Science Alert reports Dominant Coronavirus Strain Appears to Be a Mutated, More Virulent Version
The genetic variation of the novel coronavirus that dominates the world today infects human cells more readily than the original that emerged in China, according to a new study published in the journal Cell on Thursday.
”I think the data is showing that there is a single mutation that actually makes the virus be able to replicate better, and maybe have high viral loads,” Anthony Fauci, the United States’s top infectious disease specialist, who wasn’t involved in the research, commented to Journal of the American Medical Association. [See Video Below]
Researchers from the Los Alamos National Laboratory in New Mexico and Duke University in North Carolina partnered with the University of Sheffield’s COVID-19 Genomics UK research group to analyze genome samples published on GISAID, an international resource for sharing genome sequences.
They found that the current variant, called “D614G”, makes a small but potent change in the “spike” protein that protrudes from the surface of the virus, which it uses to invade and infect human cells.
Coronavirus Update With Anthony Fauci
Spike Protein Mutation
Worrisome Mutation Thread
- Worrisome Microbe mutation: “At least four lab experiments suggest that the mutation makes the virus more infectious. Another study from Los Alamos National Lab finds that patients with the G variant actually have more virus in their bodies, i.e. more likely to spread it to others.
- A change in the virus was appearing again and again. This mutation, associated with outbreaks in Europe and New York, eventually took over the city. By May, it was found in 95 percent of all the genomes Ozer sequenced.
- “At a glance, mutation seemed trivial. About 1,300 amino acids serve as building blocks for spike protein. In mutant virus, the genetic instructions for just one of those amino acids — # 614 — switched in new variant from a#”D” (aspartic acid) to “G” (glycine).”
- “But the location was significant, because the switch occurred in the part of the genome that codes for the all-important “spike protein” — the protruding structure that gives coronavirus its crownlike profile and allows it to enter human cells the way a burglar picks a lock.”
- “And its ubiquity is undeniable. Of the approximately 50,000 genomes of the new virus that researchers worldwide have uploaded to a shared database, about 70 percent carry the mutation, officially designated D614G but known more familiarly to scientists as “G.”
- “The mutation doesn’t appear to make people sicker, but a number of scientists worry that it has made it more contagious.
“epidemiological study & our data together really explain why [G variant’s] spread in Europe and U.S. was really fast… This is not just accidental.” - “But there may be other explanations for the G variant’s dominance: biases in where genetic data are being collected, quirks of timing that gave the mutated virus an early foothold in susceptible populations.”
- “The bottom line is, we haven’t seen anything definitive yet,” said Jeremy Luban, a virologist at the University of Massachusetts Medical School.
The scramble to unravel this mutation mystery embodies the challenges of science during the coronavirus pandemic.“ - “The distinctive infectiousness of the G strain is so strong that scientists have been drawn to the mutation even when they weren’t looking for it.
Neville Sanjana, a geneticist at NYU, was trying to figure out which genes enable SARS-CoV-2 to infiltrate human cells…” - “But in experiments based on a gene sequence taken from an early case of the virus in Wuhan, he struggled to get that form of the virus to infect cells. Then the team switched to a model virus based on the G variant.
“We were shocked,” Sanjana said. “Voilà!” - “It was just this huge increase in viral transduction.” They repeated the experiment in many types of cells, and every time the variant was many times more infectious.”
- “The spike protein for SARS-CoV-2 has two parts that don’t always hold together well. In version that arose in China, the outer part — which virus needs for human receptor — frequently broke off. Equipped with this faulty lock pick, it had a harder time invading host cells.”
- “Studying both versions of the gene using a proxy virus in a Petri dish, Choe and her colleagues found that viruses with G variant had more spike proteins, and outer parts of those proteins were less likely to break off. This made virus ~10 times more infectious in the lab.”
- “But New York team offers different explanation for why variant is so infectious. Whereas Choe’s study proposes that mutation made the spike protein more stable, Sanjana suggest that G variant is more efficient the process of invading & taking over its reproductive machinery”
- “Luban, who has also been experimenting with the D614G mutation, has been drawn to a third possibility: His experiments suggest that the mutation allows the spike protein to change shape as it attaches to the ACE2 receptor, improving its ability to fuse to the host cell.”
- “Although these experiments are compelling, they’re not conclusive, said Kristian Andersen, a Scripps virologist not involved in any of the studies. The scientists need to figure out why they’ve identified different mechanisms for the same effect.”
- “Even then, Andersen said, it will be too soon to say that the G variant transmits faster among people.
Cell culture experiments have been wrong before. Early experiments with hydroxychloroquine hinted that it was effective at fighting the coronavirus in a petri dish.” - “The drug was touted a lot and FDA authorized it for emergency use in hospitalized covid-19 patients. But that authorization was withdrawn this month after evidence showed that the drug was “unlikely to be effective” against the virus and posed potential safety risks.”
- “So far, the biggest study of transmission has come from Bette Korber, who built one of the world’s biggest viral genome databases for tracking HIV. In late April, she and colleagues released a draft of their work arguing that the mutation boosts transmission of the virus.”
- “Analyzing sequences from more than two dozen regions across the world, they found that most places where the original virus was dominant before March were eventually taken over by the mutated version…”
- “This switch was especially apparent in the United States: 96% of early sequences here belonged to the D variant, but by the end of March, almost 70% of sequences carried the G amino acid instead.”
- I want to add that these 4 studies are all lab studies that are computational models or in vitro studies. Not in vivo in humans or primates. So let’s wait for further in vivo studies before making formal conclusion on infectiousness.
D614G Study
Here is a link to the D614G Study, published July 2.
One interesting comment to the article.
Further mutations are quite likely to come; they could affect both, the easier spread, and the severity of the disease even in younger patients. Currently, many mammalian species can also transmit the disease within their species (cats, tigers, lions, ferrets, dogs). Despite some findings in Wuhan with 15% of tested cats (from about 100) showed antibodies against Sars-CoV-2 (but none of the reference blood samples from before the outbreak was positive), little is tested anywhere else – leading to the potentially false suggestion of the WHO that there is no evidence for a major transmission from pet-to-human. I wonder how this currently dominating mutation affects the infection rate in cats, and if this may support an easier transmission from cat to human?
What We Know
- Social distancing helps
- The recent jump in cases is from a jump in infection rates, not due to number of tests alone
- Covid-19 mutates in a fashion that newer mutations can quickly become the dominant form in an area
- The number of cases is at record highs in many Southern states
- Governors in many states, especially in the south, have walked back or even reversed reopening plans.
Unfortunately, there is too much we do not know.
I wonder if the mutations will quickly negate all the efforts in producing a vaccine.
Mish
I don’t know where this headline is coming from, but there’s error of terminology in the article referenced: the headline says “contagiousness” is worse, the byline says “virulence” is worse. These two things are generally INVERSES of each other. WHen a virus becomes more contagious, virulence goes down.
So many words wasted on unproven scientific babble.
Cell culture experiments have been wrong before. Early experiments with hydroxychloroquine hinted that it was effective at fighting the coronavirus in a petri dish.” “The drug was touted a lot and FDA authorized it for emergency use in hospitalized covid-19 patients. But that authorization was withdrawn this month after evidence showed that the drug was “unlikely to be effective” against the virus and posed potential safety risks.”
This has become the respectable position, except the studies they are referring to are deeply flawed, none mentioning that hydoxychloroquine is a zinc ionophore. Studies that do not dose properly (early disease stage, with zinc) and do not track time of onset and zinc serum levels are worthless. Studies that apply it to people on ventilators are designed to fail, like applying an air bag to a car crash victim in the hospital.
There is a lot of evidence that it does work, among them fatality rates in countries such as Morocco and Costa Rica (and Korea) where they have used it. There are also many studies that strongly support it efficacy. Any other ionophore will actually work as well.
Unfortunately, the science cudgel that people like to wield has become thoroughly politicized, on many fronts. It’s a shame that people are dying because of bureaucratic and commerical interests.
This is depressing. I didn’t know anyone with it and now I know several people including my neighbor. Our hospitals are filling up. Once hospitals are blown out, everyone freak out. Death is not the only horrible outcome. Sadly- if we had spent trillions on fighting this with testing and tracing and quarantining people then the financial losses would have been a fraction of what they are now. This is the worst, self inflicted financial disaster. Trump is the biggest destroyer of our economy there has ever been. That’s why all he talks about is hate a white supremacy now. He has nothing else to offer. We Have 100 percent broken with my husbands family and Part of mine. Culture war is real and those grandparents will never see their grandchildren again.
West coast vs East coast, particularly the Boston to D.C. corridor –
West coast younger
West coast lower BMI
West coast lower diabetes
West coast lower heart disease
West coast outdoors more
West coast eat healthier
West coast exercise more
West cost not as densely populated in cities or individual residential buildings
None of the above has anything to do with ‘response’.
Full disclosure – I am in Flyoverland, nowhere near either coast. 90 degrees, 100% sunshine and humid today, a great day to run on the trails uninterrupted.
West coast less likely to smoke / ever smoke tobacco
West coast less likely to work / ever worked in lung-damaging industry
West coast not jammed in public transportation
Can’t believe everyone believes all this propaganda and nonsense. I know nobody with this virus and ask everyone I see each day if they do. Nobody knows anyone with it.
Surprised everyone allows media and propaganda to control them like this. It’s sad.
Everything you need to know about the Global Elite can be told in the great 2020 Covid-19 hoax:
2020 Covid-19 deaths so far this year in the RICHEST nations of the world: 525k people, 85% of which have been elderly.
Meticulously tracked and hysterically reported as a mass extinction event.
2020 deaths from starvation so far this year in the POOREST nations of the world: 4.5 MILLION people, 1/3 of which have been CHILDREN dying at a rate of 1 child every 10 seconds.
Another covidiot. The global fatality rate is likely significantly higher than what has been reported. Also, the daily case and fatality rates would go through the roof without the measures taken by countries around the world to reduce the impact of the Covid virus. This has never been reported as a mass extinction event. It is however a global health crisis impacting rich and poor nations alike.
There is no doubt that the case count is climbing to new daily highs. It will be interesting to see if and how the daily death count increases relative to the daily case count. I have heard arguments that the mutated virus now seems to hit more of the younger population and that this will result in a decrease to the number of daily deaths. I guess we wait and see what the next couple of weeks brings although the cynic in me expects some of the impacted states to be less than forthcoming with actual fatality rates. It is hard to see how the economy can start to build some momentum as long as the daily case count keeps rising. No concerts, no spectator sports, no theaters, significantly reduced restaurant and bar traffic, significantly reduced foreign and domestic tourism coupled with a high unemployment rate all suggest that this recovery will be slow and a long time coming. Hope the Fed has deep pockets.
The Fed has a big printing press and an even bigger computer.
The death rates still haven’t broken from their downward trend which started after the April peak.
In terms of infection in young people.m, I suspect this is due to behavior rather than mutations.
It would seem obvious a virus can spread in the air. Nice sunshine, a breeze, perhaps it isn’t viable very long. In a warm, humid, basically still office it might float 20m and last 30 mins. Probably much less likely to get a big virus load than way but…
As more people are infected presumably the rate of mutation will increase, so more variants to come. But ones which produce worse symptoms presumably also limit themselves by making the diseased less able to spread it. So question is will getting a highly infectious, but not very deadly strain provide immunity or at least enhanced defences against other strains.
Mish, I am shocked that you haven’t triggered the Anti Fauci, Anti Virus, Anti Vaccine crowd. They must be out at the open bars testing the advanced theories of Covidiotism!
They were around for a while, but they got their feelings hurt and scampered back to their safe space at zerohedge.
We need to challenge some of the conventional wisdom about the pandemic response. If you want to label everyone who disagrees with you, have at it bucko.
I’ve noticed over the last week that Mish is approaching the virus stories from a critical lens, rather than a political one. I suspect that’s why there aren’t as many negative comments.
The coronavirus is finding new victims worldwide, in bars and restaurants, offices, markets and casinos, giving rise to frightening clusters of infection that increasingly confirm what many scientists have been saying for months: The virus lingers in the air indoors, infecting those nearby. https://www.nytimes.com/2020/07/04/health/239-experts-with-1-big-claim-the-coronavirus-is-airborne.html?smid=tw-share
This is why opening bars and other indoor venues where people cant wear masks is so dangerous.
it s all about the economy….stupid !
If it’s pure aerosol not heavy droplets, which is looking likely…. than masks won’t matter. A mask is like trying to stop a golf ball with a soccer net.
Only distancing will slow the spread, but never sought to snuff it out.
FWIW coronaviruses are always mutating. The common cold is typically a coronavirus, rhinovirus or both. I’ve said from the beginning that while vaccines would be helpful they were unlikely to prevent the mutations. Well we now know that the strain that ran through Wuhan, Italy and New York hasnt made it to most other places yet but is only now getting started. Those celebrating that a region or country has done a great job were probably celebrating too early. In reality the worse strain is only now spreading everywhere. This is precisely the wrong time to be opening or open.
About 40% of the time, the common cold is caused by a rhinovirus. Another 20% of cold are caused by 4 Cornonaviruses, the two most common of which are oc43 and 229e. Still another 20% of colds are caused by RSV, and the final 20% are caused by a variety of other viruses. The coronaviruses that cause colds do not mutate much, but we keep getting them because our bodies forget about them quickly, so immunity lasts only a few months.
This virus is more like SARS than oc43 or 229e. The immunity to SARS lasted for at least several years. There was a vaccine for SARS that was safe and effective through Phase 1 and 2 trials, but by the time it was ready to start the expensive Phase 3 trials, SARS was gone, so there was no reason for further testing. There are good reasons to believe that a vaccine for SARS-COV2 can be developed that is safe and effective, that that it will confer at least a few years of immunity.
‘There was a vaccine for SARS that was safe and effective through Phase 1 and 2 trials, but by the time it was ready to start the expensive Phase 3 trials”
If it had NOT gone thru phase 3 trials(on human beings), how did you know it was EFFECTIVE?
You are correct that it was not proven effective in humans. It was proven effective in mice, and safe in humans:
That’s what respectable people like to say, but in fact, feline trials showed problems with ADE, which means that disease severity is worse after vaccination than without.
The vaccine I was referring to was a DNA vaccine, and was described in the link in my prior post. There was also an attempt to make a vaccine from inactivated whole virus that was not successful. It did give protection to ferrets, but also caused an immune disease.
Most of the vaccines being developed for SARS-COV2 do not use inactivated whole viruses, but are based on DNA or RNA.
This story hasnt gotten enough coverage. The more virulent mutation is only now hitting places it hasnt. That’s bad news for any country that didnt get it the first time. This includes countries in Northern Europe, Iceland, Canada, the United States, Mexico and elsewhere in the Americas. Some countries like England may be opening up again at exactly the wrong time. There was a shutdown of a city of 200,000 in Spain today. I expect that as travel increases within Europe they will suffer more outbreaks of the new strain. Portions of Spain, France and Italy were ravaged but most of Europe was spared from the more virulent strain.
Europe is where the D614G evolved. That was what they had the first time.
Not all of Europe. Most places shutdown before it ravaged them. There will be more shutdowns everywhere this summer as travel inside Europe increases.
Italy, France, and Spain had the D614G mutation, and probably Portugul, UK and Switzerland as well. I don’t know about the rest of the EU.
Some would have you think Europe has been open and thriving but not so:
The UK is behind the rest of Europe.
This is pretty much old news. Since March, most of the Covid in the US has been D614G. It does explain why the West coast got the virus under control quickly, while the East Coast failed. Since the West Coast is no doubt now facing the more virulent strain, that is why this is relevant now.
It would be interesting to see the percentage of D614G by state so we could see how that matches up with the various states’ abilities to contain it.
is D614G related to DDTG? can’t believe how quickly the latter has spread.
I think you ar less forgetting the south. America isnt merely the east and west coast. 2 of 3 largest population centers are being hit hard now in Texas and Florida. They invited death and now it’s coming for their residents. I don’t believe California had the worse mutation but it is starting in LA now. This was the reason for reversing the openings of bars and restaurants in 75% of California.
I live in LA and we definately had a covid version starting as early as October but it burned way slower. I have interviewed everyone of my LA based friends that had an ILI (influenza like illness) since Oct 2019 and a bunch had covid like symptoms including myself in late December, I was a few hours away from going to the local ER when I started to get better. I suspect either the residual short lived herd immunity kept cases from spiking in a lot of the big west coast cities back in March but its worn off now or the d614g strain that is far more contagious has arrived and although not that lethal it burns so fast thru a population it overwhelms the medical system. The areas like New York that d614g burned thru already prob have some levels of herd immunity now. The serological antibody studies are prob all junk because many either have a weak antibody response or undetectable after a couple of months. If the major sewer systems like Hyperion in LA kept samples we could test my theory.
When people write about containing the virus, or suppressing it, or taming it, or getting it under control, it would be great if they defined what the end game is going to be. Nature means a virus burns through a population and eventually burns out and fades. Some disappear, others remain endemic and have a habit of coming back in hard to predict waves and cycles. None ever infects 100% of the population, due to the amount of differentiation in the population’s immune system. Herd immunity is a vaccine concept (1-1/R₀) to indicate what proportion of the population needs to get the vaccine in order to achieve immunity. Without a vaccine, you cannot really calculate herd immunity since you don’t know what percentage of the population is susceptible. With Covid, 40% of asymptomatic cases have no detectable anti-bodies 8 weeks after recovery. This could actually be higher, because asymptomatic cases are only visible to the medical community through contact tracing of symptomatic cases. Cell culture experiments show that 1 in 8 samples develop anti-bodies, the other 7 defeat the virus with T-cells activation. Modeling also shows that the curve bends way before it would if everybody as susceptible: it bends as if 80% of the population is not part of the pool. We have no means of actually establishing by serological testing what portion of the population has recovered and what portion has been exposed.
As for a vaccine, since Covid infects the epithelial cells, we don’t know whether a vaccine will prevent infection (they are hard to target, in effect being like your skin, on the outside of the body). The Oxford vaccine generated antibody response, but all the monkeys were still infected. With human subjects, the most ill show the greatest antibody response, paradoxically. And even 13% of symptomatic patients show no antibodies 8 weeks after recovery.
As for social distancing, it now seems we have to get the cat population to go along to prevent new outbreaks.
In this context, by “controlling it”, I meant reducing the case rate to a manageable level where hospitals are not over capacity. In other contexts, such as in discussion of New Zealand, I might have meant to reduce it to zero. Reducing it to zero is possible on an island, but not in a country like the US, where new infections can come from other states.
I agree that there are many questions we don’t know the answers to, and won’t know the answers for quite awhile. At some point in the future, though, when we do have more answers, we will re-visit the actions taken by various people today, and judge whether those people acted appropriately.
Interesting.. do you have a source for this?
Your reply was to me, though the information you quoted was not. Nevertheless, I will answer. I have seen speculation that this is true, notably from a Nobel winner in a non related field, math I think. The claim makes no sense, though, at least not with the 80% number. Why not? Well, if 80% were immune, we would have been at herd immunity on day one, and it would have never spread at all.
That said, it does act as if a portion of the population has some immunity. Once a country has 1-2% infections and/or 0.1-0.2% deaths, the virus seems to run out of steam. If you assume that the real infection rate is 10x higher than the detected infections, 1-2% positive tests means 10-20% infections. If 50-60% of people are immune, then 10-20% infections would be getting you close to herd immunity, and that would explain why countries and states get hit hard, and then taper off.
In other words, there is an open question, and it is important. Are the cases low now in places like New York, New Jersey, Italy, and Spain because they were this so hard that the people are behaving, and have learned how not to spread it? Or, are the cases low now because they have approached herd immunity? In time we will be able to answer this, but right now, we can’t. Some, such as Realist, believe that cases now are low in New York because they are doing a great job, and that cases in Texas and Florida are high because they are not. That’s possible, but it’s also possible that cases in New York are low because the disease has mostly run it’s course in New York, while cases are high in Texas and Florida because it has not. We could answer the question accurately if someplace such as New Jersey would simply open up completely, and see what happens, but I don’t think anyone is prepared to take that risk.
What will happen this Fall? With cooler, drier air, SARS-COV2 will become easier to spread. That, in turn, will increase the R0, which in turn will increase the percentage of the population that needs immunity before herd immunity is effective. Thus, we will almost certainly see a second wave everywhere. The size of that second wave will be smaller if there is a pool of immune people, and larger if there is not.
Thanks for the reply.. not sure how my comment was applied to yours, so sorry for the confusion.
I agree with most of what you said but would like to point out that there is a big difference between NYC (city) and NYS (state). I live in NYS, but multiple hours drive from NYC. I can tell you we never saw COVID like the city did, so it may be a case of “running its course” /herd immunity in NYC, but it’s definitely more ” people are behaving” in the rural and suburb portion of the state.
A pandemic primer on excess mortality statistics and their comparability across countries including the USA https://ourworldindata.org/covid-excess-mortality
Thank you!
This “pandemic primer” might be the best thing I’ve read since February on Covid19 statistics.
They compare a (too) few European country’s relevant numbers, explain why those numbers are what’s important, even explain why numbers for various geo-political entities should be broken out by sub-state (i.e. Comparing the US or China with, say, France or Wales begs for trouble.), etc.
There are a very few places that are trying to get overall death rates (as opposed to Covid death rates or whatnot) per various entities. Examples: