Coronavirus Sequencing


How NGS Helps Fight COVID-19

Next-generation sequencing (NGS) provides an effective, unbiased way to identify new coronavirus strains and other pathogens without prior knowledge of organisms1. Growing concern over fast spreading, novel variants of the SARS-CoV-2 coronavirus, such as the Alpha (B.1.1.7), Beta (B.1.351), Gamma (P1, Brazil), Delta (B.1.617.2) and Omicron (B.1.1.529) strains, highlights the need for more sequencing to detect mutations quickly and prevent the spread of new strains. Sequencing was used to identify the novel coronavirus causing COVID-19 (SARS-CoV-2) early in the outbreak2. NGS continues to provide public health officials, vaccine and drug developers, and researchers with critical evidence, allowing labs to:

  • Track the transmission routes of the virus globally
  • Detect mutations quickly to prevent the spread of new strain types
  • Identify viral mutations that can affect vaccine potency or avoid detection by established molecular diagnostic assays
  • Screen targets for possible COVID-19 therapeutics
  • Identify and characterize respiratory co-infections and antimicrobial resistance alleles
Surveilance of SARS-CoV-2 for Any Lab
The COVIDSeq Assay (96 samples) enables labs of any size to detect SARS-CoV-2 virus mutations and provides critical information to prevent the spread of new strain types.

Compare Coronavirus NGS Methods

  Surveillance of SARS-CoV-2 Detection and Surveillance of Respiratory Pathogens Detect Novel Virus
Testing Needs Amplicon
Illumina COVIDSeq Test (RUO)
COVIDSeq Assay
Target Enrichment Shotgun Metagenomics
Speed & Turnaround Time      
Scalable & Cost-Effective      
Identify Novel Pathogens      
Track Transmission      
Detect Mutations      
Identify Co-Infections & Complex Disease      
Detect Antimicrobial Resistance      

Adequately meets laboratory testing needs

Partially meets laboratory testing needs

More About Coronavirus Sequencing Methods

Amplicon Sequencing

Detect the presence of the SARS-CoV-2 coronavirus by sequencing specific regions of the viral genome. This method involves analyzing genomic regions of interest with ultra-deep sequencing of PCR amplicons.

Target Enrichment Sequencing

Detect and characterize coronaviruses, flu viruses, and other pathogenic respiratory tract organisms, as well as associated antimicrobial resistance alleles. These insights can help researchers monitor respiratory infections and optimize infection control strategies. This method captures genomic regions of interest via hybridization to target-specific probes.

Shotgun Metagenomics

Comprehensively sequence all organisms in a given sample and identify novel pathogens such as coronaviruses. This NGS method can help accelerate outbreak investigations and support development of new laboratory tests.

Featured SARS-CoV-2 Amplicon Sequencing Workflows

Frequently Purchased Together

COVID-19 NGS Webinars

Genomic Applications in the Fight against SARS-CoV-2

Two leading infectious disease researchers discuss how genomic sequencing technologies are tackling the COVID-19 pandemic.

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Clinical Metagenomics Analysis for SARS-CoV-2

The COVID-19 pandemic has underscored the need for tools to detect and monitor emerging pathogens like SARS-CoV-2. NGS led to the initial detection of the coronavirus, and is accelerating test and vaccine development.

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NGS for SARS-CoV-2 Detection and Monitoring

Learn about the broad applicability of NGS for responding to the COVID-19 pandemic, from initial detection and characterization of the novel coronavirus to monitoring, surveillance, and diagnostic detection.

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Coronavirus Sequencing Application Notes

Detect Respiratory Pathogens & Antimicrobial Resistance

Rapid target enrichment sequencing for broad detection of respiratory pathogens (including SARS-CoV-2, flu viruses, and fungi) and associated antimicrobial resistance alleles.

Respiratory Pathogen ID/AMR Workflow Application Note
Analytical Performance of the Respiratory Pathogen ID/AMR Workflow Application Note
Find and Characterize Respiratory Viruses

A rapid target enrichment sequencing workflow for highly sensitive detection and characterization of coronaviruses, flu viruses, and other respiratory viruses.

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Rapidly Detect Respiratory Viruses with the Illumina MiniSeq System

MiniSeq Rapid reagents reduce sequencing run times to < 5 hours, allowing fast detection of coronaviruses and other respiratory viruses.

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Coronavirus Software Tools
These tools accelerate coronavirus sequencing data analysis, simplify sample tracking, facilitate host response studies, and make it easier for scientists to contribute to public databases.


At a basic level, diagnostic testing helps clinicians manage patients, and infectious disease 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.

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. Development of PCR assays requires knowledge of the pathogen genome. NGS plays a critical role in discovering these unknown, novel pathogens; 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 address whether 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 rapidly evolving pathogen genomes. Furthermore, PCR performance can suffer if mutations occur in the primer or probe binding regions.

Epidemiologists can utilize NGS to study viral genome mutations from patient samples across the globe. They 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 allow 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 metagenomics workflow enables sequencing of both novel and known species. During an outbreak involving an unknown pathogen, multiple molecular diagnostic tests are often utilized; this may lead to unnecessary costs and delays in identifying the pathogen. Shotgun metagenomics can be used as a single comprehensive screening assay for identifying and characterizing pathogens. This research workflow can help accelerate outbreak investigations and support development of new lab 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. This information can help researchers optimize infection control strategies, including monitoring when it's 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.

The Respiratory Virus Oligo Panel includes 7,800 probes to sequence common respiratory viruses, recent flu strains, SARS-CoV-2, and other coronaviruses, 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 rapidly evolving pathogen genomes (as 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 coronavirus evolution or viral surveillance studies. 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.

Once a pathogen like the SARS-CoV-2 coronavirus has been identified, amplicon sequencing can provide cost-effective, rapid, and scalable detection of the pathogen. 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, viral whole-genome sequencing can be used to monitor viral mutations and allows phylogenetic analysis.

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

The Illumina Respiratory Virus Oligo Panel expands detection to ~30 families of respiratory viruses and allows researchers to study co-infections with other viruses in the panel.

The Illumina COVIDSeq Test (3076 samples) and COVIDSeq Assay (96 samples) are amplicon-based NGS products designed to detect RNA from the SARS-CoV-2 virus.

Learn more about: Illumina COVIDSeq Test (EUA) / Illumina COVIDSeq Test (RUO) / COVIDSeq Assay (96 samples)

Visit our Sequencing Platforms page to explore our portfolio. The choice of sequencer depends on which method(s) you use most frequently. See the workflows above for recommendations on which sequencer is optimal for which method.

Building a State-of-the-Art Clinical Research Sequencing Lab in Israel

Genomics center established in record time to combat COVID-19 pandemic.

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Paving the Way with COVID-19 Sequencing

A Utah Public Health Lab director discusses how they've expanded their NGS operations in an effort to zero in on SARS-CoV-2 outbreak clusters and establish an infrastructure for future pandemics.

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Creating an Australian COVID-19 Tracking System

In a groundbreaking initiative, public health labs use Illumina technology to sequence the viral genomes of all positive COVID-19 tests in Australia and track COVID-19 across the country, rather than state by state.

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Accelerating COVID-19 Host Response Research

A collaborative environment leveraging BaseSpace Correlation Engine helps COVID-19 researchers validate hypotheses around important pathways, biomarkers, and potential drug candidate leads.

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Improving COVID Sequencing in a Changing Pandemic

How Aegis Sciences moved with the mutations, expanded capacity, and became one of the largest COVID sequencing operations in the world.

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Technical Tips

Decontaminating Illumina Sequencers for Novel Coronavirus

In keeping with recommendations from the United States CDC and World Health Organization, Illumina recommends this procedure for decontaminating NGS instruments suspected or known to have come in contact with the novel coronavirus SARS-CoV-2 (2019-nCoV).

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Impact of Ammonium-Based Cleaning Products on Sequencing Run Performance

Use of ammonia-based cleaners and sanitizing products (frequently utilized to clean labs during the COVID-19 pandemic) in proximity to sequencing run setup can result in decreased sequencing run performance metrics. View tips on how to avoid these issues.

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Shotgun Metagenomics Supporting Products

Sequencing, RUO, RNA
Illumina Stranded Total RNA Prep with Ribo-Zero Plus

Rapid library preparation from a broad range of sample types for studying the coding and non-coding transcriptome with unparalleled study flexibility.

rRNA Depletion Kit
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
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.

Target Enrichment Supporting Products

iSeq 100
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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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

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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How Sequencing-Based Surveillance Helps Fight COVID-19

Phil Febbo, MD, Chief Medical Officer of Illumina, discusses five main ways in which next-generation sequencing-based surveillance is used to fight the SARS-CoV-2 coronavirus.

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Want to talk to someone about COVID-19 sequencing solutions for your lab?

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Related Solutions

Shotgun Metagenomics

Comprehensively sequence all organisms present in a given complex sample. Identify novel pathogens or detect microbial abundance in various environments.

Learn More
Target Enrichment

Target enrichment through hybrid–capture methods allows for highly sensitive detection, without requiring the high read depth needed for shotgun metagenomic sequencing.

Learn More
Amplicon Sequencing

Simultaneously assess a few to hundreds of genes or targets in a single run with this highly targeted multiplex PCR-based sequencing approach.

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  1. Bulcha B. Review on viral metagenomics and its future perspective in zoonotic and arboviral disease surveillance. J Biol Agr Healthc. 2017; 7(21): 35–41.
  2. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med. 2020; 382(8): 727–733.