COVIDSeq Assay (96 samples)

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.

Overview

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. 

  • 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, cost-effective sequencing

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.

Uniform genome coverage

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

Integrated solution

Kit includes all reagents 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 DRAGEN COVID Lineage App in BaseSpace Sequence Hub.


Specifications


Required products

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.

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Applications

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.

Example workflow



Related applications and methods

Documentation

Product literature
Support documentation

A dedicated support section is not currently available for this product

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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
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.
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
Method Targeted RNA Sequencing, Amplicon Sequencing Targeted RNA Sequencing, Amplicon Sequencing Target Enrichment, Targeted RNA Sequencing, Targeted DNA Sequencing
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
Nucleic acid type 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 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
Technology Sequencing Sequencing Sequencing

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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.

Library prep (4)

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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Accessory products (2)

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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Selection summary

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FAQs

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.

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

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.

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