While Americans are excited to see variants that were first distributed in the UK and South Africa in the US, scientists are finding a number of new variants that originated here. What is even more worrying is that many of these flavors are moving in the same direction and potentially becoming contagious threats themselves.
In a study published on Sunday, a team of researchers reported seven growing lineages of the novel coronavirus discovered in states across the country. All of them have developed a mutation in the same genetic letter.
“There is clearly something wrong with this mutation,” said Jeremy Kamil, a virologist at Louisiana State University’s Shreveport Health Sciences Center and co-author of the new study.
It’s unclear whether it makes the variants more contagious. However, since the mutation occurs in a gene that affects the entry of the virus into human cells, scientists are very suspicious.
“I think there is a clear signature for an evolutionary benefit,” said Dr. Kamil.
The history of life is full of examples of what is known as convergent evolution, in which different lines follow the same path. Birds were given wings when they evolved from feathered dinosaurs, for example, just as bats did when they evolved from furry, shrew-like mammals. In both cases, natural selection resulted in a pair of flat surfaces that could be fluttered to create lift. So bats and birds alike could soar in the sky and fill an ecological niche that other animals couldn’t.
Charles Darwin first recognized convergent evolution by studying living animals. In recent years, virologists have found that viruses can also develop convergently. For example, HIV emerged when several types of virus were passed from monkeys and monkeys to humans. Many of these lines of HIV received the same mutations that made them adapt to our species.
While the coronavirus is now branching into new variants, researchers observe Darwin’s theory of evolution in action every day.
Dr. Kamil stumbled upon some of the new variants while sequencing samples from coronavirus tests in Louisiana. At the end of January he observed an unfamiliar mutation in a series of samples.
The mutation changed the proteins that examine the surface of the coronavirus. Known as spike proteins, they are folded chains of more than 1,200 molecular building blocks called amino acids. Dr. Kamil’s viruses all shared a mutation that changed the 677th amino acid.
When Dr. Kamil examined these mutant viruses, he found that they all belonged to the same lineage. The earliest virus in the line dates back to December 1st. It became more common in later weeks.
On the evening of his discovery, Dr. Kamil uploaded the genomes of the viruses to an online database used by scientists around the world. The next morning he received an email from Daryl Domman of the University of New Mexico. He and his colleagues had just found the same variant in their condition with the same 677 mutation. Your samples are from October.
The scientists wondered if the line they discovered was the only one that had a 677 mutation. Dr. Kamil and colleagues examined the database and found six other lineages that independently received the same mutation.
It is difficult to answer even basic questions about the prevalence of these seven lineages because the United States sequences genomes from less than 1 percent of coronavirus test samples. The researchers found samples from the lineages that were scattered across much of the country. But they cannot tell where the mutations first originated.
Updated
Apr. 14, 2021, 3:56 p.m. ET
“At the moment I would be quite reluctant to give a place of origin for one of these lines,” said Emma Hodcroft, epidemiologist at the University of Bern and co-author of the new study.
It’s also hard to tell if the increase in variants is actually due to their being more contagious. They might have become more frequent simply because of all the travel during the holiday season. Or they exploded during superspreader events in bars or factories.
Still, scientists are concerned because the mutation could plausibly affect how easily the virus gets into human cells.
Infection begins when a coronavirus uses the tip of the spike protein to attach itself to the surface of a human cell. It then releases harpoon-like arms from the base of the spike, pulls toward the cell, and supplies its genes.
Before the virus can make this invasion, however, the spike protein must encounter a human protein on the surface of the cell. After this contact, the spike is free to rotate, exposing its harpoon tips.
The 677 mutation changes the spike protein next to where our proteins cut into the virus, which may make it easier to activate the spike.
Jason McLellan, a structural biologist at the University of Texas at Austin who was not involved in the study, called it “an important advance.” But he warned that the way the coronavirus unleashed its harpoons was still pretty mysterious.
“It’s hard to know what these substitutions do,” he said. “There really needs to be some additional experimental data added.”
Dr. Kamil and his colleagues begin these experiments in the hope that the mutation actually makes a difference to infections. If the experiments confirm their suspicions, the 677 mutation will join a small, dangerous club.
Convergent evolution has transformed several other locations on the spike protein as well. For example, the 501st amino acid is mutated in a number of lineages, including the contagious variants first seen in the UK and South Africa. Experiments have shown that the 501 mutation changes the tip of the tip. This change allows the virus to attach itself more tightly to cells and infect them more effectively.
Scientists believe that coronaviruses will converge on more mutations that will give them an advantage – not just against other viruses, but also against our own immune system. However, Vaughn Cooper, an evolutionary biologist at the University of Pittsburgh and co-author of the new study, said laboratory experiments alone could not reveal the extent of the threat.
To really understand what the mutations are doing, scientists need to analyze a much larger sample of coronaviruses from across the country. Currently, however, they can only look at a relatively small number of genomes collected from a patchwork of government and university laboratories.
“It is ridiculous that our country is not developing a national strategy for surveillance,” said Dr. Cooper.
