…New tool shows spotlights little noticed mutation that speeds viral spread
As the world has learned to its cost, the Delta variant of the pandemic coronavirus is more than twice as infectious as previous strains. Just what drives Delta’s ability to spread so rapidly hasn’t been clear, however. Now, a new lab strategy that makes it possible to quickly and safely study the effects of mutations in SARS-CoV-2 variants has delivered one answer: a little-noticed mutation in Delta that allows the virus to stuff more of its genetic code into host cells, thus boosting the chances that each infected cell will spread the virus to another cell.
That discovery, published today in Science, is “a big deal,” says Michael Summers, a structural biologist at the University of Maryland, Baltimore County—not just because it helps explain Delta’s ravages. The new system, developed by Nobel Prize winner Jennifer Doudna of the University of California (UC), Berkeley, and her colleagues, is a powerful tool for understanding current SARS-CoV-2 variants and exploring how future variants might affect the pandemic, he says. “The system she has developed allows you to look at any mutation and its influence on key parts of viral replication. … That can now be studied in a much easier way by a lot more scientists.”
Researchers analyzing how mutations in the coronavirus’ genome affect its activity have concentrated on the spike protein, which studs the virus’ surface and allows it to invade human cells. That’s partly because, short of deliberately mutating the virus and testing it—research that requires high-level biosafety facilities—the best tool for probing individual mutations has been what’s called a “pseudovirus,” a construct made from a different virus, called a lentivirus, that can express a coronavirus protein on its surface. But lentiviruses only express spike, not SARS-CoV-2’s other three structural proteins.
Doudna and her team made the new tool by tweaking lab constructs called viruslike particles (VLPs), which contain all the virus’ structural proteins but lack its genome. From the outside, a SARS-CoV-2 VLP looks exactly like the full-fledged virus. It can bind with cells in a laboratory and invade them. But because it is stripped of the virus’ RNA genome, it can’t hijack a cell’s machinery to replicate and burst out of the host cell to infect more cells. “It’s a one-way ticket. It doesn’t spread,” says Charles Rice, a molecular virologist at Rockefeller University.
Doudna and her colleagues, including co–senior author Melanie Ott, a virologist and director of the Gladstone Institute of Virology, added a new innovation to the VLP system. They inserted a snippet of messenger RNA (mRNA) that causes cells invaded by the VLPs to light up and glow. The brighter the cells glow after being infected with the VLPs, the more mRNA the VLPs have successfully delivered.
Next, the researchers tweaked the VLP’s proteins with various mutations. One was R203M, a mutation found in Delta that alters the nucleocapsid (N), a protein tucked inside the virus that packages its RNA genome. The N protein is a central player in viral replication, with roles that include stabilizing and releasing the virus’ genetic material. And it contains a mutational hot spot: a seven–amino acid stretch that is mutated in every SARS-CoV-2 variant of interest or concern in most samples studied. R203M is one mutation in this hot spot.
That work “revealed a surprise,” Doudna says. According to the intensity of the VLP’s glow, “A single amino acid change found in Delta’s nucleocapsid protein supercharged the particles with 10 times more mRNA compared with the original virus!” Cells infected with VLPs carrying N mutations found in the Alpha and Gamma variants glowed 7.5 and 4.2 times brighter, respectively.
The scientists next tested a real coronavirus engineered to include the R203M mutation, in appropriate lab biosafety conditions. After invading lung cells in the lab, the mutated virus produced 51 times more infectious virus than an original SARS-CoV-2 strain.
In people infected with the coronavirus, a very small proportion of viral particles produced by a cell actually go on to infect another cell, in part because many viral particles lack parts or all of the viral RNA genome. So mutations that make the virus more efficient at putting RNA inside host cells can boost the number of infectious particles produced.
“This mutation that’s found in Delta … makes the virus better at making infectious particles and because of that, it spreads more quickly,” says Abdullah Syed, a biomedical engineer at the Gladstone Institute of Data Science and Biotechnology, and one of the paper’s first authors.
The finding has implications for treatments, says Shan Lu, a cell biologist at UC San Diego who studies the N protein. “The field could think more about targeting the nucleocapsid protein to really help control infection and help treat patients.”
The researchers are now trying to understand just how Delta’s R203M mutation and others in N improve the assembly of viral particles and their mRNA delivery to host cells. They will probe whether a host protein is involved. If so, targeting it with a drug could be an effective way to stall Delta’s spread.
Scientists are also excited by the new VLP system, which will allow researchers without high-level biosafety access to study how all four coronavirus structural proteins work to assemble the virus, help it bud from cells, and invade other cells. Jasmine Cubuk, a biochemist and biophysicist at Washington University in St. Louis who studies the SARS-CoV-2 N protein, calls it “a fascinating and a very powerful tool.”
Rice cautions the new VLPs are a model system that may not always mimic the real thing. Researchers will still need to work with the real virus in advanced biosafety labs. “At the end of the day if you really want to understand how these mutations are affecting basic viral replicative processes, you have to put [a mutation] in the virus and study it.”
But he praises the new tool. “It really provides a wonderful system to study coronavirus assembly and also to look for drugs, for inhibitors that interfere with these processes.”
