The danger lurking in the mutations in the highly contagious delta COVID variant

Upon first inspection, the mutations in the highly contagious delta COVID variant don't look that worrisome.

For starters, delta has fewer genetic changes than earlier versions of the coronavirus.

"When people saw that the epidemic in India was driven by delta, they did not suspect it would be so bad or overtake other variants," said Trevor Bedford, an evolutionary biologist at the Fred Hutchinson Cancer Research Center.

But those expectations were wrong.

Delta has kept some of the most successful mutations found in earlier variants, but also contains new genetic changes that enable it to spread twice as fast.

Delta is more dangerous in many ways. It has an incubation period of four days, rather than six, making people contagious sooner. When the pandemic began, people spread the original coronavirus to an average of two or three people. Today, people infected with delta infect six people, on average.

As of late July, the delta variant had caused at least 92% of the new infections in the United States, according to covariants.org, a research firm in Bern, Switzerland.

Although delta isn't necessarily any more lethal than other variants, it can kill huge numbers of people simply because it infects so many more, said Dr. Eric Topol, founder and director of the Scripps Research Translational Institute.

Scientists have sequenced delta's mutations but are still trying to understand their significance, said Angela Rasmussen, a virologist at the University of Saskatchewan's Vaccine and Infectious Disease Organization. "When we see the same mutations appearing repeatedly and independently, that suggests they're important," she said.

Scientists have the best understanding of mutations on the so-called spike protein — which sticks out from the surface of the virus like a club — and which have been studied the most intensely, Rasmussen said. The coronavirus uses the spike protein to enter human cells, and changes in the spike can help the virus evade antibodies.

Scientists believe one of the most important areas of the spike is the receptor-binding domain, the specific part of the protein that allows the virus to latch onto a receptor on the surface of our cells, said Vaughn Cooper, a professor of microbiology and molecular genetics at the University of Pittsburgh. Receptors are like sockets or docking stations that allow proteins to interact with the cell. Once the virus gains entry to the cell, it can hijack the cell's genetic machinery and turn it into a virus-making factory.

Delta, like all the identified variants in circulation, contains a spike mutation called D614G, sometimes known as "Doug," which became ubiquitous last year.

Scientists think Doug increases the density of spike protein on the surface of viral particles and makes it easier for the virus to enter cells.

Delta also has a spike mutation called P681R, which closely resembles a mutation in the alpha variant that appears to produce higher viral loads in patients, Cooper said. People infected with delta have 1,000 times more virus in their respiratory tract, making them more likely to spread the virus when they sneeze, cough or talk.

The P681R mutation, also found in the kappa variant, is located at a part of the genome called the furin cleavage site, Cooper said.

Furin is a naturally occurring human enzyme that gets hijacked by the coronavirus, which uses it to slice the spike protein into the optimal shape for entering the cell, Rasmussen said. The new mutation makes that sculpting more efficient.

Another delta mutation is called L452R. Experiments suggest this mutation acts to prevent antibodies from neutralizing the virus, Cooper said.

These mutations appear to be more formidable as a team than alone.

The genetic changes "are certainly doing something, but why that combination makes the delta variant more fit is not entirely obvious," Bedford said.

Delta also has developed genetic changes not seen in other variants.

One such spike mutation is called D950N. "This might be unique," Cooper said. "We don't see that anywhere else."

The D950N mutation is different from other mutations because it's located outside the receptor-binding domain in an area of the coronavirus genome that helps the virus fuse with human cells, Cooper said. Fusing allows the coronavirus to dump its genetic material into those cells.

This mutation could affect which types of cells the virus infects, potentially allowing it to harm different organs and tissues. Mutations in this region are also associated with higher viral loads, Cooper said.

Delta also contains mutations in a part of the spike protein called the N-terminal domain, which provides a "supersite" for antibodies to latch onto the virus and prevent it from entering cells, said Dr. Hana Akselrod, an infectious diseases specialist at the George Washington University School of Medicine & Health Sciences.

Mutations in this region increases the delta variant's ability to escape vaccine-generated antibodies, Akselrod said. That may explain why vaccinated people are slightly more likely to become infected with delta.

The best way to slow down the evolution of variants is to share vaccines with the world, vaccinating as many people as possible, Bedford said. Because viruses undergo genetic changes only when they spread from one host to another, stopping transmission denies them a chance to mutate.

Whether the coronavirus evolves more deadly variants "is totally in our hands," Cooper said.