run.
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.
Don’t take our word for it: Hear what our customers have to say
“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
Resource library for SARS-CoV-2 data analysis
QIAGEN CLC Genomics resources and tutorials for SARS-CoV-2
- Analysis of SARS-CoV-2 using MinION sequences: This tutorial covers the analysis of metatranscriptomic Oxford Nanopore MinION reads from SARS-CoV-2 samples. The tutorial dataset includes an example workflow, allowing the analysis to be run in a reproducible, hands-off manner.
- De novo assembly using long reads and short read polishing: This tutorial is focused on hybrid assembly of long, error-prone reads, and read polishing with high-quality short reads. It includes assessment of assembly quality, and how and when to perform long read error correction.
- Tutorials on QIAGEN CLC Genomics for SARS-CoV-2 bioinformatics
- General tutorials: There are many tutorials available to introduce other functionalities, as well as publicly available manuals for QIAGEN CLC core products and plugins.
QIAGEN CLC resources for microbial and viral genomics
Webinars
- Wastewater and COVID-19 data analysis using QIAGEN CLC Genomics Workbench
- Sample to Insight: Using Targeted whole viral genome sequencing to analyze and understand COVID-19 (Sept. 25, 2020)
- QIAGEN CLC User Group Meeting (May 26 and 27, 2020) Watch the on-demand presentations from this online event, including talks on QIAGEN CLC core and advanced capabilities, use cases from KOLs and a discussion on SARS-CoV-2 analysis using CLC Genomics Workbench
- Using QIAGEN Digital Insights to research coronavirus fusion and immune control (May 6, 2020)
- Bioinformatics analysis of Nanopore sequencing data for SARS-CoV-2 (April 2, 2020)
- Bacterial strain typing and genomics characterization of multi-drug resistance with QIAGEN CLC Genomics Workbench (March 9, 2020)
Blogs
- Genomics analysis of wastewater for SARS-CoV-2 tracking
- Get the job done: How to maximize productivity in the Nevada SARS-CoV-2 reinfection case study
- Highlights of the latest update to QIAGEN CLC Microbial Genomics Module: Using viral reference databases for phylogeny construction and taxonomic profiling of samples with low viral load
- De novo assembly of Oxford Nanopore MinION reads with QIAGEN CLC Genomics Workbench
- Comparative analysis of whole genomes using QIAGEN CLC Workbenches
Other resources/external tools
- GitHub resource maintained by Duncan MacCannell (CDC Office of Advanced Molecular Detection)
- GISAID Initiative for rapid and open access to influenza virus data
- Latest news from QIAGEN on the fight against coronavirus
Select publications using QIAGEN IPA and/or QIAGEN CLC Genomics to study COVID-19
- Characterisation of SARS-CoV-2 variants in Beijing during 2022: an epidemiological and phylogenetic analysis
- Therapeutic efficacy of monoclonal antibodies and antivirals against SARS-CoV-2 Omicron BA.1 in Syrian hamsters
- Conserved microRNAs in human nasopharynx tissue samples from swabs are differentially expressed in response to SARS-CoV-2
- Genomic surveillance of SARS-CoV-2 lineages indicates early circulation of P.1 (gamma) variant of concern in southern Brazil
- Impact of ADAR-induced editing of minor viral RNA populations on replication and transmission of SARS-CoV-2
- COVID-19 cluster linked to aerosol transmission of SARS-CoV-2 via floor drains
- SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung
- Unique evolution of SARS-CoV-2 in the second large cruise ship cluster in Japan
- Identification of a novel SARS-CoV-2 P. 1 sub-lineage in Brazil provides new insights about the mechanisms of emergence of variants of concern
- Near-complete genome of SARS-CoV-2 delta (AY.3) variant identified in a dog in Kansas, USA
- Monitoring the circulation of SARS-CoV-2 variants by genomic analysis of wastewater in Marseille, south east France
- Variations among viruses in influent water and effluent water at a wastewater plant over one year as assessed by quantitative PCR and metagenomics
- Drug repurposing for COVID-19 based on an integrative meta-analysis of SARS-CoV-2 induced gene signature in human airway epithelium
- An outbreak of SARS-CoV-2 infections among hospital personnel with high mRNA vaccine uptake
- Management following the first confirmed case of SARS-CoV-2 in a domestic cat associated with a massive outbreak in South Korea
- mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates
- Detection of SARS-CoV-2 derived small RNAs and changes in circulating small RNAs associated with COVID-19
- Distribution of SARS-CoV-2 lineages in the Czech Republic, analysis of data from the first year of the pandemic
- Recurrent and persistent infection with SARS-CoV-2 – epidemiological data and case reports from Western Sweden, 2020
- An epidemiological analysis of SARS-CoV-2 genomic sequences from different regions of India
- SARS-CoV-2 spike mutations, L452R, T478K, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India
- Nosocomial outbreak of COVID-19 in a hematologic ward
- Mutational asymmetries in the SARS-CoV-2 genome may lead to increased hydrophobicity of virus proteins
- The Coronavirus Network Explorer: Mining a large-scale knowledge graph for effects of SARS-CoV-2 on host cell function
- Favipiravir antiviral efficacy against SARS-CoV-2 in a hamster model
- Possible involvement of central nervous system in COVID-19 and sequence variability of SARS-CoV-2 revealed in autopsy tissue samples: A case report
- Detection of SARS-CoV-2 lineage P.1 in patients from Rio Grande do Sul, Southern Brazil
- Molecular adaptive evolution of SARS-COV-2 spike protein in Saudi Arabia
- Two distinct immunopathological profiles in autopsy lungs of COVID-19
- A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm
- Genomic evidence for reinfection with SARS-CoV-2: a case study
- Proteomic and metabolomic characterization of COVID-19 sera
- Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins
- LY6E impairs coronavirus fusion and confers immune control of viral disease
- Focusing on pathways to reposition common approved drugs against COVID-19
- Ultrarapid diagnosis, microscope imaging, genome sequencing, and culture isolation of SARS-CoV-2
- A novel coronavirus from patients with pneumonia in China, 2019
- Genomic and protein structure modelling analysis depicts the origin and pathogenicity of 2019-nCoV
- Virtual screening and repurposing of FDA approved drugs against COVID-19 main protease
- A comparative analysis for SARS-CoV-2
- Focusing on the unfolded protein response and autophagy-related pathways to reposition common approved drugs against COVID-19
- Overly exuberant innate immune response to SARS-CoV-2 infection