Viral Surveillance Panel

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

The Illumina Viral Surveillance Panel v1 is still available through My Illumina or customer service. Please contact your sales rep for more information.

Overview

The Viral Surveillance Panel v2 Kit allows researchers to obtain whole-genome sequencing (WGS) data that can characterize a wide-range of viruses, including SARS-CoV-2, influenza, arboviruses, and hepatitis.

  • 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 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


Required products

The complete kits include everything needed for library prep and enrichment, including purification beads and index adapters. Use up to 4 kits for larger runs up to 384 samples.

  • Illumina Viral Surveillance Panel v2 Kit, Set A (96 samples)
  • Illumina Viral Surveillance Panel v2 Kit, Set B (96 samples)
  • Illumina Viral Surveillance Panel v2 Kit, Set C (96 samples)
  • Illumina Viral Surveillance Panel v2 Kit, Set D (96 samples)
/ Results

Applications

The 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


Related applications and methods

Documentation

Product literature
Support documentation

A dedicated support section is not currently available for this product

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 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. 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, iSeq 100 System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiniSeq 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 Targeted DNA sequencing, Whole-genome sequencing, Targeted RNA sequencing, Target enrichment Targeted DNA 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 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 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 (4)

Illumina Viral Surveillance Panel v2 Kit, Set A (96 samples)

20108081

Viral Surveillance Panel V2 Kit (VSP V2) is a hybrid capture enrichment kit that provides whole genome sequencing of over 200 viruses and subtypes of public health concern.

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Illumina Viral Surveillance Panel v2 Kit, Set B (96 samples)

20108082

Viral Surveillance Panel V2 Kit (VSP V2) is a hybrid capture enrichment kit that provides whole genome sequencing of over 200 viruses and subtypes of public health concern.

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Illumina Viral Surveillance Panel v2 Kit, Set C (96 samples)

20108083

Viral Surveillance Panel V2 Kit (VSP V2) is a hybrid capture enrichment kit that provides whole genome sequencing of over 200 viruses and subtypes of public health concern.

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Illumina Viral Surveillance Panel v2 Kit, Set D (96 samples)

20108084

Viral Surveillance Panel V2 Kit (VSP V2) is a hybrid capture enrichment kit that provides whole genome sequencing of over 200 viruses and subtypes of public health concern.

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Panel (1)

Illumina Viral Surveillance Panel v2 (96 samples)

20123403

Oligo probe panel for hybrid capture whole genome sequencing of over 200 viruses and subtypes. Library prep and indexes sold separately.

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Selection summary

Product

Qty

Unit Price

FAQs

Viral Surveillance Panel v1 provides results for 66 viruses of public health concern.  Viral Surveillance Panel v2 expands this target list to over 200 viruses and subtypes.  Viral Surveillance Panel v2 includes Illumina Purification Beads, which are not included in Viral Surveillance Panel v1.

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 8M 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.

The standard workflow is to pool 3 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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