Where Do COVID Variants Come From?

Since December 2020, the World Health Organization (WHO) has designated five COVID-19 variants as Variants of Concern (VOC): Alpha, Beta, Gamma, Delta, and Omicron. While experts are keen on tracking how long these variants persist, they’re not certain how exactly new variants arise.

Since COVID-19 cannot transmit without a host, some researchers suspect new variants may arise in people who’re infected with the virus.

Pavitra Roychoudhury, PhD, MSc, instructor at the department of laboratory medicine and pathology at the University of Washington, said research has suggested that variants may arise in infected immunocompromised individuals as they’re at risk of longer-lasting infection.

“You can have significant divergence within an immunocompromised person,” Roychoudhury told Verywell. “There’s this more rapid accumulation of mutations just because they’re infected for so long, and the number of cycles of replication are so many compared to the typical course of infection.”

A study in the United Kingdom looked into the possibility of variants emerging from immunocompromised patients, noting that mutational COVID-19 variants can arise during the course of “persistent cases of coronavirus disease.”

Another recent study in France evaluated a scenario where a 72-year-old man was initially infected with the Alpha variant. Several mutations were found as the virus replicated, but the mutations didn’t evolve into a dangerous variant.

Roychoudhury and her team have studied mutation accumulation in people with more typical courses of infection. In these studies, viral mutations occurred “at a lower frequency,” but weren’t strong enough to form a new variant.

“In the typical course of infection, the number of variants that arises and reaches high frequency is low, but you can have certain mutations that linger at the lower frequencies,” she said.

Impacting the Consensus Genome

The frequency level of a variant is key in determining its ability to transmit to other people, or become widespread enough to be labeled as a VOC. For either of the two to occur, the variant most likely needs to impact the virus’s consensus genome, which can be found in any person infected with COVID-19.

A consensus genome, or consensus sequence, is a string of proteins that represents the most common amino acids or nucleotides in a molecule. For instance, in terms of COVID-19, a consensus genome that contains mostly Delta mutations would be considered a Delta variant.

“A consensus genome is like a ‘majority wins’ view of what’s in that person,” Roychoudhury said. If there’s a mutation that can outcompete the original strain, then the “beneficial” mutations will eventually be reflected in the patient’s consensus genome.

Even if a variant doesn’t rise to high enough frequencies to change the consensus genome, there’s still a chance a person could transmit the variant to another host, she added.

Scientists predict that there are thousands of viral particles with unique mutations that are not widespread enough to be recognized as variants of interest or concern. But the good news is that our immune system may be evolving to fight off variants.

“Usually, what happens is the person’s immune system is also playing a role in trying to clear this virus at the same time,” Roychoudhury said, adding that the virus usually doesn’t stay in the body long enough to become a new variant.

Antivirals could be critical in helping infected people who are immunocompromised fight off COVID-19 quickly, she added, to reduce the risk of further variant accumulation.

The information in this article is current as of the date listed, which means newer information may be available when you read this. For the most recent updates on COVID-19, visit our coronavirus news page.