Virus Variants and the Pandemic

Virus Variants

The COVID-19 pandemic that spread across the planet in 2020 sparked a global disaster. Then came the variants.

The Delta variant spreads faster and may cause twice as many infections as the original version. The latest identified variant, Omicron, is fast-growing with a large number of mutations that are being studied to determine whether it, too, may be a greater threat than earlier strains. And the virus is still evolving. How do these dangerous variants come about, and what can be done to stop them?

On the left, two model renderings depict the Delta spike, and on the right, two model renderings depict the Omicron spike.
The Delta and Omicron variants of the coronavirus SARS-CoV-2 exhibit mutations on their spike proteins. In this rendering, blue indicates single point amino acid mutations, red indicates amino acid deletions, and light grey represents amino acid insertions. Those differences may explain why some variants are more transmissible than others.
Image credit: Mia Rosenfeld, Fiona Kearns. Modeling credit: Mia Rosenfeld, Fiona Kearns, Lorenzo Casalino, Rommie Amaro, UC San Diego
Viruses turn living cells into tiny virus-copying factories, forcing them to do the work of viral reproduction.

Viruses replicate by entering living cells and turning them into tiny virus-copying factories, forcing them to do the work of viral reproduction. “A virus is just a very, very small packet of genetic information,” says Michael Tessler, assistant professor of biology at St. Francis College and a Museum research associate.

In the case of SARS-CoV-2, the virus that causes COVID-19, this genetic material takes the form of RNA. Like its more famous double-stranded counterpart, DNA, RNA consists of a long chain of chemical components called nucleic acids. These act like letters, spelling out coded instructions for building proteins. The infected cell “reads” some of the RNA instructions and follows them, building the proteins necessary to make copies of the virus. It also replicates the virus’s RNA, the most essential piece of the new viral particle. That’s the key to viral evolution. 

This cross-section of the measles virus particle is depicted by a protein-studded, ovoid shape containing six strands of RNA in the interior.
This illustration shows a cross-section of the measles virus particle, with a strand of RNA, shown in yellow, protected by nucleoproteins, shown in green.
Courtesy of D. Goodsell/Wikimedia Commons

“Anytime there's replication, there's a certain error rate,” says Tessler. “Some percentage of the time you're going to get a change in the genetic sequence—a mutation. This is true when sperm or egg cells are made in humans. And it's true when viruses replicate as well.” 

These mutations are random mistakes. “It’s like, if you were cracking eggs to make an omelet, occasionally you're going to get an eggshell in there,” Tessler explains. The mistakes might take the form of chunks of RNA omitted or duplicated, or one nucleic acid might be substituted for another. Most of these errors will be neutral or harmful for the virus, messing up its ability to replicate, for example. Virus particles with negative mutations won’t go on to infect new cells and new people. 

But very occasionally, a mutation will improve the virus, and the improved variant will prosper. Improvements could include an ability to spread faster, and spread in greater numbers, as is the case with the Delta variant, says Tessler. They could include an ability to survive in warmer or colder temperatures, or at higher or lower humidity; to travel farther through the air; to delay symptoms, so that infected people feel healthy, go out with their friends, and pass the virus on. Some mutations could allow a variant to slip past the defenses of our immune system, to infect people of different ages, or even people who have been vaccinated.

Because variants can change the virus’s behavior, which in turn could affect strategies for addressing the pandemic, it’s important to detect and track variants. But the process is not straightforward. “We can't use a microscope and see the genetic code,” says Tessler. Scientists have to extract viral RNA from samples taken from people’s noses, use molecular techniques to sequence the RNA, and compare the resulting sequences to discover where they differ. This process is expensive and time consuming; most samples are never sequenced. 

To find where to concentrate their efforts, scientists start by observing the behavior of the virus—noticing where it’s spreading faster, for example, or causing more deaths or hospitalizations, which may signal the arrival of a new variant. But variants aren’t the only possible explanation for differences in how the virus affects different communities. Some differences are due to biological factors, such as whether members of the community have ever before encountered the virus or a related one. Public health issues, such as levels of vaccination and masking, also play a role, as do social factors such as population density, age, access to health care, and preexisting health conditions. All these issues can make variants harder to spot.

“It takes a lot of hard work, and a lot of tracking, and a lot of comparisons to various symptoms to be able to tell when there’s a new variant, and what its characteristics are,” says Tessler.

Tiny spherical virus particles clumped together in the middle of tendril-like cell surface.
This scanning electron microscope image shows SARS-CoV-2 (orange)—also known as 2019-nCoV, the virus that causes COVID-19—isolated from a patient in the U.S., emerging from the surface of cells (green) cultured in the lab.
Courtesy of NIAID

The best way to stop dangerous variants from arising is to stop the virus from spreading. “Every time a person is infected, they're going to replicate the virus,” says Tessler. “And by replicating the virus, you're giving it another opportunity to mutate, which ultimately gives it more opportunities to evolve.”

And viruses evolve fast. Unlike, say, an elephant, which takes two years to produce a single baby, the SARS-CoV-2 virus can produce trillions of copies of itself in a single infected person—trillions of opportunities for a dangerous mutation to appear.

That’s one reason vaccination, masking, testing, and other measures that reduce the spread of COVID-19 are so important. Keeping the virus under control with vaccines and other tools doesn’t just protect individual people from illness and death. It also keeps a lid on killer variants, stopping them before they start.

Created with the support of the City of New York Department of Health and Mental Hygiene. © 2021 City of New York 

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