This low- to mid-throughput NGS assay enables labs of any size to identify and track the emergence and prevalence of novel SARS-CoV-2 variants.
COVIDSEQ Assay (96 samples) is a comprehensive amplicon-based next-generation sequencing (NGS) assay designed to help research labs identify novel SARS-CoV-2 variants.
Designed to run a low number of samples, the COVIDSeq Assay (96 samples) offers a low-throughput configuration ideal for Illumina benchtop sequencing systems, enabling smaller labs to perform decentralized surveillance of new variants.
Coverage is focused on the spike protein locus. For detailed sequencing, the optional ARTIC v4 primer pool provides in-depth characterization of new variants.
Kit includes all reagents for cDNA conversion, amplification, and library prep. A 63°C annealing temperature during PCR improves variant analysis and insights.
Assess lineage and annotate mutations with open software tools, including the DRAGEN COVID Lineage App in BaseSpace Sequence Hub.
| Automation capability | Liquid handling robots |
|---|---|
| Automation details | Explore available automation methods |
| Content specifications | Uniform viral genome coverage across the spike protein locus |
| Description | 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. |
| 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 |
| Method | Amplicon sequencing, Targeted RNA sequencing |
| Multiplexing | 8-plex on the iSeq System 30–48 plex on the MiSeq System 48-plex on the MiniSeq System |
| Nucleic acid type | RNA |
| Sample type details | Nasopharyngeal, oropharyngeal, and mid-turbinate nasal swab samples |
| Species category | Human, Virus |
| Species details | SARS-CoV-2 (SARS-CoV-2_ MN908947v3) |
| Strand specificity | Non-stranded |
| Technology | Sequencing |
One COVIDSeq Assay (96 samples) is required. There are four options available, all identical except for the included index plate.
The COVIDSeq Positive Control is an optional product.
The Illumina COVIDSeq v4 Primer Pools, 384 Samples RUO is an optional replacement for the v3 primer pool. v4 was updated in response to additional mutations in the Delta and Omicron variants and delivers improved coverage in the spike protein locus.
The COVIDSeq Assay (96 Samples) enables labs using benchtop sequencing systems to perform genomic surveillance of SARS-CoV-2 variants and lineages to identify and monitor new strains.
Illumina COVIDSeq Assay (96 samples)
NGS can identify novel coronavirus variants, track COVID-19 transmission, and more. Compare NGS methods for various coronavirus sequencing goals.
NGS supports effective genomic surveillance strategies through identification of novel strains of coronavirus and other emerging infectious disease agents.
Genomics can advance public health and wellness by detecting and characterizing new, emerging, and circulating pathogens.
| COVIDSeq Assay (96 samples) | COVIDSeq Test (RUO Version) | Respiratory Pathogen ID/AMR Enrichment Panel Kit | Pan-Coronavirus Panel | ||
|---|---|---|---|---|---|
| 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 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 COVIDSeq Test (RUO Version) is a scalable high-throughput NGS assay (up to 3072 samples) intended for research applications. | 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. | 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. | |
| 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, MiniSeq System | MiSeq System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiniSeq System | |
| Method | Amplicon sequencing, Targeted RNA sequencing | Amplicon sequencing, Targeted RNA sequencing | Targeted DNA sequencing, Targeted RNA sequencing, Target enrichment | Whole-genome sequencing, Target enrichment | |
| Multiplexing | 8-plex on the iSeq System 30–48 plex on the MiSeq System 48-plex on the MiniSeq System | 384-plex on NextSeq 384-plex on NovaSeq | 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 | DNA, RNA | 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 | Fungal, Virus, Bacteria | Virus | |
| 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 |
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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.
COVIDSeq Assay (96 samples) index 1
20049393
Includes reagents for preparing 96 samples for detection of SARS-CoV-2. Includes index plate 1 with 96 unique dual indexes. Purchase optional positive control and optional v4 primer pools separately
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COVIDSeq Assay (96 samples) index 2
20051772
Includes reagents for preparing 96 samples for detection of SARS-CoV-2. Includes index plate 2 with 96 unique dual indexes. Purchase optional positive control and optional v4 primer pools separately
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COVIDSeq Assay (96 samples) index 3 RUO
20051773
Includes reagents for preparing 96 samples for detection of SARS-CoV-2. Includes index plate 3 with 96 unique dual indexes. Purchase optional positive control and optional v4 primer pools separately
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COVIDSeq Assay (96 samples) index 4 RUO
20051774
Includes reagents for preparing 96 samples for detection of SARS-CoV-2. Includes index plate 4 with 96 unique dual indexes. Purchase optional positive control and optional v4 primer pools separately
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COVIDSeq Positive Control
20051775
Includes 100 uL of COVIDSeq Positive Control to support quality control
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Illumina COVIDSeq v4 Primer Pools, 384 Samples RUO
20065135
Includes optional ARTIC v4 primer pools reagents sufficient for up to 384 samples. Replaces v3 primer pools included in the COVIDSeq Test (RUO) and COVIDSeq Assay (96 samples).
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The primary difference is the number of samples each assay can run. The COVIDSeq Assay (96 samples) runs up to 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.
Prepared libraries can be sequenced on any Illumina sequencing system. However, the low-throughput configuration of the COVIDSeq Assay (96) samples is ideal for Illumina benchtop sequencing systems, including the iSeq 100, MiniSeq, MiSeq, NextSeq 550, NextSeq 1000, and NextSeq 2000 Systems.
The ARTIC v3 primer pool is included with the COVIDSeq Assay (96 samples) kit. It contains primers for 98 amplicons and 11 human genes, designed against the original strain of SARS-CoV-2. The optional ARTIC v4 primer 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.
Advanced chemistry, optics, and informatics combine to deliver exceptional speed and data quality, outstanding throughput and scalability.
Optimized reagent kit that provides increased cluster density and read length, improving sequencing quality scores compared to earlier versions.
Enable CGP with a large pan-cancer panel covering all major variant classes plus gene signatures (TMB, MSI, and HRD) from FFPE tissue.
A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.
This high-throughput NGS assay enables labs to detect SARS-CoV-2 mutations to identify and track the emergence and prevalence of novel variants.
Library prep and enrichment kit that delivers highly sensitive, comprehensive respiratory pathogen identification and antimicrobial resistance insights.
A streamlined workflow offering highly sensitive detection and characterization of common respiratory viruses, including SARS-CoV-2 strains.
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