Illumina COVIDSeq Test

This high-throughput next-generation sequencing (NGS) test detects SARS-CoV-2 in nasopharyngeal, oropharyngeal, and mid-turbinate nasal swabs from patients suspected of COVID-19. Read More...


Key Features and Benefits
  • Accuracy: Detects 98 targets on SARS-CoV-2 for highly accurate detection
  • Quality Control: Internal control consists of 11 human mRNA targets in every reaction
  • Flexibility: Available on NovaSeq 6000 S4 and SP flow cells and on NextSeq 500/550/550Dx (in RUO mode) HO flow cell


The Illumina COVIDSeq Test is the first NGS test approved for use under the U.S. Food and Drug Administration’s Emergency Use Authorization (EUA). 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 in 12 hours on NovaSeq 6000 system using two SP or S4 reagent kits, respectively or 384 results in 12 hours using 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 the 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.

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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 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 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.

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

This test utilizes an amplicon approach for target resequencing of SARS-CoV-2. Refer to the Instructions for Use document for workflow instructions and other details.

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 available as Research Use Only (RUO) in non-U.S. countries. Depending on the region and country, additional data may be required to enable COVIDSeq to be used as a diagnostic test.

COVIDSeq Workflow

This assay is only authorized for use with NovaSeq 6000 v1.0 S4 and SP reagent kits 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 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.

COVIDSeq Instructions for Use

This document describes the step-by-step process of the workflow, from sample collection to data analysis and report generation, and lists the required materials and equipment.

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