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HomeCOVID19Genomic sequencing: This is how researchers determine omicron and different COVID-19 variants

Genomic sequencing: This is how researchers determine omicron and different COVID-19 variants


How do scientists detect new variants of the virus that causes COVID-19? The reply is a course of referred to as DNA sequencing.

Researchers sequence DNA to find out the order of the 4 chemical constructing blocks, or nucleotides, that make it up: adenine, thymine, cytosine and guanine. The thousands and thousands to billions of those constructing blocks paired up collectively collectively make up a genome that accommodates all of the genetic info an organism must survive.

When an organism replicates, it makes a replica of its whole genome to go on to its offspring. Generally errors within the copying course of can result in mutations through which a number of constructing blocks are swapped, deleted or inserted. This will likely alter genes, the instruction sheets for the proteins that permit an organism to perform, and might in the end have an effect on the bodily traits of that organism. In people, for instance, eye and hair coloration are the results of genetic variations that may come up from mutations. Within the case of the virus that causes COVID-19, SARS-CoV-2, mutations can change its capability to unfold, trigger an infection and even evade the immune system.

We’re each biochemists and microbiologists who train about and research the genomes of micro organism. We each use DNA sequencing in our analysis to know how mutations have an effect on antibiotic resistance. The instruments we use to sequence DNA in our work are the identical ones scientists are utilizing proper now to check the SARS-CoV-2 virus.

The primary human genome took 20 years to sequence. With advances in know-how, scientists at the moment are in a position to sequence DNA in a matter of hours.

How are genomes sequenced?

One of many earliest strategies scientists used within the Nineteen Seventies and Eighties was Sanger sequencing, which entails slicing up DNA into quick fragments and including radioactive or fluorescent tags to determine every nucleotide. The fragments are then put by means of an electrical sieve that types them by measurement. In contrast with newer strategies, Sanger sequencing is gradual and might course of solely comparatively quick stretches of DNA. Regardless of these limitations, it supplies extremely correct knowledge, and a few researchers are nonetheless actively utilizing this technique to sequence SARS-CoV-2 samples.

Because the late Nineteen Nineties, next-generation sequencing has revolutionized how researchers accumulate knowledge on and perceive genomes. Often known as NGS, these applied sciences are in a position to course of a lot greater volumes of DNA on the similar time, considerably decreasing the period of time it takes to sequence a genome.

There are two primary varieties of NGS platforms: second-generation and third-generation sequencers.

Second-generation sequencing marks every nucleotide with a particular coloration.

Second-generation applied sciences are in a position to learn DNA immediately. After DNA is minimize up into fragments, quick stretches of genetic materials referred to as adapters are added to offer every nucleotide a unique coloration. For instance, adenine is coloured blue and cytosine is coloured purple. Lastly, these DNA fragments are fed into a pc and reassembled into your entire genomic sequence.

Third-generation applied sciences just like the Nanopore MinIon immediately sequence DNA by passing your entire DNA molecule by means of {an electrical} pore within the sequencer. As a result of every pair of nucleotides disrupts {the electrical} present in a specific approach, the sequencer can learn these adjustments and add them on to a pc. This permits clinicians to sequence samples at point-of-care scientific and remedy amenities. Nonetheless, Nanopore sequences smaller volumes of DNA in contrast with different NGS platforms.

Third-generation sequencing detects adjustments in {an electrical} present to determine nucleotides.

Although every class of sequencer processes DNA otherwise, they will all report the thousands and thousands or billions of constructing blocks that make up genomes in a short while – from just a few hours to a couple days. For instance, the Illumina NovaSeq can sequence roughly 150 billion nucleotides, the equal of 48 human genomes, in simply three days.

Utilizing sequencing knowledge to battle coronavirus

So why is genomic sequencing such an vital software in combating the unfold of SARS-CoV-2?

Speedy public well being responses to SARS-CoV-2 require intimate data of how the virus is altering over time. Scientists have been utilizing genome sequencing to trace SARS-CoV-2 virtually in actual time because the begin of the pandemic. Tens of millions of particular person SARS-CoV-2 genomes have been sequenced and housed in numerous public repositories just like the International Initiative on Sharing Avian Influenza Information and the Nationwide Heart for Biotechnology Data.

Genomic surveillance has guided public well being choices as every new variant has emerged. For instance, sequencing the genome of the omicron variant allowed researchers to detect over 30 mutations within the spike protein that enables the virus to bind to cells within the human physique. This makes omicron a variant of concern, as these mutations are recognized to contribute to the virus’s capability to unfold. Researchers are nonetheless studying about how these mutations may have an effect on the severity of the infections omicron causes, and the way effectively it’s in a position to evade present vaccines.

This picture exhibits a DNA readout of the alpha variant of SARS-CoV-2. A mutation is marked by dotted traces.
Sebastian Gollnow/image alliance by way of Getty Photos

Sequencing additionally has helped researchers determine variants that unfold to new areas. Upon receiving a SARS-CoV-2 pattern collected from a traveler who returned from South Africa on Nov. 22, 2021, researchers on the College of California, San Francisco, have been in a position to detect omicron’s presence in 5 hours and had almost your entire genome sequenced in eight. Since then, the Facilities for Illness Management and Prevention has been monitoring omicron’s unfold and advising the federal government on methods to forestall widespread neighborhood transmission.

The fast detection of omicron worldwide emphasizes the ability of sturdy genomic surveillance and the worth of sharing genomic knowledge throughout the globe. Understanding the genetic make-up of the virus and its variants provides researchers and public well being officers insights into find out how to greatest replace public well being tips and maximize useful resource allocation for vaccine and drug growth. By offering important info on find out how to curb the unfold of latest variants, genomic sequencing has saved and can proceed to avoid wasting numerous lives over the course of the pandemic.

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