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Supporting Global COVID-19 Efforts

Testing can make all the difference
COVIDSeq, the first diagnostic NGS test to receive emergency use authorization from the FDA.
UCSF Charles Chiu with NextSeq
In sequencing the coronavirus, Dr. Chiu could have keys to the disease

When UCSF's Charles Chiu was tapped by the CDC to sequence viral strains from throughout the state, he knew he needed more capacity.

Dr Bedform of Washington
Dr. Bedford helps trace and halt community spread in Washington

With the help of Illumina NextSeq 550 and reagents, Dr. Bedford was able to identify one of the first COVID-19 clusters in the US.

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How next-generation sequencing can help identify and track SARS-CoV-2

Illumina has developed two workflows to detect and track SARS-CoV-2 from clinical samples.

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The power of NGS: from identification to vaccine development to outbreak control

Next-generation sequencing (NGS) has the unique ability to support scientists, researchers, public health officials and health care professionals on the front lines. It helps us understand transmission routes, comorbidities, mutation rates, serves as a foundation for vaccine development and therapies, and ultimately helps predict and prevent future outbreaks.

Learn More from CMO Phil Febbo
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Connecting those who look for answers with the technology to find them

We believe access to the best technologies, global networks, and genomic insights are crucial to stop this pandemic and keep it from coming back. This is why we work with researchers, the CDC, the Chinese CDC, the NIH, GISAID, Stanford, the Broad Institute, and more to make sure they have the genomic and sequencing support they need to succeed.

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Global needs are our responsibility

We are a global company championing the greater good, committed to supporting COVID-19 efforts around the world. We are proud to partner to fund the Africa Centre of Excellence for Genomics of Infectious Diseases as well as the Milken Institute to develop global surveillance networks.

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Our unique ability to help

With our decades of experience, vast global reach, support across countries and languages, as well as data transparency, we are afforded a humbling opportunity to quickly connect and support local and global resources to fight this pandemic across the world.

How We Support the Fight Against COVID-19

Global
Illumina makes software toolkit available free of charge to support worldwide efforts to combat COVID-19
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Africa
Illumina’s Donation to the Africa Centre for Disease Control and Prevention Expands their Capability for Sequencing-Based COVID-19 Surveillance
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UK
UK launches whole genome sequence alliance to map spread of coronavirus
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China
Providing the system used to sequence the first COVID‑19 genome in Wuhan
Cambodia
iSeq 100 System + iSeq cloud metagenomic platform to allow characterization of Cambodian COVID‑19
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USA
New York COVID-19 Genomics Research Network Coalesces to Battle Pandemic
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Comprehensive and integrated testing methods can aid in management of COVID-19. Pathogen genomics is complementary to traditional methods and Illumina NGS is uniquely positioned in an infectious disease surveillance and outbreak model.

Workflow Comparison Table

  Detect Novel Virus Detect SARS-COV-2 and Diagnose COVID-19 Detect Co-Infections and Monitor Viral Evolution Detect Patient Immunity
Testing Needs Metagenomics PCR/qPCR Amplicon Illumina COVIDSeq Test Targeted Enrichment Respiratory Virus Oligo Panel Serology
Speed and TAT          
Scalable and Cost Effective          
Identification of Novel Pathogen          
Track Transmissions          
Unaffected by Mutational Changes          
Identify Co-Infection and Complex Disease          
Identifies Pathogens Present at Low Levels in Samples With High Background          

Adequately meets laboratory testing needs based on phase of outbreak

Partially meets laboratory testing needs based on phase of outbreak

Illumina COVID-19 Application Notes & Customer Guide

How to Detect Coronavirus Using Illumina Systems

A shotgun metagenomics sequencing workflow for effective detection and characterization of coronavirus strains.

Read Application Note
Targeted Sequencing with the Respiratory Virus Panel on Illumina Systems

Effective detection of coronavirus using a comprehensive targeted enrichment worklflow.

Read Application Note
Detect Coronavirus with the Respiratory Virus Panel

A resource guide for detection and full genome sequencing of SARS-CoV-2 and a broad spectrum of respiratory viruses.

Read Customer Guide
Illumina and IDbyDNA Partner to Deliver NGS Infectious Disease Solutions

Partnership aims to accelerate NGS adoption for clinical infectious disease testing.

Read the Article
Join the conversation

Register now for a conversation with former U.S. FDA Commissioner Dr. Scott Gottlieb: “Genomics’ Role in Global COVID-19 Surveillance”

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FAQs

At a basic level, diagnostic testing helps clinicians manage patients and surveillance is required to manage populations.

Diagnostic testing provides important yes/no answers for individual patients so that appropriate management can be provided.

Surveillance helps public health officials track the path of the epidemic, understand transmission routes, perform contact tracing, determine the rate of viral evolution, and understand if the virus is changing in ways that could impact diagnostic or therapeutic effectiveness.

Very early in an outbreak, when traditional methods such as culture, PCR/qPCR or ELISA are unable to identify a pathogen causing illness in the first cluster of patients, NGS plays a critical role in identification of the novel pathogen. Once the pathogen is identified and the genome is shared publicly, diagnostic tests (PCR) can be developed based on the pathogen’s genomic sequence to help clinicians manage patients.

After pathogen identification, NGS continues to play an important role by providing public health officials, vaccine and drug developers, and researchers with critical evidence that enables:

  • Tracking the transmission route of the virus globally, which can enable containment and control measures
  • Determining how quickly the virus is mutating as it spreads
  • Identifing targets for therapies
  • Understanding the role of co-infection

NGS can provide unbiased detection of a novel pathogen in patient samples without prior knowledge of the organism.

A key challenge in infectious disease detection is that many of the microbes, including viruses, that cause respiratory, digestive, and other diseases in humans, have not been researched and characterized and thus are not known or detected by targeted approaches, such as PCR, the development of which require knowledge of the pathogen genome. NGS plays a critical role in discovering these unknown, novel pathogens and the resulting genome sequence can then be used to develop routine tests such as PCR to help clinicians manage patients.

NGS can be used to track the evolution of the pathogen genome to help public health officials monitor the spread of infection and determine the best isolation plan at a population level. Sequencing the virus from different patients over time can determine the rate of viral evolution and understanding if the virus is changing in ways that could impact pathogenicity as well as diagnostic or therapeutic effectiveness. PCR is designed to detect the presence of specific regions of the pathogen genome and will not identify new mutations across these rapidly evolving pathogen genomes. Furthermore, PCR performance can suffer if mutations occur in the primer or probe binding regions.

Epidemiologists study the mutations of the viral genome from patient samples across the globe and can use this information to build a genetic tree (or map) that can indicate the path of transmission between patients. Clusters due to genetic similarities in the pathogen belong to patients within the same transmission chains. These transmission chains enable public health officials to quickly determine the pathogen origin, track the path of the epidemic, understand transmission routes and inform appropriate containment measures.

A shotgun metagenomic workflow enables detection of both novel and known species. When faced with an unknown outbreak, multiple molecular diagnostic tests are often used which may lead to unnecessary cost and delays in identifying the pathogen. Shotgun Metagenomics can be used as a single comprehensive screening test for identifying and characterizing pathogens. This research workflow can help accelerate outbreak investigations and support development of new laboratory tests for large scale screening efforts.

Once a pathogen, such as SARS-CoV-2 is identified, a target enrichment workflow can provide the high sensitivity needed to detect the virus and provide information about its epidemiology and evolution to help researchers optimize infection control strategies including monitoring when its acceptable to de-escalate isolation mechanisms and resume normal activities, and aid in the development of vaccines.

These complementary workflows using Illumina sequencing can be performed alongside traditional testing methods and integrated into a comprehensive outbreak response model.

Illumina has made several solutions available for SARS-CoV-2 detection and analysis.

To support researchers with the analysis and sharing of genomic data related to the severe acute respiratory syndrome coronavirus outbreak, Illumina has released the Illumina SARS-CoV-2 NGS Data Toolkit – a new suite of data analysis tools for researchers working with the virus. These tools make it simpler for researchers to detect and identify the SARS-CoV-2 viral sequence in their samples and contribute their findings to critical public databases.

Learn More About the Illumina SARS-CoV-2 NGS Data Toolkit

For users looking to generate clinical reporting of SARS-CoV-2 detection to diagnose COVID-19 in symptomatic patients, the DRAGEN COVIDSeq test pipeline is used in conjunction with the Illumina COVIDSeq test.

For users looking to generate clinical reports for shotgun metagenomics or for the respiratory virus oligo panel, Illumina's partnership with IDbyDNA delivers simple, powerful bioinformatics software to turn the data generated by our sequencers into actionable insights.

IDbyDNA’s proven, automated Explify platform analysis supports the detection of 35 respiratory viruses, including genomic characterization of SARS-CoV-2. Contact IDbyDNA Client Services at 833-397-5439 or clientservices@idbydna.com to learn more.

Tool/Pipeline Overview
DRAGEN COVIDSeq Test Pipeline
  • For use with the Illumina COVIDSeq Test (EUA) for clinical analysis and reporting of SARS-CoV-2 detection to aid in the diagnosis of COVID-19
  • An RUO version of this pipeline is available for use with the Illumina COVIDSeq Test (RUO and PEO)
DRAGEN Metagenomics
  • Host removal & taxonomic classification w/ Kraken 2
  • Rich reporting including organism detection report
  • Updated 2020 database with SARS-Cov-2
DRAGEN RNA Pathogen Detection
  • Custom human + virus references
  • Integrates DRAGEN k-mer Matcher for viral detection
GISAID Submission App
  • Push-button submission to GISAID public database
IDbyDNA Explify
  • Easy to use, clinical analysis and reporting of shotgun metagenomic data and/or respiratory viral oligo panel results (IDbyDNA Explify RVOP platform)
SRA Submission
  • Push-button submission of raw read data to NCBI's SRA (Short Read Archive) database
SRA Import
  • Push-button import of data from NCBI's SRA database

Identification & Detection

Data Sharing

There are 7,800 probes to detect common respiratory viruses, recent flu strains, and SARS-CoV-2 as well as human probes to act as positive controls. These probes are 80-mer oligos, spaced very close together providing full genome coverage of all viruses in the panel. Table of viruses in the panel:

  • Human coronavirus 229E
  • Human coronavirus NL63
  • Human coronavirus OC43
  • Human coronavirus HKU1
  • SARS-CoV-2
  • Human adenovirus B1
  • Human adenovirus C2
  • Human adenovirus E4
  • Human bocavirus 1 (Primate bocaparvovirus 1 isolate st2)
  • Human bocavirus 2c PK isolate PK-5510
  • Human bocavirus 3
  • Human parainfluenza virus 1
  • Human parainfluenza virus 2
  • Human parainfluenza virus 3
  • Human parainfluenza virus 4a
  • Human metapneumovirus (CAN97-83)
  • Respiratory syncytial virus (type A)
  • Human Respiratory syncytial virus 9320 (type B)
  • Influenza A virus (A/Puerto Rico/8/1934(H1N1))
  • Influenza A virus (A/Korea/426/1968(H2N2))
  • Influenza A virus (A/New York/392/2004(H3N2))
  • Influenza A virus (A/goose/Guangdong/1/1996(H5N1))
  • Human bocavirus 4 NI strain HBoV4-NI-385
  • KI polyomavirus Stockholm 60
  • WU Polyomavirus
  • Human parechovirus type 1 PicoBank/HPeV1/a
  • Human parechovirus 6
  • Human rhinovirus A89
  • Human rhinovirus C (strain 024)
  • Human rhinovirus B14
  • Human enterovirus C104 strain: AK11
  • Human enterovirus C109 isolate NICA08-4327
  • Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
  • Influenza A virus (A/Hong Kong/1073/99(H9N2))
  • Influenza A virus (A/Texas/50/2012(H3N2))
  • Influenza A virus (A/Michigan/45/2015(H1N1))
  • Influenza B virus (B/Lee/1940)
  • Influenza B virus (B/Wisconsin/01/2010)
  • Influenza B virus (B/Brisbane/60/2008)
  • Influenza B virus (B/Colorado/06/2017)
  • Influenza B virus (B/Washington/02/2019)
  • Human control genes

Target enrichment is a resequencing method that captures genomic regions of interest by hybridization to target-specific biotinylated probes. Target enrichment through hybrid–capture methods allows for highly sensitive detection and therefore does not require high read depth. Additionally, the target enrichment NGS workflow allows for near-complete sequence data of targets and opens up applications such as variant analysis for viral evolution or viral surveillance.

Alternatively, amplicon sequencing is designed to detect the presence of the target pathogen in a sample by identifying specific regions of the pathogen genome. This method does not enable identification of new mutations across these rapidly evolving pathogen genomes which is required for viral evolution or viral surveillance studies.

The target enrichment NGS workflow allows for near-complete sequence data of targets and opens up applications such as variant analysis for viral evolution or viral surveillance. Compared to other targeted resequencing methods, such as amplicon sequencing, enrichment through hybrid capture allows for dramatically larger probe panels with more comprehensive profiling of the target regions. Additionally, the oligo probes used for hybrid–capture protocols remain effective, even within highly mutagenic regions, which can be difficult for amplicon-based assays such as qPCR, allowing targeting of rapidly evolving viruses, such as RNA viruses.

When traditional methods such as culture, PCR/qPCR or ELISA are unable to identify the pathogen causing the illness, Shotgun Metagenomics (mNGS) is a sequencing method that comprehensively examines all organisms present in a given complex sample to enable researchers to identify the novel pathogen causing the disease, like SARS-CoV-2.

Beyond merely detecting viral particles, Shotgun Metagenomics can provide the full genome sequence of pathogens like SARS-CoV-2 virus at high titer to help accelerate outbreak investigations.

By identifying known and novel pathogens in a sample (virus + bacteria + fungal), researchers can use this information to study and identify co-infections associated with a target pathogen like SARS-CoV-2.

Once the pathogen has been identified, amplicon can provide cost effective, rapid, and scalable detection of SARS-CoV-2. When used as a general whole genome sequencing diagnostic approach, it allows for broader target coverage, making it less susceptible to mutational effects. For research, whole genome sequencing can be used to monitor viral mutations and allows phylogenetic analysis.

Once the pathogen has been identified, the viral enrichment panel provides high sensitivity detection coupled with epidemiology information by detecting the full SARS-CoV-2 genome and the genomic mutations found across different samples. This information helps define the epidemiology of transmission and public officials can optimize infection control strategies.

When used with Illumina’s Respiratory Virus Oligo Panel, detection is expanded to ~30 families of respiratory viruses and allows researchers to study and identify co-infections with other viruses in the panel.

The Illumina COVIDSeq Test is the first NGS test to receive emergency use authorization (EUA) from FDA to be used in the U.S. for detection of SARS-CoV-2 and diagnosis of COVID-19 in symptomatic patients.

We offer a Performance Evaluation Only (PEO) version of the Illumina COVIDSeq Test for European countries regulated by CE-IVD, and a Research Use Only (RUO) version for other countries outside of the U.S. These products can be used for detection of SARS-CoV-2 in research settings.

Shotgun Metagenomics Supporting Products

TruSeq Stranded Total RNA

This library prep kit is a robust, highly scalable whole-transcriptome analysis (RNA-Seq) solution for a variety of species and sample types.

rRNA Depletion Kit

The stand-alone Illumina Ribo-Zero Plus kit allows for ribosomal RNA removal in human, mouse, rat, and bacterial samples.

NextSeq 2000

Groundbreaking benchtop sequencers allow you to explore new science across a variety of current and emerging applications, with higher efficiency and fewer restraints.

Enrichment Supporting Products

iSeq 100

The iSeq 100 system leverages the speed and affordability of complementary metal-oxide-semiconductor (CMOS) technology and the accuracy of sequencing by synthesis (SBS) chemistry.

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MiSeq

The MiSeq benchtop sequencer enables targeted and microbial genome applications, with high-quality sequencing, simple data analysis, and cloud storage.

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Illumina RNA Prep with Enrichment

Illumina RNA Prep with Enrichment is the fastest and most flexible targeted sequencing solution for RNA in the Illumina library prep portfolio.

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