The Times Australia
The Times World News

.
The Times Real Estate

.

Here's how researchers identify omicron and other COVID-19 variants

  • Written by Andre Hudson, Professor and Head of the Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology
Here's how researchers identify omicron and other COVID-19 variants

How do scientists detect new variants of the virus that causes COVID-19? The answer is a process called DNA sequencing[1].

Researchers sequence DNA to determine the order of the four chemical building blocks, or nucleotides[2], that make it up: adenine, thymine, cytosine and guanine. The millions to billions[3] of these building blocks paired up together collectively make up a genome[4] that contains all the genetic information an organism needs to survive.

When an organism replicates[5], it makes a copy of its entire genome to pass on to its offspring. Sometimes errors in the copying process can lead to mutations in which one or more building blocks are swapped, deleted or inserted. This may alter genes[6], the instruction sheets for the proteins that allow an organism to function, and can ultimately affect the physical characteristics of that organism. In humans, for example, eye and hair color[7] are the result of genetic variations that can arise from mutations. In the case of the virus that causes COVID-19, SARS-CoV-2[8], mutations can change its ability to spread, cause infection or even evade the immune system.

We are both biochemists[9] and microbiologists[10] who teach about and study the genomes of bacteria. We both use DNA sequencing in our research to understand how mutations affect antibiotic resistance. The tools we use to sequence DNA in our work are the same ones scientists are using right now to study the SARS-CoV-2 virus.

The first human genome took two decades to sequence. With advances in technology, scientists are now able to sequence DNA in a matter of hours.

How are genomes sequenced?

One of the earliest methods scientists used in the 1970s and 1980s was Sanger sequencing[11], which involves cutting up DNA into short fragments and adding radioactive or fluorescent tags to identify each nucleotide. The fragments are then put through an electric sieve that sorts them by size. Compared with newer methods, Sanger sequencing is slow and can process only relatively short stretches of DNA. Despite these limitations, it provides highly accurate data[12], and some researchers are still actively using this method to sequence SARS-CoV-2 samples[13].

Since the late 1990s[14], next-generation sequencing[15] has revolutionized how researchers collect data on and understand genomes. Known as NGS, these technologies are able to process much higher volumes of DNA at the same time, significantly reducing the amount of time it takes to sequence a genome.

There are two main types of NGS platforms: second-generation and third-generation sequencers.

Second-generation sequencing marks each nucleotide with a specific color.

Second-generation technologies[16] are able to read DNA directly. After DNA is cut up into fragments, short stretches of genetic material called adapters are added to give each nucleotide a different color. For example, adenine is colored blue and cytosine is colored red. Finally, these DNA fragments are fed into a computer and reassembled into the entire genomic sequence.

Third-generation technologies[17] like the Nanopore MinIon[18] directly sequence DNA by passing the entire DNA molecule through an electrical pore in the sequencer. Because each pair of nucleotides disrupts the electrical current in a particular way, the sequencer can read these changes and upload them directly to a computer. This allows clinicians to sequence samples at point-of-care clinical and treatment facilities. However, Nanopore sequences smaller volumes of DNA compared with other NGS platforms.

Third-generation sequencing detects changes in an electrical current to identify nucleotides.

Though each class of sequencer processes DNA in a different way, they can all report the millions or billions of building blocks that make up genomes in a short time – from a few hours to a few days. For example, the Illumina NovaSeq[19] can sequence roughly 150 billion nucleotides, the equivalent of 48 human genomes, in just three days.

Using sequencing data to fight coronavirus

So why is genomic sequencing such an important tool in combating the spread of SARS-CoV-2?

Rapid public health responses to SARS-CoV-2 require intimate knowledge of how the virus is changing over time. Scientists have been using genome sequencing to track SARS-CoV-2[20] almost in real time since the start of the pandemic. Millions of individual SARS-CoV-2 genomes have been sequenced and housed in various public repositories like the Global Initiative on Sharing Avian Influenza Data[21] and the National Center for Biotechnology Information[22].

Genomic surveillance has guided public health decisions as each new variant has emerged. For example, sequencing the genome of the omicron variant[23] allowed researchers to detect over 30 mutations in the spike protein that allows the virus to bind to cells in the human body. This makes omicron a variant of concern[24], as these mutations are known to contribute to the virus’s ability to spread. Researchers are still learning[25] about how these mutations might affect the severity of the infections omicron causes, and how well it’s able to evade current vaccines.

A screen showing sequences of the letters T, C, A and G.
This image shows a DNA readout of the alpha variant of SARS-CoV-2. A mutation is marked by dotted lines. Sebastian Gollnow/picture alliance via Getty Images[26]

Sequencing also has helped researchers identify variants that spread to new regions. Upon receiving a SARS-CoV-2 sample collected from a traveler who returned from South Africa on Nov. 22, 2021, researchers at the University of California, San Francisco, were able to detect omicron’s presence in five hours[27] and had nearly the entire genome sequenced in eight. Since then, the Centers for Disease Control and Prevention has been monitoring omicron’s spread[28] and advising the government on ways to prevent widespread community transmission.

The rapid detection of omicron worldwide[29] emphasizes the power of robust genomic surveillance and the value of sharing genomic data across the globe. Understanding the genetic makeup of the virus and its variants gives researchers and public health officials insights into how to best update public health guidelines and maximize resource allocation for vaccine and drug development. By providing essential information on how to curb the spread of new variants, genomic sequencing has saved and will continue to save countless lives over the course of the pandemic.

[Get the best of The Conversation, every weekend. Sign up for our weekly newsletter[30].]

References

  1. ^ DNA sequencing (www.genome.gov)
  2. ^ nucleotides (www.genome.gov)
  3. ^ millions to billions (dx.doi.org)
  4. ^ genome (www.nature.com)
  5. ^ an organism replicates (sciencing.com)
  6. ^ genes (medlineplus.gov)
  7. ^ eye and hair color (www.doi.org)
  8. ^ SARS-CoV-2 (doi.org)
  9. ^ biochemists (scholar.google.com)
  10. ^ microbiologists (scholar.google.com)
  11. ^ Sanger sequencing (www.nature.com)
  12. ^ highly accurate data (doi.org)
  13. ^ sequence SARS-CoV-2 samples (doi.org)
  14. ^ late 1990s (dx.doi.org)
  15. ^ next-generation sequencing (dx.doi.org)
  16. ^ Second-generation technologies (doi.org)
  17. ^ Third-generation technologies (dx.doi.org)
  18. ^ Nanopore MinIon (nanoporetech.com)
  19. ^ Illumina NovaSeq (www.illumina.com)
  20. ^ using genome sequencing to track SARS-CoV-2 (www.who.int)
  21. ^ Global Initiative on Sharing Avian Influenza Data (www.gisaid.org)
  22. ^ National Center for Biotechnology Information (www.ncbi.nlm.nih.gov)
  23. ^ omicron variant (www.cdc.gov)
  24. ^ variant of concern (www.who.int)
  25. ^ still learning (doi.org)
  26. ^ Sebastian Gollnow/picture alliance via Getty Images (www.gettyimages.com)
  27. ^ detect omicron’s presence in five hours (sanfrancisco.cbslocal.com)
  28. ^ monitoring omicron’s spread (www.cdc.gov)
  29. ^ rapid detection of omicron worldwide (www.cnn.com)
  30. ^ Sign up for our weekly newsletter (memberservices.theconversation.com)

Read more https://theconversation.com/genomic-sequencing-heres-how-researchers-identify-omicron-and-other-covid-19-variants-172935

The Times Features

Why Regional Small Businesses in Bendigo Deserve Better Access to Finance in 2025

In the heart of regional Victoria, Bendigo has long stood as a beacon of innovation, resilience and community spirit. As we step further into 2025, the importance of nurturing sm...

Is It Time for a Deep Cleaning? Signs You Shouldn’t Ignore

Most people know they should visit the dentist for a regular check-up and cleaning every six months. But sometimes, a standard cleaning isn’t enough. When plaque and tartar build...

The Hidden Meaning Behind Popular Engagement Ring Cuts

When it comes to engagement rings, the cut of the diamond is not just about aesthetics. Each shape carries its own symbolism and significance, making it an important decision for...

Annual Health Exams in the Office: How They Can Reduce Sick Days and Healthcare Costs

Regular health check-ups, especially annual health exams in the office, can significantly impact the overall well-being of your workforce. A proactive approach to employee health...

Best Deals on Home Furniture Online

Key Highlights Discover the best deals on high-quality outdoor furniture online. Transform your outdoor space into a stylish and comfortable oasis. Explore a wide range of d...

Discover the Best Women's Jumpers for Every Season

Key Highlights Explore lightweight jumpers for spring and summer, ensuring breathability and ease. Wrap up warm with cozy wool jumpers for the chilly autumn and winter season...

Times Magazine

The Essential Guide to Transforming Office Spaces for Maximum Efficiency

Why Office Fitouts MatterA well-designed office can make all the difference in productivity, employee satisfaction, and client impressions. Businesses of all sizes are investing in updated office spaces to create environments that foster collaborat...

The A/B Testing Revolution: How AI Optimized Landing Pages Without Human Input

A/B testing was always integral to the web-based marketing world. Was there a button that converted better? Marketing could pit one against the other and see which option worked better. This was always through human observation, and over time, as d...

Using Countdown Timers in Email: Do They Really Increase Conversions?

In a world that's always on, where marketers are attempting to entice a subscriber and get them to convert on the same screen with one email, the power of urgency is sometimes the essential element needed. One of the most popular ways to create urg...

Types of Software Consultants

In today's technology-driven world, businesses often seek the expertise of software consultants to navigate complex software needs. There are several types of software consultants, including solution architects, project managers, and user experienc...

CWU Assistive Tech Hub is Changing Lives: Win a Free Rollator Walker This Easter!

🌟 Mobility. Independence. Community. All in One. This Easter, the CWU Assistive Tech Hub is pleased to support the Banyule community by giving away a rollator walker. The giveaway will take place during the Macleod Village Easter Egg Hunt & Ma...

"Eternal Nurture" by Cara Barilla: A Timeless Collection of Wisdom and Healing

Renowned Sydney-born author and educator Cara Barilla has released her latest book, Eternal Nurture, a profound collection of inspirational quotes designed to support mindfulness, emotional healing, and personal growth. With a deep commitment to ...

LayBy Shopping