How scientists are tracking the coronavirus through its own genetic makeup

This is a COVID detective story.

"In epidemiology, we track diseases in populations to ultimately try to prevent it, hopefully," says Dr. Catherine McCarty, with the University of Minnesota Medical School, Duluth Campus. "Here with COVID, we’re looking at a molecular fingerprint."

In this microscopic world, the coronavirus leaves a genetic trail of clues, mutating about every other time it’s transmitted from one person to another.

"We have the technology to recognize, to be more precise, and much more potent," says Roberto Cattaneo, a molecular biology and biochemistry professor at the Mayo Clinic. "Now we see differences between viruses, between the genome of the virus that we were not able to detect only a few years ago."

KSTP medical expert Dr. Archelle Geogiou says the replication and mutation process triggers a slightly different genetic code.

"When a virus replicates, it mostly stays the same, that’s why we can make vaccines that work," she explains. "But there are subtle little changes that occur in its genetic makeup, that give it a unique signature. You can track the virus, and where it’s gone, and who has transmitted it by looking at these subtle changes, and that’s called genomic sequencing."

Here’s how genomic sequencing works:

The virus’s genetic makeup starts with four building blocks called nucleotides.

About 30,000 of them are strung together.

When there’s a mutation, the sequence of those nucleotides changes.

One way to look at it is to liken the process to a typo in a book.

"In a tightly written book page, or in a journal article, you will have about 10,000 letters, so there are three pages in small characters," Cattaneo says. "There will be an average one, two, or three characters that are different, so it’s just much more subtle, these changes."

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"A sequence is like the equivalent of a word. So when the virus replicates, it replicates with each word being exactly the same," Dr. Georgiou adds. "But once in a while, a letter in one of those words is going to mutate or change, and so that gets passed on along when that mutated virus then replicates itself."

Experts say the mutations don’t change the functionality of the virus itself.

But scientists can look at the chemical structures of the sequences, in order to learn more about these sub-strains— or variants, as the scientific community calls them.

"Every time it replicates, there are some changes to its genome," McCarty says. "We can track that as a molecular fingerprint, and know where the strain came from. So if we have a super-spreader event for instance, we’re able to identify the signature of whatever very specific strain of the COVID virus, that caused that super-spreader to happen."

This sequencing science is also proving useful in other ways.

For example, if there’s a COVID outbreak at a school, researchers can get students tested, and find out if the strain came from the school or somewhere else.

"If all the children have one sub-type, then maybe they’re giving it to each other, and it would be important to close the school," Dr. Georgiou says.

"However, if there are four or five different sub-types, maybe they’re not giving it to each other— and all of those children got it from the outside, in the community, from their own environments— and happened to be in the same classroom. That would make a difference about whether or not you close the school, or how long you close the school."

The idea of a continually mutating virus sounds concerning.

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But McCarty says there is some encouraging news.

"That ‘more mutation’ sounds so gosh-darn scary, lots of movies out there for mutated viruses," she exclaims. "Usually a virus gets less virulent over time as they’re mutating because it’s in their best interest not to hurt their host, because they want to live forever."

Scientists say the sharing of gene sequences is an invaluable tool in tracking the coronavirus.

But unlike in countries like the United Kingdom and Germany, there’s no national database in the U.S. for this information.

Much of the work is being done by private research labs and at academic institutions, including at the University of Minnesota Genomics Center.

The Centers for Disease Control and Prevention launched a national sequencing effort in May.

But funding for that began just a short time ago.

Dr. Georgiou believes genomic sequencing will prove even more important as vaccines begin to be used in the fight against COVID-19.

"It’s important right now so we can better figure out how to control the pandemic," she says. "And it’s going to be important in the future to understand which vaccines work, which ones the virus has already mutated against, and where the outbreaks are."