The Illumina COVIDSeq Test (RUO version), an amplicon-based NGS assay, includes 2019-nCoV primers designed to detect mutations and characterize RNA from the SARS-CoV-2 virus to help clinical research labs identify and track the emergence and prevalence of novel strains of SARS-CoV-2.
The Illumina COVIDSeq Test (RUO version) can be scaled up or down to accommodate different numbers of samples. 1536 to 3072 results can be processed in 12 hours on NovaSeq 6000 system using two SP or S4 reagent kits, respectively or 384 results in 12 hours using NextSeq 2000 P2 v3 reagent kits or NextSeq 500/550/550Dx (in Research Mode) HO reagent kit.
The workflow includes steps for viral RNA extraction, RNA-to-cDNA conversion, PCR, library preparation, sequencing, analysis, and report generation. Key components include the high-throughput NovaSeq 6000 System or the NextSeq 2000 System or the NextSeq 500/550/550Dx (in Research Mode) Systems, coupled with the Illumina COVIDSeq Test (RUO version) and the DRAGEN COVIDSeq Test App (RUO version) in BaseSpace Sequence Hub for rapid analysis.
The Illumina COVIDSeq Test (RUO version) leverages a modified version of the validated, publicly available ARTIC multiplex PCR protocol, with 98 amplicons designed to amplify SARS-CoV-2 virus-specific sequences, combined with proven Illumina sequencing technology. COVIDSeq provides consensus sequence information when +90 amplicons are detected. A 63°C annealing temperature at the PCR step improves variant analysis—providing important insight into the SARS-CoV-2 strain present in the sample, and enabling tracking of virus strains.
The COVIDSeq V4 Primer Pool is available as an RUO product. It is based on ARTIC network V4 design and includes 99 amplicons and no human controls. The kit volume is sufficient for 384 samples. This product is not available in all countries/regions. Please contact your local sales representative for availability.
Consensus sequence information (FASTA file) can be uploaded into open software tools to assign lineage and annotate mutations. FASTA files can be easily uploaded to the NCBI and/or GISAID App directly through BaseSpace Sequencing Hub for added convenience.
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This document describes the step-by-step workflow process and lists the required materials and equipment.View Document
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Illumina COVIDSeq Test (Research Use Only)
Data Sheet | PDF < 1 MB
Automated processing for COVIDSeq™ workflow flexibility
Brochure | PDF < 1 MB
Surveillance of infectious disease through wastewater sequencing
Application Note | PDF < 1 MB
Aliquot procedure for Illumina COVIDSeq Test (RUO Version) kit reagents
Technical Note | PDF < 1 MB
Sequencing guidelines for COVID-19 surveillance using the Illumina COIVDSeq Test (RUO Version)
Technical Note | PDF 1 MB
Technical Note | PDF | 2 versions
Illumina Adapter Sequences Documentation
Illumina DRAGEN COVID Pipeline Software Guide Documentation
Illumina DRAGEN COVIDSeq Test App Guide (RUO) Documentation
Illumina DRAGEN COVIDSeq Test Pipeline Software Guide (RUO) Documentation
Illumina COVIDSeq RUO Kits Reference Guide Documentation
Index Adapters Pooling Guide Documentation
All Illumina COVIDSeq Test RUO Support All Illumina COVIDSeq Test RUO Documentation Support