Description
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 v5.4.2 primers
Supports a seamless and flexible end-to-end workflow
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.
96 amplicons provide full coverage across SARS-CoV-2 genome for 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 Microbial Amplicon App in BaseSpace Sequence Hub.
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
Illumina COVIDSeq Assay (96 samples)
iSeq 100 System
MiniSeq System
MiSeq System
DRAGEN Microbial Amplicon App
Related applications and methods
Coronavirus sequencing
NGS can identify novel coronavirus variants, track COVID-19 transmission, and more. Compare NGS methods for various coronavirus sequencing goals.
Genomic surveillance
NGS supports effective genomic surveillance strategies through identification of novel strains of coronavirus and other emerging infectious disease agents.
Public health surveillance
Genomics can advance public health and wellness by detecting and characterizing new, emerging, and circulating pathogens.
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.
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 View less
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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 View less
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 View less
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 View less
COVIDSeq Positive Control
20051775
Includes 100 uL of COVIDSeq Positive Control to support quality control View less
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How are COVIDSeq Assay (96 samples) and COVIDSeq Test (RUO) different?
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.
Which Illumina sequencing systems are used for the COVIDSeq Assay (96 samples)?
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.
What is the difference between the ARTIC v5.4.2 primer pools and prior ARTIC pools like v3 and v4?
As SARS-CoV-2 mutates, updates to the primer pools are occasionally necessary to ensure complete coverage across the genome and improved analytical sensitivity for SARS-CoV-2 variant detection. The v5.4.2 primers provide increased coverage for recent Omicron variants.
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