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SARS-CoV-2 sequencing: A Way for Researchers to Identify Omicron and Other COVID-19 variants

Scientists employ a variety of methods to identify new strains of the virus that produces COVID-19, and the method has been known as SARS-CoV-2 sequencing.


To be able to discover the sequence of the four basic chemical building blocks or nucleotides (adenine, thymine, cytosine, and guanine) that are making it up, researchers sequence DNA. When linked together, these nucleotides, each of these building components that are in millions to billions, will be forming into a genome, including all of the genetic information that an organism is required to thrive.


The process by which an organism reproduces is to create a duplicate of its whole genome, which it will then pass on to its children. Mutations can occur when mistakes occur during the copying process, resulting in swapping, removing, or adding one or more building blocks. Genetic changes can modify genes, which serve as the blueprints for the proteins that allow an organism to operate. They can eventually alter the physical traits of the creature in question. Eye and hair color, for example, are the product of genetic changes that can occur as a result of mutations in human beings. Virus mutations can alter the capacity of a virus to disseminate, produce illness, or even avoid the immune system, as is the case with the virus that causes COVID-19, SARS-CoV2.


In addition to being biochemists and microbiologists, we are also interested in and educating about bacterial genomes and their evolution. When it comes to understanding how mutations cause antibiotic resistance, we both employ DNA sequencing in our study. We use the same technologies that scientists are utilizing to research the SARS-CoV-2 virus to sequence DNA in our work, which is a good thing.


Methods Used to Sequence Genomes


Sanger sequencing was one of the first ways scientists used in the 1970s and 1980s to identify individual nucleotides in DNA. This approach includes breaking DNA into short pieces and attaching radioactive or fluorescent tags to each nucleotide to identify each nucleotide. The shards are subsequently passed through an electric sieve, which separates them according to their size. Sanger sequencing is a slow approach that can only analyze small sections of DNA compared to newer technologies such as next-generation sequencing. Despite these drawbacks, it produces extremely precise data, and some researchers are still actively utilizing this approach to sequence SARS-CoV-2 samples today.


Since its introduction in the late 1990s, next-generation sequencing has transformed how scientists gather information about and analyze genomes. Known as next-generation sequencing (NGS), these technologies are capable of processing considerably more significant amounts of DNA at the same time, resulting in a dramatic reduction in the length of time required to sequence a genome.


In the field of next-generation sequencing (NGS), there are two primary types of platforms: second-generation sequencers and third-generation sequencers.


Second-generation technology has the ability to read DNA directly from the source. A brief piece of genetic material called an adaptor is added to each nucleotide after it has been split up into fragments in order to give each nucleotide a distinct color. In the case of adenine, the color is blue, whereas the color of cytosine is red. Last but not least, these DNA fragments are input into a computer, where they are reconstructed into the whole genomic sequence.


The Nanopore Minion is an example of third-generation technologies (the second type of NGS), this type of method uses direct sequencing of DNA by bypassing the entire DNA molecule through an electrical pole in the sequencer, compared to the second-generation technologies. Because each pair of nucleotides causes a distinct disruption in the electrical current, the sequencer can detect these changes and upload them straight to a computer without needing additional equipment. Point-of-care clinical and therapeutic facilities allow doctors to sequence samples on the spot. Compared to other NGS systems, Nanopore sequences a lesser amount of DNA than the competition.


Despite the fact that each type of sequencer analyzes DNA in a somewhat different manner, they are all capable of reporting the millions or billions of building blocks that constitute genomes in a relatively short period – ranging from a few hours to a few days. For example, the Illumina NovaSeq is capable of sequencing around 150 billion nucleotides in three days, which is the same as of 48 human genomes.


Utilization of sequencing data in the battle against coronavirus


So why is genome sequencing such a critical tool in the fight against SARS-CoV-2 spread?


Rapid public health countermeasures to SARS-CoV-2 require an extensive understanding of the virus’s evolution. Ever since the pandemic has started, scientists have been tracking SARS-CoV-2 by way of genome sequencing, and there have been thousands of SARS-CoV-2 genomes have been sequenced and are being stored in so many public sources, which includes Global Initiative for Sharing Avian Influenza Data as well as the National Center for Biotechnology Information.


Genomic monitoring has guided public health choices with the emergence of each novel variation. For instance, analyzing the omicron variant’s genome enabled researchers to identify over 30 spike protein changes that will allow the virus to connect to human cells. This makes omicron a concerning variety, as it is known that these changes contribute to the virus’s capacity to propagate. Researchers are still investigating how these alterations may impact the severity of the illnesses caused by omicron and its ability to escape existing vaccinations.


Additionally, sequencing has aided researchers in identifying variations that have migrated to new locations. The University of California researchers at San Francisco were able to detect the presence of omicron in five hours and sequence them virtually the whole genome in just eight hours after being able to receive a sample of the SARS-CoV-2 from a tourist who returned from South Africa on Nov. 22, 2021. Since then, the CDC has been monitoring omicron’s progress and advising the government on measures to prevent broad community transmission.


The quick discovery of omicron around the world demonstrates the benefits of thorough genomic surveillance and the importance of global data exchange. Understanding the virus’s genetic makeup and variations enables researchers and public health officials to make the most effective use of available resources for vaccine and treatment development. So much has been saved and will continue to save countless lives throughout the pandemic by way of genomic sequencing by giving out critical information on how to contain the spread of new variations.


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