Explaining SARS-CoV-2 Sequencing

The Covid-19 omicron variant was first detected in California on December 2021. Since then, nearly half of states in the country reported cases of omicron infection. People wonder why, despite many measures to curb infection, cases are still increasing, and Covid-19 variants still keep popping up. There are a lot of misunderstandings and false information about how Covid-19 and its variants spread. This article will take a look into SARS-CoV-2 sequencing and find out the answers to many of our questions concerning Covid-19.

People, states, and countries that detect new Covid-19 variants, like omicron, doesn’t necessarily mean they are the first people or places to have it. It simply means that they were the first ones to detect it. For example, Minnesota was the one of the first states to detect the presence the omicron variant because they were able to sequence a large number of Covid-19 positive specimens. When there’s a good sequencing system in place, it’s so easy to detect newer Covid-19 variants immediately.

State health officials in Minnesota are constantly working and analyzing the virus’ genetic code to detect new variants.

This article will try to give you a better understanding of what genome sequencing is and how it works, and how SARS-CoV-2 sequencing can help in our fight against infectious viruses like Covid-19.

1. What does it mean when you track a variant or sequence a genome?

When identifying variants or tracking different virus variants, we actually refer to analyzing the virus’ genetic codes to see if it’s a variant and which variant it is.

To explain the molecular process, we start with a positive sample. Let’s take a patient sample containing the SARS-CoV-2 (Covid-19 virus), then you extract that sample’s genetic code and purify it, together with human DNA and RNA.

Next, you subject the sample to a PCR or polymerase chain reaction. The PCR are tests that amplify minute pieces of the entire virus, or almost all of the virus’ genetic code in order to produce millions of copies. The amplified pieces must then be sequenced after.

After that, the genetic code is created, letter by letter. Then you compare the code to one that’s available in a public sequence library to see if it matches with any of the known variants. If it doesn’t come up with a match, it means it might be a completely new variant.

This is what we consider next-generation-sequencing: sequencing DNA or RNA through the production of millions of sequence reads in a largely parallel manner. This method is also called deep sequencing and it lets you sequence the entire genome of a microorganism.

1. How do you use genetic sequencing to monitor and track new stains?

This is done by using the information you have gathered from sequencing in different ways. This way you can determine what variants are spreading in the community and if there are new variants showing up. This is one of the reasons SARS-CoV2 sequencing is important—it helps you to identify new variants. It’s also used to track the spread of known variants as they spread around different communities around the world.

1. How long does it take to sequence samples and how much is the capacity of sequencing machines?

Genomic sequencing is a complicated process that involves numerous steps. Some clinics use two different tests to sequence genomes; one done in a clinical laboratory and the other in a research laboratory. The test done in a clinical laboratory is mostly for infection prevention and control purposes, and the results have no bearing on treatment. The second test is capable of sequencing over 700 specimens at the same time. This process takes a lot longer to get done because there are multiple teams involved.

1. All positive tests do not get sequenced. Why?

Identifying the variant does not have any bearing or impact on treatment. However, it’s a great way to put a name to what variant of the virus is currently spreading in the community and to track how it is spreading. By monitoring different variants and exchanging information in public databases, sequencing can be a big help to public health officials, especially in their attempts to understand viral outbreaks better. It will also help them make informed decisions on how to contain them.

For example, if a person tested positive for Covid-19, they are advised to stay away from other people until a certain amount of time has passed by, to ascertain that they are not infectious. There is no need to know what variant of the virus they carry. But, if a Covid-positive person was with a group of people and they all got infected at a party or event, then it will be helpful to know what variant of the virus it is so they can track the spread from a public health point of view. This also helps them understand how that variant spread across different groups of people.

1. What should people keep in mind with different Covid-19 variants popping up?

People may be confused with all the different variants of Covid-19 showing up, but people should remember that it is a virus, and because it is ‘alive’ it’s definitely prone to evolving and mutating. Some mutations may be significant, and others not at all. A new variant may appear and then go away on its own without any major impact. For example, some of Covid-19’s earlier variants—beta and gamma—have already disappeared. The Delta variant, on the other hand, spread very quickly, but also disappeared. It’s important to remember that every time there is a new variant, it doesn’t necessarily have to be an immediate concern. We must observe it first and follow its progress over time.

The most effective way to stop the virus and prevent new mutations from appearing is to get the entire population vaccinated. People are also advised to continue following all necessary preventive measures (observing social distance, wearing masks), because the virus only mutates when it gets inside people’s immune systems. The fewer people are infected, the less chances a mutation happens, and a new variant appears. Until then, our scientists will continue using SARS-CoV-2 sequencing to find a treatment for the Covid-19.