How do researchers discover new variants of the virus that causes COVID-19? The response is a procedure called DNA sequencing.
Scientist series DNA to figure out the order of the 4 chemical structure blocks, or nucleotides, that make it up: adenine, thymine, cytosine, and guanine. The millions to billions of these foundation combined up together jointly make up a genome which contains all the hereditary info an organism requires to endure.
When an organism duplicates, it makes a copy of its entire genome to hand down to its offspring. Sometimes mistakes in the copying procedure can result in mutations in which one or more foundation are switched, deleted or placed. This might alter genes, the guideline sheets for the proteins that allow an organism to work, and can eventually impact the physical qualities of that organism. In human beings, for eye, hair and example color are the result of genetic variations that can develop from mutations. In the case of the infection that causes COVID-19, SARS-CoV-2, anomalies can change its capability to spread out, cause infection and even evade the immune system.
We are both microbiologists and biochemists who teach about and study the genomes of germs. We both use DNA sequencing in our research to understand how mutations impact antibiotic resistance. The tools we use to series DNA in our work are the same ones scientists are using right now to study the SARS-CoV-2 virus.
The very first human genome took twenty years to series. With advances in innovation, scientists are now able to series DNA in a matter of hours.
How are genomes sequenced?
One of the earliest techniques scientists utilized in the 1970s and 1980s was Sanger sequencing, which includes cutting up DNA into short fragments and including fluorescent or radioactive tags to identify each nucleotide. The pieces are then executed an electrical sieve that sorts them by size. Compared to newer approaches, Sanger sequencing is sluggish and can process only fairly short stretches of DNA. In spite of these limitations, it supplies highly precise information, and some scientists are still actively utilizing this method to sequence SARS-CoV-2 samples.
Because the late 1990s, next-generation sequencing has actually changed how scientists collect data on and comprehend genomes. Called NGS, these technologies are able to process much greater volumes of DNA at the exact same time, considerably reducing the amount of time it requires to series a genome.
There are two main kinds of NGS platforms: third-generation and second-generation sequencers.
Second-generation sequencing marks each nucleotide with a specific color.
After DNA is cut up into fragments, brief stretches of hereditary material called adapters are included to provide each nucleotide a various color. These DNA fragments are fed into a computer and reassembled into the whole genomic series.
Third-generation innovations like the Nanopore MinIon directly sequence DNA by passing the entire DNA particle through an electrical pore in the sequencer. Due to the fact that each set of nucleotides disrupts the electrical existing in a specific method, the sequencer can check out these modifications and submit them straight to a computer system. This allows clinicians to sequence samples at point-of-care clinical and treatment facilities. Nanopore series smaller volumes of DNA compared with other NGS platforms.
Third-generation sequencing spots modifications in an electrical current to identify nucleotides.
Though each class of sequencer procedures DNA in a various method, they can all report the millions or billions of building obstructs that comprise genomes in a short time– from a few hours to a couple of days. The Illumina NovaSeq can sequence roughly 150 billion nucleotides, the equivalent of 48 human genomes, in just 3 days.
Utilizing sequencing data to fight coronavirus
So why is genomic sequencing such an essential tool in combating the spread of SARS-CoV-2?
Fast public health actions to SARS-CoV-2 need intimate understanding of how the infection is changing in time. Researchers have been using genome sequencing to track SARS-CoV-2 almost in genuine time since the start of the pandemic. Millions of specific SARS-CoV-2 genomes have been sequenced and housed in numerous public repositories like the Global Initiative on Sharing Avian Influenza Data and the National Center for Biotechnology Information.
Sequencing the genome of a virus offers scientists info on how mutations can impact its transmissibility and virulence.
Sequencing the genome of the omicron version permitted researchers to discover over 30 anomalies in the spike protein that allows the infection to bind to cells in the human body. This makes omicron a variant of concern, as these anomalies are understood to contribute to the infections capability to spread.
Sequencing also has assisted researchers determine versions that spread out to new areas. Upon getting a SARS-CoV-2 sample gathered from a traveler who returned from South Africa on Nov. 22, 2021, scientists at the University of California, San Francisco, were able to spot omicrons presence in five hours and had nearly the entire genome sequenced in 8. Ever since, the Centers for Disease Control and Prevention has been keeping track of omicrons spread and encouraging the government on ways to avoid extensive community transmission.
The quick detection of omicron around the world stresses the power of robust genomic surveillance and the worth of sharing genomic information around the world. Understanding the genetic makeup of the infection and its variants provides scientists and public health authorities insights into how to best update public health standards and make the most of resource allocation for vaccine and drug development. By providing necessary info on how to curb the spread of brand-new versions, genomic sequencing has actually conserved and will continue to save many lives throughout the pandemic.
Written by:
Andre Hudson, Professor and Head of the Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology
Crista Wadsworth, Assistant Professor in the Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology
This article was first published in The Conversation.
We both utilize DNA sequencing in our research study to understand how anomalies impact antibiotic resistance. The tools we use to sequence DNA in our work are the very same ones researchers are using right now to study the SARS-CoV-2 infection.
One of the earliest methods scientists utilized in the 1980s and 1970s was Sanger sequencing, which includes cutting up DNA into brief pieces and adding fluorescent or radioactive tags to determine each nucleotide. Compared with more recent approaches, Sanger sequencing is slow and can process just relatively short stretches of DNA. Third-generation technologies like the Nanopore MinIon straight sequence DNA by passing the whole DNA particle through an electrical pore in the sequencer.
