Scientist explains genome sequencing of SARS-CoV-2


Credit: AIXabay / CC0 public domain

A variant of COVID-19 Omicron has been reported in almost half of the states of the United States since it was first detected in California on December 1. The second most known case of Omicron in the country was identified in Minnesota.

“People who detect Omicron (states, counties, countries) don’t necessarily mean they had it first,” says Dr. Bobby Plit, director of the Mayo Clinic Department of Clinical Microbiology. “That’s the only thing they first detected. In Minnesota, we were one of the first states to detect the presence of Omicron. Mutant.. This is due to the large number of COVID-19 positive samples sequenced. It has a very good sequence system. ”

Mayo Clinic Laboratories is working with Minnesota health authorities and other academic medical centers to look for new variants by virus analysis. Genetic code..

To help you understand better Genome sequencing And how it works, Dr. Plit answers in this Q & A.

What does variant tracking or genomic sequencing mean?

When talking about variant identification or virus variant tracking, it usually refers to analyzing the genetic code of a virus to see if it is a variant and which variant it is.

Could you explain the molecular sequencing process?

First, we need to start with a positive sample. There is a patient sample containing SARS-CoV-2 (a virus that causes COVID-19), and a positive sample is taken and subjected to what is called extraction to extract and purify the genetic code of the virus. With all of human DNA and RNA.

Then it is subjected to PCR (Polymerase Chain Reaction). And for the test used at the Mayo Clinic, PCR is a test that amplifies a small fragment of the entire virus or almost the entire genetic code of the virus to produce millions of copies. Next, you need to sequence all the small pieces that have been amplified.

Next, a genetic code is created for each character. The code is then compared to a publicly available sequence library to see if it matches one of the known variants, or if it could be entirely new.

This is next generation sequencing. The process of sequencing DNA or RNA by generating millions of sequence reads in a massively parallel manner. Next-generation sequencing, also known as deep sequencing, enables sequencing of the entire microbial genome.

Credit: Mayo Clinic

How is gene sequencing used to monitor COVID-19 to track these new strains?

Use the information you get from sequencing in different ways to see which variants are in circulation in your community. If you have a new variant, it may not be named yet. This is one of the reasons for creating a sequence, but usually to track the spread of known variants as they traverse the community.

How long does the sequencing machine take and how long does it take?

As mentioned above, genome sequencing is a complex process involving multiple steps.

Here at the Mayo Clinic, we use two different tests for the sequence. One is done in our clinical laboratory and is mainly used for infection prevention and control purposes. At this point, the results have not been used as a therapeutic guide. Another test we use is done in a much larger laboratory. You can sequence more than 700 samples at one time. This process takes a much longer time due to the involvement of multiple teams.

Why are all positive tests not ordered?

Now that we know that variants do not affect treatment, we would like to know what is circulating in the community to track how the virus is spreading. Sequencing helps public health authorities better understand and make decisions about outbreaks by monitoring variants and sharing information in public databases.

For example, if you test positive for COVID-19, you know that you are not infectious because you have been away from others until a certain amount of time has passed. You don’t need to know the variant I have. But if I’m with a group of people and all of us get infected, I think it might be useful to know the variant at a particular party or event like you would see in New York City at an anime conference. You can track the spread from a public health perspective and understand how the variant is spreading to multiple people.

What should people keep in mind now about the new COVID-19 variant?

It should be remembered that this is a virus and tends to continue to mutate. Some mutations may be clinically important, others may not be at all important. A new variant can occur, then it can disappear and it can be meaningless. For example, some of the previous variants (beta, gamma) are no longer visible, while delta variants have spread very rapidly. Keep in mind that whenever a new variant is available, it may not be an immediate problem. You need to monitor and track its progress over time.

The most important thing to stop this virus and prevent new mutations is to vaccinate everyone and mutate only when the virus is inside a person, so all precautions (wearing a mask) , Social distance) is to continue to use. The fewer people infected, the less likely it is that a mutation will occur and a new variant will appear.

Everyone needs to be vaccinated, stay at a social distance and continue to wear masks. It’s hard and we’re all tired of pandemics, but we have to be vigilant.

Improved tracking of US virus variants after slow start

Quote: Scientists obtained SARS-CoV-2 (2021, 2021) from https: // on December 14, 2021. I will explain the genome sequencing of (December 14th)

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