Illumina COVIDSeq Test

This high-throughput, next-generation sequencing test detects SARS-CoV-2 in patients suspected of COVID-19 and enables virus genome analysis in research use. Read More...


Key Features and Benefits
  • Accurate: Detects 98 targets on SARS-CoV-2 for highly accurate detection
  • Comprehensive: Detects SARS-CoV-2 virus RNA; reports consensus genome calling for virus analysis under research use
  • Quality Controlled: Built in quality control features in every reaction
  • Flexible: Seamless end-to-end workflow. Temperature specification allows use of different thermocyclers.
  • Scalable: Available on NovaSeq 6000, NextSeq 2000, or NextSeq 500/550/550Dx (in RUO mode) systems.

Product Highlights

The Illumina COVIDSeq Test is intended for detection of SARS-CoV-2 virus RNA in authorized countries* and virus genome analysis for research use. Insight into the SARS-CoV-2 strain present in the sample enables tracking of virus strains.  This amplicon-based NGS test includes 2019-nCoV primers designed to detect RNA from the SARS-CoV-2 virus in nasopharyngeal, oropharyngeal, and mid-turbinate nasal swabs from patients with signs and symptoms of infection who are suspected of COVID-19.

Rapid, Scalable SARS-CoV-2 Detection

The Illumina COVIDSeq Test can be scaled up or down to accommodate different numbers of samples. 1536 to 3072 results can be processed on the NovaSeq 6000 system in 12 hours using two SP or S4 reagent kits, or 384 results in 12 hours using the NextSeq 2000 or the NextSeq 500/550/550Dx (in RUO 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 NextSeq 2000 System or NextSeq 500/550/550Dx (in RUO mode) Systems, coupled with the Illumina COVIDSeq Test and the DRAGEN COVIDSeq Test Pipeline or DRAGEN COVIDSeq Test App in BaseSpace Sequence Hub for rapid analysis.

Design and Quality Control

The Illumina COVIDSeq Test 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. As a quality feature, an internal control consisting of 11 human mRNA targets is included in every sample. The test reports consensus sequence when +90 amplicons are detected, which enables virus genome analysis to help track virus strains in research settings.

Frequently Purchased Together


Intended Use

EUA Approved Intended Use

The Illumina COVIDSeq Test is a Next-Generation Sequencing (NGS) in vitro diagnostic test on the Illumina NovaSeq 6000 Sequencing System, NextSeq 2000 Sequencing System, NextSeq 500 Sequencing System, NextSeq 550 Sequencing System, or NextSeq 550Dx Instrument intended for the qualitative detection of SARS-CoV-2 RNA from nasopharyngeal (NP) swabs, oropharyngeal (OP) swabs, anterior nasal swabs, mid-turbinate nasal swabs, nasopharyngeal wash/aspirates, nasal aspirates, and bronchoalveolar lavage (BAL) specimens from individuals suspected of COVID-19 by their healthcare provider.

Testing is limited to laboratories certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA), 42 U.S.C. §263a, to perform high complexity tests.

Results are for the identification of SARS-CoV-2 RNA. The SARS-CoV-2 RNA is generally detectable in respiratory specimens during the acute phase of infection. Positive results are indicative of the presence of SARS-CoV-2 RNA; clinical correlation with patient history and other diagnostic information is necessary to determine patient infection status. Positive results do not rule out bacterial infection or co-infection with other viruses. Laboratories within the United States and its territories are required to report all positive results to the appropriate health authorities.Negative results do not preclude SARS-CoV-2 infection and should not be used as the sole basis for patient management decisions.

Negative results must be combined with clinical observations, patient history, and epidemiological information. The Illumina COVIDSeq Test is intended for use by qualified and trained clinical laboratory personnel specifically trained in the use of the NovaSeq 6000 Sequencing System, the NextSeq 2000 Sequencing System, the NextSeq 500 Sequencing System, the NextSeq 550 Sequencing System, or the NextSeq 550Dx Instrument, as well as Next-Generation Sequencing workflows and in vitro diagnostic procedures. The Illumina COVIDSeq Test is only for use under the Food and Drug Administration’s Emergency Use Authorization.

Contact an Illumina representative for regional availability.

High-Level Workflow

Frequently Asked Questions

About the COVIDSeq Test

This test has been authorized by FDA under an emergency use authorization (EUA) for use as an in vitro diagnostic test for detection and/or diagnosis of COVID-19.

COVIDSeq can be used to perform strain typing for monitoring virus evolution and epidemiology. It can be used to report virus sequence in a clinical sample for Public Health and research applications.

The Illumina COVIDSeq test does not provide information on the role of specific mutations detected and its risk to reduced vaccine efficacy, impact on transmissibility, or impact on patient.

No, this test only detects SARS-CoV-2, the virus causing COVID-19.

This test uses an amplicon approach for target resequencing of SARS-CoV-2. Consensus sequence is reported when +90 amplicons are detected. This information enables virus genome analysis for research use and provides insight into the SARS-CoV-2 strain present in the sample to help researchers track virus strains.

Emergency Use Authorization authorizes the FDA to facilitate the availability of an unapproved product, or an unapproved use of an approved product, during a declared state of emergency. When the state of emergency ends, the test is no longer authorized for clinical use and defaults to standard regulatory requirements.

Testing is limited to laboratories certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA), 42 U.S.C. §263a, to perform high complexity tests.

More testing is necessary to control the global pandemic and return to work, school, and normal activities. However, there is a major shortage in COVID-19 testing-related products, and many clinical labs are facing capacity and resource constraints. COVIDSeq, leveraging highly scalable and accurate sequencing technology, is enabling labs to ramp up and diversify testing, contributing to improving testing capacity for COVID-19.

This product is intended for detection of SARS-CoV-2 virus RNA in authorized countries (Canada, Japan, Philippines, Singapore, and U.S.) under each country’s respective authorizing agency.* Depending on the region and country, additional data may be required to enable COVIDSeq to be used as a diagnostic test. A Research Use Only (RUO) version of this product is available for virus genome analysis for research use.

COVIDSeq Workflow

This assay is only authorized for use with NovaSeq 6000 v1.0 S4 and SP reagent kits, with NextSeq 2000, and with NextSeq 500, 550, 550Dx (in RUO mode) v2.5 HO reagent kit. Use of other systems and/or reagent kits would require independent validation and a separate Emergency Use Authorization submission.

This test is authorized for use with nasopharyngeal (NP), oropharyngeal (OP), and mid-turbinate (MT) nasal swabs.

Up to 384 samples can be loaded per lane on a NovaSeq S4 and SP flow cell for a total of 1536 samples per S4 flow cell and 768 per SP flow cell. Two flow cells can be run simultaneously for a total of 3072 or 1536 samples per run respectively.

Up to 384 samples per run on the NextSeq 2000.

Up to 384 samples can be loaded per HO flow cell.

Up to 384 unique dual indexes (IDT for Illumina PCR Indexes Sets 1-4) are available through Illumina.

Analysis and Reporting

Analysis is performed by the DRAGEN COVIDSeq Test Pipeline installed on the local DRAGEN server or by the DRAGEN COVIDSeq Test App on BaseSpace Sequence Hub.

A positive test result for COVID-19 indicates that RNA from SARS-CoV-2 was detected, and the patient is infected with the virus and presumed to be contagious. Laboratory test results should always be considered in the context of clinical observations and epidemiological data in making a final diagnosis and patient management decisions. Patient management should follow current CDC guidelines.

A negative test result for this test means that SARS-CoV-2 RNA was not present in the specimen above the limit of detection. However, a negative result does not rule out COVID-19 and should not be used as the sole basis for treatment or patient management decisions. A negative result does not exclude the possibility of COVID-19.

*Authorizing agencies: Health Canada in Canada, the Pharmaceuticals and Medical Devices Agency (PMDA) in Japan, the Food and Drug Administration in the Philippines, the South African Health Products Authority (SAHPRA) in South Africa, and the Food and Drug Administration in the U.S.