Pan-Coronavirus Panel

This panel supports characterization and genomic surveillance of 225 known and novel coronaviruses from humans and animal reservoirs.

< 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 Pan-Coronavirus Panel (Pan-CoV) allows for detection and sequencing of known human and animal coronaviruses and closely related novel coronaviruses with the potential to become infectious to humans. It includes hybrid–capture oligos that span across reference genomes of multiple coronavirus strains and various known animal hosts. 

When combined with Illumina RNA Prep with Enrichment, the Pan-Coronavirus Panel enables whole-genome sequencing (WGS) of 225 known human and animal coronaviruses. The targeted enrichment approach captures mutations and variants throughout the viral genome, enabling sequencing of novel coronavirus strains and detection of recombination between strains. 

The panel can be used for multiple applications, including:

  • Surveillance to identify and monitor coronaviruses in animal hosts

  • Track transmission patterns and viral mutations

  • Guide vaccine and therapeutic developments

Integrated viral sequencing solution

The Pan-Coronavirus Panel can integrate into a comprehensive workflow that includes library preparation, target enrichment, next-generation sequencing (NGS), and powerful data analysis, providing a simple means to obtain robust and reliable viral results.

Specifications

Assay time < 9 hr library prep time
Automation capability Liquid Handling Robots
Description The Pan-Coronavirus Panel is part of an integrated workflow that allows for the detection and whole-genome sequencing of over 200 known and novel coronavirus strains in various animal hosts.
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, MiniSeq System
Mechanism of action On-bead tagmentation followed by a single hybridization step
Method Target Enrichment, Whole-Genome Sequencing
Multiplexing Up to 384 samples in a single run with unique dual indexes
Nucleic acid type RNA
Species category Virus
Strand specificity Non-Stranded
Technology Sequencing

Required products

Illumina RNA Prep with Enrichment, (L) Tagmentation (16 or 96 Samples) needs to be ordered separately as well as index adapters. Illumina DNA/RNA Indexes Set A, B, C, or D can be used.

We recommend ordering the Illumina DNA/RNA UD Indexes Sets A-D (20091654, 20091656, 20091658, 20091660) since the IDT for Illumina DNA/RNA UD Indexes Sets A-D (20027213, 20027214,20042666, 20042667) are being discontinued.

 

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Applications

Target enrichment through hybrid–capture allows for detection and sequencing of 225 known human and animal coronaviruses and closely related novel coronaviruses for surveillance of animal reservoirs, tracking transmissions, and therapeutic and vaccine development.

Example workflow

1
Prep

Pan-Coronavirus Panel

2
Sequence
3
Analyze

Project recommendations

Instrument Recommended number of samples Read length
MiSeq System

6–12 samples using MiSeq Reagent Kit v2 (1–2M reads/sample) 

2 × 150 bp
NextSeq 550 System

65–130 samples using NextSeq 500/550 Mid-Output Kit (1–2M reads/sample)

2 × 150 bp
NextSeq 1000 System

100–200 samples using P2 Reagent Kit (1–2M reads/sample)

2 × 150 bp
NextSeq 2000 System

100–200 samples using P2 Reagent Kit (1–2M reads/sample)

2 × 150 bp

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.

Microbial genomics

Use NGS to discover novel microbes, monitor outbreaks, analyze food sources, and more.

How others use this product
Building a state-of-the-art clinical research sequencing lab in Israel
Leaders in COVID surveillance: Utah Public Health Laboratory

Documentation

Product literature
Support documentation

Compare

Pan-Coronavirus Panel Viral Surveillance Panel Illumina Respiratory Virus Enrichment Kit
Assay time < 9 hr library prep time < 9 hr library prep time
Automation capability Liquid Handling Robots Liquid Handling Robots
Description The Pan-Coronavirus Panel is part of an integrated workflow that allows for the detection and whole-genome sequencing of over 200 known and novel coronavirus strains in various animal hosts.

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 < 2 hr library prep time
Input quantity 10-100 ng 10-100 ng
Instruments MiSeq System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiniSeq System MiSeq System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System
Mechanism of action On-bead tagmentation followed by a single hybridization step On-bead tagmentation followed by a single hybridization step
Method Target Enrichment, Whole-Genome Sequencing Target Enrichment, Targeted RNA Sequencing, Whole-Genome 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
Nucleic acid type RNA DNA, RNA
Species category Virus Virus
Strand specificity Non-Stranded Non-Stranded
Technology Sequencing Sequencing

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Figures

Coronavirus strains covered in panel

Pan-Coronavirus Panel includes hybrid–capture oligos that capture 225 known human and animal coronaviruses.

Host-associated coronavirus genomes

Pan-Coronavirus Panel includes various known animal hosts.

Enrichment of Coronaviridae reads

The Pan-Coronavirus Panel successfully enriched Coronaviridae reads in all libraries tested across a range of viral copy number input.

Improved coronavirus genome coverage

Median coverage of synthetic viral RNA controls (SARS-CoV-2 and HCoV229E) in 10 ng UHR after enrichment with the Pan-Coronavirus Panel. Increased read depth (top) and read length (bottom) resulted in improved genome coverage. Read lengths were trimmed to 36, 74, 100, and 149 bp.

Panel (1)

Pan-Coronavirus Panel, RUO 96 Rxns

20088155

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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Library prep (2)

Illumina® RNA Prep with Enrichment, (L) Tagmentation (16 Samples)

20040536

Includes reagents for preparing and enriching 16 libraries (16, 1-plex enrichment reactions). Purchase enrichment probe panel, Purification Beads and index adapters separately.

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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

The panel is built with enrichment probes that allows for most variants to be captured effectively. In addition, the Pan-Coronavirus Panel was designed to enrich for 225 coronavirus genotypes from various animal sources and expected to capture most novel coronaviruses. For example, the Pan-Coronavirus Panel was designed before the Omicron variant but was still shown to enrich for the entire genome with high coverage (see data sheet for details).

Yes, the Pan-Coronavirus Panel was designed to work on environmental samples and samples from various animal sources. In fact, the panel is to be used for sequencing of coronviruses from diverse sample types such as bats, wastewater, and any potential coronavirus host. To maximize success with the panels, use the highest quality RNA you can obtain.

There is a free DRAGEN Microbial Enrichment BaseSpace App that can assemble contigs and explore genome coverage/depth, in addition to other outputs.

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

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