COVIDSeq Test (RUO Version)

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.

Rapid, Scalable SARS-CoV-2 Detection

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.

Workflow and Components

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.

Design and Quality Control

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 PCR annealing temperature setting generates more complete genomes—providing important insight into the SARS-CoV-2 strain present in the sample, and enabling tracking of virus strains.

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.