Different variants of the virus behind the COVID-19 pandemic are swapping chunks of genetic material, but it’s not yet clear what implications that may have for public health.

By Abby Olena

Recombination—the exchange of genetic material between genomes—is common in coronaviruses because of the way they copy their RNA genomes. During replication, the RNA-synthesizing enzyme these viruses use duplicates shorter sections close to the end of the genome in addition to making the long template it needs for generating whole-genome copies. Furthermore, the enzyme is prone to switching from one template to another, so if a cell has multiple viral genomes in it, the enzyme may stitch together bits from different viruses to create a kind of Frankenstein genome.

RNA viruses can leverage recombination to fix deleterious mutations or acquire new characteristics, which is why virologists say it’s important to keep tabs on any recombination events that may be occurring in SARS-CoV-2. While it’s not yet clear exactly what role recombination is playing in the virus’s evolution, researchers are continuing to monitor and investigate it in an effort to better understand its biology—and, perhaps, develop novel strategies for fighting it.

Recombination from the beginning

Early on in the pandemic, research suggested recombination likely played a pivotal role in SARS-CoV-2’s emergence as a human pathogen. In a study published in July 2020, for instance, Bette Korber, a researcher at Los Alamos National Laboratory, and colleagues reported that a portion of the receptor binding domain of SARS-CoV-2’s spike protein—the part of the spike that directly interacts with the ACE2 receptor that the virus uses to gain entry into cells—came from recombination with pangolin coronaviruses.

It’s no surprise, then, that the virus continued to recombine after it began infecting people. “It should be happening because it’s a very important evolutionary mechanism for these viruses,” explains Korber. At the same time, she adds, “quantifying how much it’s there can be tricky because . . . it’s computationally not easy to look at vast data sets,” and the search can be confounded by genetic changes that can come about in the lab.

Recombination happens in many viruses, including influenza, HIV, and other coronaviruses. It “could, in principle, be a meaningless event where two viruses swap some pieces of RNA, but they don’t really change themselves,” says Penn State biologist Maciej Boni. But researchers want to keep an eye on recombination in SARS-CoV-2 because it’s one way the virus could evolve to be more virulent or to infect more people—potentially faster than mutating one nucleotide at a time. 

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