Massive Genetic Study Shows Coronavirus Mutating And Potentially Evolving Amid Rapid U.S. Spread

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Scientists in Houston on Wednesday released a study of more than 5,000 genetic sequences of the coronavirus, which reveals the virus’s continual accumulation of mutations, one of which may have made it more contagious.

That mutation is associated with a higher viral load among patients upon initial diagnosis, the researchers found.

The study, which has not been peer-reviewed, was posted Wednesday on the preprint server MedRxiv. It appears to be the largest single aggregation of genetic sequences of the virus in the United States thus far. A larger batch of sequences was published earlier this month by scientists in the United Kingdom, and, like the Houston study, concluded that a mutation that changes the structure of the “spike protein” on the surface of the virus may be driving the outsized spread of that particular strain.

The tiny mutation found in the dominant

coronavirus variant

Like all coronaviruses, SARS-CoV-2 has a series of characteristic spikes surrounding its core. These spikes are what allow the virus to attach to human cells.

SPIKE

Spike

SARS-CoV-2

Amino acid 614

A mutation affecting the spike protein changed amino acid 614 from “D” (aspartic acid) to “G” (glycine). Research suggests that this small change — which affects three identical amino acid chains — might enhance the virus’s transmissibility.

Source: Global Initiative on Sharing All Influenza Data

The new report, however, did not find that these mutations have made the virus deadlier. All viruses accumulate genetic mutations, and most are insignificant, scientists say. Coronaviruses such as SARS-CoV-2 are relatively stable as viruses go, because they have a proofreading mechanism as they replicate.

But every mutation is a roll of the dice, and with transmission so widespread in the United States — which continues to see tens of thousands of new, confirmed infections daily — the virus has had abundant opportunities to change, potentially with troublesome consequences, said study author James Musser of Houston Methodist Hospital.

“We have given this virus a lot of chances,” Musser told The Washington Post. “There is a huge population size out there right now.”

Scientists from Weill Cornell Medicine, the University of Chicago, Argonne National Laboratory and the University of Texas at Austin also contributed to the study.

David Morens, a virologist at the National Institute of Allergy and Infectious Diseases, reviewed the new study and said the findings point to the strong possibility that the virus, as it has moved through the population, has become more transmissible, and that this “may have implications for our ability to control it.”

Morens noted that this is a single paper, and “you don’t want to over-interpret what this means.” But the virus, he said, could potentially be responding — through random mutations — to such interventions as mask-wearing and social distancing, Morens said Wednesday.

“Wearing masks, washing our hands, all those things are barriers to transmissibility, or contagion, but as the virus becomes more contagious it statistically is better at getting around those barriers,” said Morens, senior adviser to Anthony S. Fauci, the director of NIAID.

This has implications for the formulation of vaccines, he said. As people gain immunity, either through infections or a vaccine, the virus could be under selective pressure to evade the human immune response.

“Although we don’t know yet, it is well within the realm of possibility that this coronavirus, when our population-level immunity gets high enough, this coronavirus will find a way to get around our immunity,” Morens said. “If that happened, we’d be in the same situation as with flu. We’ll have to chase the virus and, as it mutates, we’ll have to tinker with our vaccine.”

At Houston Methodist, whose main hospital is part of the Texas Medical Center in central Houston but also includes hospitals around the city, scientists have been sequencing the 30,000-character genome of the coronavirus since early March, when the virus first appears to have arrived in the metropolitan area of 7 million. The paper documents 5,085 sequences.

The research shows that the virus disseminated across Houston neighborhoods in two waves, first striking wealthier and older individuals but then spreading, in the second wave, to younger people and lower income neighborhoods — affecting many Latino city residents.

At the same time, as the virus spread Zip code by Zip code, it also compiled a catalogue of mutations, many affecting the spike protein. That structure on the surface of the virus, which resembles a tree decked with curled ribbons, enables the virus to enter cells.

The genetic data show the virus arrived in Houston many times, presumably at first by air travel. Notably, 71 percent of the viruses that arrived initially were characterized by a now famous mutation, which appears to have originated in China, that scientists increasingly suspect may give the virus a biological advantage in how it spreads. It is called D614G, referring to the substitution of an amino acid called aspartic acid (D) for one called glycine (G) in a region of the genome that encodes for the spike protein.

By the second wave of the outbreak in Houston, the study found that this variant had leaped to 99.9 percent prevalence — completing its domination of the outbreak. The researchers found that people infected with the strain had higher loads of virus in their upper respiratory tracts, a potential factor in making the strain spread more effectively.


A medical worker walks past ambulances parked outside of Houston Methodist Hospital amid the global coronavirus outbreak in Houston in June. (Callaghan O’hare/Reuters)

Kristian Andersen, an immunologist at the Scripps Research Institute in California, who was not involved in the new research, downplayed the significance of the new study. He said it “just confirms what has already been described — G increased in frequency over time.” As for the numerous other mutations the study finds, “they just catalogue them, but we don’t know if any of them have any functional relevance.”

Musser said his interpretation is that D614G has been increasingly dominant in Houston and other areas because it is better adapted to spreading among humans. He acknowledged that the scientific case is not closed on this matter.

“This isn’t a murder trial,” Musser said. “We’re not looking for beyond a reasonable doubt. This is a civil trial, and clearly, it’s the preponderance of the evidence that I think forces all of us into the same conclusion, which is there’s something biologically different about that strain, that family of strains.”

Recently, the even larger study of the spread of the coronavirus in the United Kingdom, based on some 25,000 genomes, also found evidence that this variant of the virus outdistances its competitors “in a manner consistent with a selective advantage.”

In general, scientists would expect natural selection to favor mutations that help the virus spread more effectively — since that allows it to make more copies of itself — but not necessarily ones that make it more virulent. Killing or incapacitating the host would generally not help the virus spread to more people.

The study found 285 separate mutation sites that actually change a physical building block of the spike protein, which is the most important part of the coronavirus in the sense that it is what allows it to infect and harm humans. Forty-nine of the changes at these sites had not been seen before in other genomes sequenced around the world.

The study characterizes some of the spike protein mutations as “disconcerting.” While the paper does not present strong proof that any additional evolution of the spike protein is occurring, it suggests that these repeated substitutions provide a hint that, as the virus interacts with our bodies and our immune systems, it may be learning new tricks that help it respond to its host.

“I think there’s pretty good evidence that’s consistent with immunologic selection acting on certain regions of the spike protein,” Musser said.

The actual mutations in the virus occur randomly as it makes mistakes trying to copy its genome within our cells. But every new case gives a chance for more mutations to occur, which in turn increases the chance that one of these mutations will be useful to the virus, just as D614G apparently already has been.

6 COMMENTS

  1. “Massive study…POTENTIALLY spreading…”
    “Not peer-reviewed”
    “He acknowledged that the science is not closed on the matter”
    WHY IS THIS STUDY IN GREAT DETAIL ON THIS WEBSITE?
    Are you trying to give more אימת הדין before Yom Kippur?
    Enough with trying to instill PANIC and confusion to the public!

    Why not inform the public that a study of 37 universities found over 48,000 college students who were tested positive and ONLY 2 (TWO!) were hospitalized and ZERO died!

    Why not inform the public that children aged 0-19 have THREE chances in 10,000,000 (ten million!!!) of dying from COVID 19.

    Stop the fear mongering! Please!

  2. Its official, ALL Lakewood schools will be closing for 3 weeks in order to stem the spread of corona. What are we gonna do with the kids?

    • During a war children do not go to school. Yes, there is a war, a real war, actually a world war with armed forces, and many troops are getting killed. Just because you don’t know about it, doesn’t mean the government should allow children to go to school. Remember how Trump said it’s a war against invisible enemies?

      You should thank Hashem that Hillary is not president. Had she been president, she was planning on starting WWIII. Then you certainly wouldn’t dream of sending your children to school even for a day.

      The Deep State Cabal criminals were desperate for President Trump to go into war and were delighted when he fired a missile on Syria in April 2017, 3 months into his first term. They were hoping it’ll be a full fledged war but they didn’t know this new POTUS. President Trump only fired it at the Deep State region. Syria’s President, Bashar, was not even involved. There were photos of him going to work as usual on that day. Boy were they mad when he called the troops home after his mission was completed.

  3. Intensifying the panic to keep innocent people safe, out of harms way, while they complete President Trump’s mission of eradicating the elite corona criminals globally that have infected the world for hundreds of years, especially in the last century. IF YOU DON’T BELIEVE IT, how can you justify military troops, marines and tanks rolling down the streets? Do you really think the army can shoot the fevers and flu out of the people all over the world and nobody will ever get sick again?

    Don’t you think we’d have heard something from honest doctors and and professors of hospitals had it been a medical issue, like after the Chernobyl nuclear disaster?

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