COVIDSeq Test (RUO Version)

This high-throughput NGS assay enables labs to detect SARS-CoV-2 mutations to identify and track the emergence and prevalence of novel variants.

This product is available for Research Use Only (RUO). An in vitro diagnostic version of this product is available for use in Japan, Philippines, and the US under each country's respective authorizing agency. 

Overview

COVIDSeq Test (RUO Version) is a next-generation sequencing (NGS) assay that enables researchers to detect and characterize novel variants of SARS-CoV-2.

  • Detects genome of SARS-CoV-2 RNA using ARTIC v3 primers 

  • Reports consensus sequence when ≥ 90 amplicons detected

  • Supports a seamless and flexible end-to-end workflow 

Rapid and scalable sequencing

The Illumina COVIDSeq Test (RUO version) accommodates 384 to 3072 samples, depending on throughput needs. 

Uniform genome coverage

Coverage is particularly focused on the spike protein locus. For detailed sequencing, the optional ARTIC v4 primer pool provides in-depth characterization of new variants. 

Integrated solution

The kit includes all reagents needed for cDNA conversion, amplification, and library prep. A 63°C annealing temperature during PCR improves variant analysis and insights. 

Streamlined data analysis

Assess lineage and annotate mutations with open software tools, including the Illumina DRAGEN COVID Lineage App in BaseSpace Sequence Hub.  


Specifications


Required products

In addition to the Illumina COVIDSeq Test (3072 samples), you will need: 

  • IDT for Illumina PCR Indexes Sets 1–4 (384 Indexes, 384 samples) 

  • Flow cell for your sequencing system  

  • Sequencing reagent kit for your sequencing system 

  • Viral RNA extraction kit (eg, QIAamp Viral RNA Mini Kit) 

/ Results

Applications

The COVIDSeq Test (RUO Version) is an integrated NGS research solution for detection and characterization of SARS-CoV-2, not for use in diagnostic procedures or patient management. 

Example workflow


Application notes


Related applications and methods

Compare

COVIDSeq Test (RUO Version) COVIDSeq Assay (96 samples) Pan-Coronavirus Panel Respiratory Pathogen ID/AMR Enrichment Panel Kit
Automation capability Liquid handling robots Liquid handling robots Liquid handling robots Liquid handling robots
Automation details Explore available automation methods Explore available automation methods Explore available automation methods
Content specifications

Uniform viral genome coverage across the spike protein locus 

Uniform viral genome coverage across the spike protein locus 

Detects respiratory pathogen DNA and RNA simultaneously and profiles antimicrobial resistance (AMR) gene expression concurrently.
Description

The COVIDSeq Test (RUO Version) is a scalable high-throughput NGS assay (up to 3072 samples) intended for research applications.  

The COVIDSeq Assay (96 samples) is a low- to mid-throughput NGS assay intended to be processed on any Illumina benchtop sequencing system for research applications. 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. 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.
Instruments MiSeq System, iSeq 100 System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiSeqDx in Research Mode, MiniSeq System, NextSeq 550Dx in Research Mode, NovaSeq 6000Dx in Research Mode, NextSeq 500 System, NovaSeq 6000 System MiSeq System, iSeq 100 System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiSeqDx in Research Mode, MiniSeq System, NextSeq 550Dx in Research Mode, NovaSeq 6000Dx in Research Mode, NextSeq 500 System, NovaSeq 6000 System MiSeq System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiniSeq System MiSeq System, NextSeq 550 System, MiniSeq System
Method Amplicon sequencing, Targeted RNA sequencing Amplicon sequencing, Targeted RNA sequencing Whole-genome sequencing, Target enrichment Targeted DNA sequencing, Targeted RNA sequencing, Target enrichment
Multiplexing

384-plex on NextSeq

384-plex on NovaSeq

8-plex on the iSeq System

30–48 plex on the MiSeq System

48-plex on the MiniSeq System

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 RNA RNA DNA, RNA
Sample type details

Nasopharyngeal, oropharyngeal, and mid-turbinate nasal swab samples 

Nasopharyngeal, oropharyngeal, and mid-turbinate nasal swab samples 

Species category Human, Virus Human, Virus Virus Fungal, Virus, Bacteria
Species details SARS-CoV-2 (SARS-CoV-2_ MN908947v3) SARS-CoV-2 (SARS-CoV-2_ MN908947v3) Detects respiratory pathogens (180+ bacteria, 50+ fungi, and 40+ viruses, including SARS-CoV-2) and antimicrobial resistance alleles (1200+).
Strand specificity Non-stranded Non-stranded Non-stranded
Technology Sequencing Sequencing Sequencing Sequencing

Selection Tools:

Figures

Genomic coverage performance

Heat map plotting performance as a function of read length and depth shows significant improvement with paired-end reads over single reads. The fraction of genomes > 0.99 confident is shown, with values close to 1 representing more complete coverage of the SARS-CoV-2 genome. 

FAQs

The COVIDSeq Test (RUO Version) is intended for the NovaSeq 6000 Sequencing System. It can also be run on the iSeq 100, MiniSeq, MiSeq, MiSeqDx in Research Mode, NextSeq 500, NextSeq 550, NextSeq 550Dx in Research Mode, NextSeq 1000, or NextSeq 2000 Systems.

The primary difference is the number of samples each assay can run. The COVIDSeq Assay (96 samples) runs 96 samples on Illumina benchtop sequencing systems to accommodate smaller research labs. In contrast, the COVIDSeq Test (RUO) runs up to 3072 samples on the NovaSeq 6000 System or NextSeq line of sequencing systems.

Yes, an in vitro diagnostic (IVD) test is available for use in authorized countries (Japan, Philippines, and the US) under each country’s respective authorizing agency.  

The ARTIC v3 primer pool is included with the COVIDSeq Test (RUO) kit. It contains primers for 98 amplicons and 11 human genes, designed against the original strain of SARS-CoV-2. The optional ARTIC v4 pool includes 99 amplicons and no human controls, designed against the Delta variant. It delivers improved genomic coverage across the spike protein locus and better analytical sensitivity for SARS-CoV-2 variant detection. Read technical note.

/ Results

Order the NovaSeq X Series

Advanced chemistry, optics, and informatics combine to deliver exceptional speed and data quality, outstanding throughput and scalability.

MiSeq Reagent Kit v3

Optimized reagent kit that provides increased cluster density and read length, improving sequencing quality scores compared to earlier versions.

TruSight Oncology 500

Enable CGP with a large pan-cancer panel covering all major variant classes plus gene signatures (TMB, MSI, and HRD) from FFPE tissue.

Illumina DNA Prep

A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.

Contact us

Interested in bringing the Illumina COVIDSeq Test into your lab for surveillance applications?