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Whole-genome sequencing and characterization of > 200 viruses and subtypes, including SARS-CoV-2, influenza, arboviruses, and hepatitis.
Rapid Viral Surveillance Panel v2
Whole-genome sequencing and characterization of > 200 viruses and subtypes, including SARS-CoV-2, influenza, arboviruses, and hepatitis.
Rapid Viral Surveillance Panel v2

Rapid Viral Surveillance Panel v2

Whole-genome sequencing and characterization of > 200 viruses and subtypes, including SARS-CoV-2, influenza, arboviruses, and hepatitis.

6.5 hr library prep time

Assay time

< 1.5 hr library prep time

Hands-on time

10–100 ng

Input quantity

See full details in the specifications table

The Illumina Viral Surveillance Panel v2 with standard IRPE remains available for purchase.

Overview

The Rapid Viral Surveillance Panel v2 Kit allows researchers to perform whole-genome sequencing (WGS) that can characterize a wide range of viruses, including SARS-CoV-2, influenza, arboviruses, and hepatitis, with target enrichment. The kit is available with the rapid, single reaction library prep or a standard library prep option.

  • Coverage of more than 200 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 clinical research

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 to monitor multiple high-risk viruses with one panel/workflow.

The Rapid Viral Surveillance Panel v2 option provides a single tube library prep reaction that simplifies the workflow and reduces cleanup steps, potentially improving detection of low-frequency targets.

Specifications

Assay time 6.5 hr library prep time
Automation capability Liquid handling robot(s)
Automation details Explore available automation methods
Description The Rapid Viral Surveillance Panel v2 Kit provides an optimized workflow that supports viral outbreak detection and monitoring of more than 200 RNA and DNA viral pathogens
Hands-on time < 1.5 hr library prep time
Input quantity 10–100 ng
Instruments MiSeq System, iSeq 100 System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiniSeq System, MiSeq i100 Plus System, MiSeq i100 System
Mechanism of action On-bead tagmentation followed by a single hybridization step
Method Targeted DNA sequencing, Whole-genome sequencing, Targeted RNA sequencing, Target enrichment
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

The kit includes the oligo panel, Illumina Rapid RNA Prep with Enrichment library prep, and purification beads needed for library prep and enrichment of 96 three-plex samples (32 hybridization reactions).

  • Illumina Rapid Viral Surveillance Panel v2 Kit
  • Illumina DNA/RNA Unique Dual Index Plate (Set A, B, C, or D)
/ Results

Applications

The Rapid Viral Surveillance Panel v2 Kit provides an optimized workflow that supports viral outbreak detection and monitoring of over 200 RNA and DNA viral pathogens.

Example workflow

1
Prep

Rapid Viral Surveillance Panel v2

2
Sequence
3
Analyze

Project recommendations

Instrument Recommended number of samples Read length
MiSeq i100 System, NextSeq 550 System, MiSeq System, iSeq 100 System, MiSeq i100 Plus System, NextSeq 1000 System, NextSeq 2000 System, MiniSeq System

1M paired-end reads for high-concentration low-complexity samples
4M paired-end reads for low-concentration high-complexity samples such as wastewater

2 × 150 bp

Related applications and methods

Genomic surveillance

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

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

Rapid Viral Surveillance Panel v2 Viral Surveillance Panel Illumina Respiratory Virus Enrichment Kit
Assay time 6.5 hr library prep time < 9 hr library prep time < 9 hr library prep time
Automation capability Liquid handling robot(s) Liquid handling robot(s) Liquid handling robot(s)
Automation details Explore available automation methods Explore available automation methods Explore available automation methods
Description The Rapid Viral Surveillance Panel v2 Kit provides an optimized workflow that supports viral outbreak detection and monitoring of more than 200 RNA and DNA viral pathogens The Viral Surveillance Panel v2 Kit provides an optimized workflow that supports viral outbreak detection and monitoring of more than 200 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
Hands-on time < 1.5 hr library prep time < 2 hr library prep time < 2 hr library prep time
Input quantity 10–100 ng 10–100 ng 10–100 ng
Instruments MiSeq System, iSeq 100 System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiniSeq System, MiSeq i100 Plus System, MiSeq i100 System MiSeq System, iSeq 100 System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiniSeq System, MiSeq i100 Plus System, MiSeq i100 System MiSeq System, NextSeq 550 System, NextSeq 2000 System, MiniSeq System, MiSeq i100 Plus System, MiSeq i100 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 Targeted DNA sequencing, Whole-genome sequencing, Targeted RNA sequencing, Target enrichment Targeted DNA sequencing, Whole-genome sequencing, Targeted RNA sequencing, Target enrichment Targeted DNA sequencing, Targeted RNA sequencing, Target enrichment
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 Virus Human, Virus
Strand specificity Non-stranded Non-stranded
Technology Sequencing Sequencing Sequencing

Selection tools:

NGS Workflow Finder

Your go-to hub to find end-to-end next-generation sequencing workflows. Customize recommendations based on your exact laboratory needs.

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 v2 Kit 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 v2 Kit workflow.

 

Wastewater surveillance

Viruses detected in wastewater using Viral Surveillance Panel v2 Kit or shotgun sequencing.a Samples with low viral concentrations are easily detectable when using the Viral Surveillance Panel v2 Kit.

See the data sheet or Virus List Spreadsheet for the full list of viruses detected.

Download the Viral Surveillance Panel v2 Virus List Spreadsheet

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 v2 Kit

The panel detects over 200 viruses and subtypes, including the 66 viruses identified as important risks to public health by the World Health Organization (WHO).2

Included on the Viral Surveillance Panel  
  Adeno-associated virus 2 Human adenoviruses (species A - G) Mamastrovirus "Rotaviruses (species A, B, C, H)
  Aichi virus 1 Human bocavirus Marburg virus Rubella virus
  Aigai virus Human coronaviruses (4 species) Mayaro virus Sabia virus
  Bombali virus Human cytomegalovirus Measles virus Salivirus A
  Bourbon virus Human immunodeficiency viruses (1 and 2) Menangle virus Sandfly fever Sicilian virus
  Cache Valley virus Human metapneumovirus MERS-CoV Sapovirus
  California encephalitis virus Human papillomaviruses (28 types) Mpox virus SARS-CoV
  Chapare virus Human parainfluenza viruses (types 1 - 4) Mumps virus SARS-CoV-2
  Chikungunya virus Human parechovirus Murray Valley encephalitis virus Semliki Forest virus
  Colorado tick fever virus Human parvovirus B19 Nipah virus Severe fever with thrombocytopenia syndrome virus
  Coxsackieviruses (A and B) Influenza A virus (20 subtypes) Norovirus Sindbis virus
  Crimean-Congo hemorrhagic fever virus Influenza B virus (both lineages) Omsk hemorrhagic fever virus Snowshoe hare virus
  Dengue viruses (4 types) Influenza C virus Onyong-nyong virus Sosuga virus
  Ebola viruses (6 species) Jamestown Canyon virus Oropouche virus St. Louis encephalitis virus
  Echovirus Japanese encephalitis virus Poliovirus Tacheng tick virus 2
  Enteroviruses (A - D) Junin virus Polyomavirus (13 species) Tahyna virus
  Epstein-Barr virus Kyasanur Forest disease virus Powassan virus Tick-borne encephalitis virus
  Equine encephalitis viruses (3 species) La Crosse virus Punta Toro virus Torque teno virus (Anelloviruses)
  Guanarito virus Lassa virus Rabies virus Toscana virus
  Hantaviruses (22 species) Lloviu virus Ravn virus Usutu virus
  Heartland virus Lujo virus Respiratory syncytial virus (types A and B) Varicella-zoster virus
  Hendra virus Lymphocytic choriomeningitis virus Rhinoviruses (species A - C) Variola virus
  Hepatitis viruses (A - E) Lyssavirus Rift Valley fever virus West Nile virus
  Herpes simplex viruses (1 and 2) Machupo virus Ross River virus Yellow fever virus
        Zika virus

Library prep (1)

Illumina Rapid Viral Surveillance Panel v2 Kit (96 samples)

20158826

Includes reagents for preparing and enriching 96 samples of Rapid RNA libraries (32 hybridization reactions with 3 libraries each), with Viral Surveillance Panel V2, and Illumina Purification Beads. UD Indexes sold separately. Viral Surveillance Panel V2 (VSP V2) provides whole genome sequencing of over 200 viruses and subtypes of public health concern.

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Index adapters (4)

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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FAQs

The Rapid Viral Surveillance Panel v2 Kit is a single reaction library prep that significantly reduces hands‑on time and overall assay time compared to the standard version. Both kits use the same oligo panel and detect the same viruses. The standard kit includes a 96‑sample index plate, while the rapid version requires purchasing the plate separately, providing greater flexibility in run planning.

Download the full list of viruses and subtypes and viruses.

For good quality samples, the read depth is a minimum of 1M fragments at 2 x 150 bp read length per sample. For more complex samples, such as wastewater, a minimum of 4M fragments at 2 x 150 bp read length is recommended per sample.

Yes. Whole-genome sequencing of multiple viruses at once can be done using the Rapid Viral Surveillance Panel v2. This makes the panel ideal for viral surveillance and analysis of viral evolution.

Yes, dsRNA, ssRNA, dsDNA, and ssDNA viruses are detected.

The standard workflow is to pool three samples per one hybridization (3-plexing).

/ Results

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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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