Viral Surveillance Panel

Whole-genome sequencing and characterization of 66 viruses including SARS-CoV-2, influenza, and polio with target enrichment.

< 9 hr library prep time

Assay time

< 2 hr library prep time

Hands-on time

10-100 ng

Input quantity

See full details in the specifications table

Overview

The Viral Surveillance Panel and Illumina RNA Prep with Enrichment kit allows researchers to obtain whole-genome sequencing (WGS) data that can characterize a wide-range of viruses, including SARS-CoV-2, influenza, and poliovirus.

  • Coverage of 66 viruses identified as high-risk to public health 

  • Concurrent enrichment for RNA and DNA viruses 

  • Compatible with a range of samples, including wastewater, environmental, and post-clinical 

Target enrichment for virus detection

Target enrichment through a hybrid–capture method allows for WGS of multiple viruses, without requiring the high read depth needed for shotgun metagenomic sequencing, providing insight to viral evolution and broad viral surveillance.1 Additionally, as compared to other targeted resequencing methods, such as amplicon sequencing, hybrid–capture provides greater ability to capture, sequence and identify mutations, making it ideal for outbreak surveillance of rapidly evolving viruses.

Streamlined solution for viral applications

This comprehensive workflow integrates library preparation, target enrichment, sequencing, and data analysis, allowing researchers and public health scientists the ability to monitor multiple high-risk viruses with one panel/workflow. 

Specifications

Assay time < 9 hr library prep time
Automation capability Liquid Handling Robots
Automation details Explore available automation methods
Description

The Viral Surveillance Panel with the Illumina RNA Prep with Enrichment provides an optimized workflow that supports viral outbreak detection and monitoring of 66 RNA and DNA viral pathogens.
Hands-on time < 2 hr library prep time
Input quantity 10-100 ng
Instruments MiSeq System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System
Mechanism of action On-bead tagmentation followed by a single hybridization step
Method Target Enrichment, Targeted RNA Sequencing, Whole-Genome Sequencing, Targeted DNA Sequencing
Multiplexing Up to 384 samples in a single run with unique dual indexes
Nucleic acid type DNA, RNA
Species category Virus
Strand specificity Non-Stranded
Technology Sequencing

Required products

Two complete kits are available that include the library prep, probe panel, and index adapters: 

  • VSP w ILMN RNA Prep w Enrich A (Index set A) 

  • VSP w ILMN RNA Prep w Enrich B (Index set B) 

For index set C and D, or for multiplexing, the  Viral Surveillance Panel, Illumina RNA Prep with Enrichment, and index adapters will need to be ordered separately. 

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Applications

The Viral Surveillance Panel with the Illumina RNA Prep with Enrichment provides an optimized workflow that supports viral outbreak detection and monitoring of 66 RNA and DNA viral pathogens.

Example workflow

1
Prep

Viral Surveillance Panel 

2
Sequence
3
Analyze

Related applications and methods

Genomic surveillance of infectious diseases

NGS supports effective genomic surveillance strategies through identification of novel strains of coronavirus and other emerging infectious disease agents.

Coronavirus sequencing

NGS can identify novel coronavirus variants, track COVID-19 transmission, and more. Compare NGS methods for various coronavirus sequencing goals.

Wastewater surveillance

Learn about wastewater surveillance with NGS for community-level monitoring of infectious diseases, mutation tracking, and variant trend tracking.

Documentation

Product literature
Support documentation

Compare

Viral Surveillance Panel Illumina Respiratory Virus Enrichment Kit Respiratory Pathogen ID/AMR Enrichment Panel Kit
Assay time < 9 hr library prep time < 9 hr library prep time < 9 hr library prep time
Automation capability Liquid Handling Robots Liquid Handling Robots Liquid Handling Robots
Automation details Explore available automation methods Explore available automation methods Explore available automation methods
Description

The Viral Surveillance Panel with the Illumina RNA Prep with Enrichment provides an optimized workflow that supports viral outbreak detection and monitoring of 66 RNA and DNA viral pathogens.

 A streamlined workflow for detecting and analyzing SARS-CoV-2 and other common respiratory viruses. The agnostic design allows for widespread identification of pathogenic viruses across multiple sample types of interest. Identify respiratory infections and co-infections, detect antimicrobial resistance markers, and perform strain typing of critical pathogens (SARS-CoV-2 and Flu A/B viruses) to study viral evolution and transmission.
Hands-on time < 2 hr library prep time < 2 hr library prep time < 2 hr library prep time
Input quantity 10-100 ng 10-100 ng Based on volume (not concentration dependent)
Instruments MiSeq System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System MiSeq System, NextSeq 550 System, NextSeq 2000 System, MiniSeq System MiSeq System, NextSeq 550 System, MiniSeq System
Mechanism of action On-bead tagmentation followed by a single hybridization step On-bead tagmentation followed by a single hybridization step On-bead tagmentation followed by a single hybridization step
Method Target Enrichment, Targeted RNA Sequencing, Whole-Genome Sequencing, Targeted DNA Sequencing Target Enrichment, Targeted RNA Sequencing, Targeted DNA Sequencing Target Enrichment, Targeted RNA Sequencing, Targeted DNA Sequencing
Multiplexing Up to 384 samples in a single run with unique dual indexes Up to 384 samples in a single run with unique dual indexes Up to 384 samples in a single run with unique dual indexes
Nucleic acid type DNA, RNA DNA, RNA DNA, RNA
Species category Virus Human, Virus Fungal, Virus, Bacteria
Strand specificity Non-Stranded
Technology Sequencing Sequencing Sequencing

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Figures

Read counts and viral genome coverage gains

Compared to shotgun metagenomic sequencing, where all RNA/DNA is sequenced, targeted hybrid–capture reduces unnecessary sequencing of host and nontargeted microbes.

Uniform viral genome coverage

Target enrichment probes in the Viral Surveillance Panel provide uniform coverage of whole virus genomes. Virus controls were prepared by mixing virus controls at known copy numbers with 10 ng human RNA/DNA mix. Libraries were prepared and sequenced following the Viral Surveillance Panel workflow.

 

Wastewater surveillance

Viruses detected in wastewater using Viral Surveillance Panel or shotgun sequencing.a Samples with low viral concentrations are easily detectable when using the Viral Surveillance Panel.  

a. Samples were collected by researchers at Colorado State University and purified total nucleic acids were shipped to Illumina for testing. Libraries were prepared and sequenced using 100 ng total nucleic acids 

Viruses detected by the Viral Surveillance Panel

List of 66 viruses identified as important risks to public health by the World Health Organization (WHO).2

Included on the Viral Surveillance Panel
Adenovirus Hepatitus B virus Parechovirus
Aichivirus Hepatitus C virus Parvovirus
Astrovirus Hepatitus E virus Poliovirus
Chapare virus Human Immunodeficiency Virus 1 Polymavirus
Chikungunya virus Human Immunodeficiency Virus 2 Respiratory syncytial virus
Coronavirus-229E Influenza A Virus Rhinovirus
Coronavirus-HKU1 Influenza B Virus Rift Valley fever virus
Coronavirus-OC43 Japanese encephalitis virus Rotavirus
Coronavirus-NL63 Junin virus Rubella virus
Coxsackievirus Kyasanur Forest disease virus Sabia virus
Crimean-congo haemorrhagic fever virus Lassa fever virus Salivirus
Dengue virus 1 Lujo hemorrphagic fever virus Sapovirus
Dengue virus 2 Machupo virus SARS-COV
Dengue virus 3 Marburg virus SARS-COV-2
Dengue virus 4 MERS-CoV Tick-borne encephalitis virus
Eastern equine encephalitis virus Metapneumovirus Torque Teno virus
Ebola virus Monkeypox virus Variola virus
Enterovirus Nipah virus Venezuelan equine encephalitis virus
Guanarito virus Norovirus West Nile virus
Hantavirus Omsk hemorrhagic fever virus Western equine encephalitis virus
Hendra henipavirus Oncolytic human papillomavirus Yellow fever virus
Hepatitis A virus Parainfluenza virus Zika virus
 

Library prep (4)

Viral Surveillance Panel, RUO 96 Rxns

20088154

Includes Viral Surveillance Panel sufficient for 32, 3-plex enrichment reactions when paired with Illumina RNA Prep with Enrichment kit. Purchase library prep and enrichment kit and index adapters separately.

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VSP w ILMN RNA Prep w Enrich A, 96 Rxns

20087932

Includes all reagents necessary for library prep and enrichment including Illumina RNA Prep with Enrichment kit reagents, Viral Surveillance Panel, IDT for Illumina DNA/RNA UD Indexes Set A for preparation of 96 libraries followed by enrichment in 32, 3-plex enrichment reactions.

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VSP w ILMN RNA Prep w Enrich B, 96 Rxns

20087929

Includes all reagents necessary for library prep and enrichment including Illumina RNA Prep with Enrichment kit reagents, Viral Surveillance Panel, IDT for Illumina DNA/RNA UD Indexes Set B for preparation of 96 libraries followed by enrichment in 32, 3-plex enrichment reactions.

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Illumina® RNA Prep with Enrichment, (L) Tagmentation (96 Samples)

20040537

Includes reagents for preparing and enriching 96 libraries (32, 3-plex enrichment reactions). Purchase enrichment probe panel, Purification Beads and index adapters separately.

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Index adapters (8)

Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples)

20091654

Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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Illumina® DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples)

20091656

Illumina® DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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Illumina® DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples)

20091658

Illumina® DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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Illumina® DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples)

20091660

Illumina® DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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IDT® for Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples)

20027213

Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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IDT® for Illumina® DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples)

20027214

Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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IDT® for Illumina® DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples)

20042666

Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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IDT® for Illumina® DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples)

20042667

Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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FAQs

For good quality samples, the read depth is a minimum of 2M paired-end reads per sample with a read length of 150 bp. For more complex samples, such as wastewater, a minimum of 4M paired-end reads is recommended per sample.

Yes. Whole-genome sequencing of multiple viruses at once can be done using the Viral Surveillance Panel. This makes the panel ideal for viral surveillance and analysis of viral evolution. 

Yes, dsRNA, ssRNA, dsDNA, and ssDNA viruses are detected using a library prep.

The standard workflow is to pool 3 samples per one hybridization (3-plexing).
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References
  1. Gaudin M, Desnues C. Hybrid Capture-Based Next Generation Sequencing and Its Application to Human Infectious Diseases. Front Microbiol. 2018;9:2924. Published 2018 Nov 27. doi:10.3389/fmicb.2018.02924
  2. Bloom DE, Cadarette D. Infectious Disease Threats in the Twenty-First Century: Strengthening the Global Response. Front Immunol. 2019;10:549. Published 2019 Mar 28. doi:10.3389/fimmu.2019.00549

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