Barbed and ready

It starts with the spikes. Each SARS-CoV-2 virion (virus particle) has an outer surface peppered with 24–40 haphazardly arranged spike proteins that are its key to fusing with human cells2. For other types of virus, such as influenza, external fusion proteins are relatively rigid. SARS-CoV-2 spikes, however, are wildly flexible and hinge at three points, according to work published in August 2020 by biochemist Martin Beck at the Max Planck Institute of Biophysics in Frankfurt, Germany, and his colleagues3.

That allows the spikes to flop around, sway and rotate, which could make it easier for them to scan the cell surface and for multiple spikes to bind to a human cell. There are no similar experimental data for other coronaviruses, but because spike-protein sequences are highly evolutionarily conserved, it is fair to assume the trait is shared, says Beck.

Cryo-electron tomography images of SARS-CoV-2 virions. (Scale bar: 30 nanometres.)Credit: B. Turoňová et al./Science

Early in the pandemic, researchers confirmed that the RBDs of SARS-CoV-2 spike proteins attach to a familiar protein called the ACE2 receptor, which adorns the outside of most human throat and lung cells. This receptor is also the docking point for SARS-CoV, the virus that causes severe acute respiratory syndrome (SARS). But compared with SARS-CoV, SARS-CoV-2 binds to ACE2 an estimated 2–4 times more strongly4, because several changes in the RBD stabilize its virus-binding hotspots5.

Worrying variants of SARS-CoV-2 tend to have mutations in the S1 subunit of the spike protein, which hosts the RBDs and is responsible for binding to the ACE2 receptor. (A second spike subunit, S2, prompts viral fusion with the host cell’s membrane.)

The Alpha variant, for example, includes ten changes in the spike-protein sequence, which result in RBDs being more likely to stay in the ‘up’ position6. “It is helping the virus along by making it easier to enter into cells,” says Priyamvada Acharya, a structural biologist at the Duke Human Vaccine Institute in Durham, North Carolina, who is studying the spike mutations.

The Delta variant, which is now spreading around the world, hosts multiple mutations in the S1 subunit, including three in the RBD that seem to improve the RBD’s ability to bind to ACE2 and evade the immune system7.

Restricted entry

Once the viral spikes bind to ACE2, other proteins on the host cell’s surface initiate a process that leads to the merging of viral and cell membranes (see ‘Viral entry up close’).

Source: Janet Iwasa, Univ. Utah; Graphic: Nik Spencer/Nature

The virus that causes SARS, SARS-CoV, uses either of two host protease enzymes to break in: TMPRSS2 (pronounced ‘tempress two’) or cathepsin L. TMPRSS2 is the faster route in, but SARS-CoV often enters instead through an endosome — a lipid-surrounded bubble — which relies on cathepsin L. When virions enter cells by this route, however, antiviral proteins can trap them.

SARS-CoV-2 differs from SARS-CoV because it efficiently uses TMPRSS2, an enzyme found in high amounts on the outside of respiratory cells. First, TMPRSS2 cuts a site on the spike’s S2 subunit8. That cut exposes a run of hydrophobic amino acids that rapidly buries itself in the closest membrane — that of the host cell. Next, the extended spike folds back onto itself, like a zipper, forcing the viral and cell membranes to fuse.

An animation of the way SARS-CoV-2 fuses with cells.Credit: Janet Iwasa, University of Utah

The virus then ejects its genome directly into the cell. By invading in this spring-loaded manner, SARS-CoV-2 infects faster than SARS-CoV and avoids being trapped in endosomes, according to work published in April by Barclay and her colleagues at Imperial College London9.

The virus’s speedy entry using TMPRSS2 explains why the malaria drug chloroquine didn’t work in clinical trials as a COVID-19 treatment, despite early promising studies in the lab10. Those turned out to have used cells that rely exclusively on cathepsins for endosomal entry. “When the virus transmits and replicates in the human airway, it doesn’t use endosomes, so chloroquine, which is an endosomal disrupting drug, is not effective in real life,” says Barclay.

The discovery also points to protease inhibitors as a promising therapeutic option to prevent a virus from using TMPRSS2, cathepsin L or other proteases to enter host cells. One TMPRSS2 inhibitor, camostat mesylate, which is approved in Japan to treat pancreatitis, blocked viral entry into lung cells8, but the drug did not improve patients’ outcomes in an initial clinical trial11.

“From my perspective, we should have such protease inhibitors as broad antivirals available to fight new disease outbreaks and prevent future pandemics at the very beginning,” says Stefan Pöhlmann, director of the Infection Biology Unit at the German Primate Center in Göttingen, who has led research on ACE2 binding and the TMPRSS2 pathway.

Source: Structural image from Lorenzo Casalino, Univ. California, San Diego (Ref. 1); Graphic: Nik Spencer/Nature

In Amaro’s simulation, when the RBD lifted up above the glycan cloud, two glycans swooped in to lock it into place, like a kickstand on a bicycle. When Amaro mutated the glycans in the computer model, the RBD collapsed. McLellan’s team built a way to try the same experiment in the lab, and by June 2020, the collaborators had reported that mutating the two glycans reduced the ability of the spike protein to bind to a human cell receptor1 — a role that no one has previously recognized in coronaviruses, McLellan says. It’s possible that snipping out those two sugars could reduce the virus’s infectivity, says Amaro, although researchers don’t yet have a way to do this.

Since the start of the COVID-19 pandemic, scientists have been developing a detailed understanding of how SARS-CoV-2 infects cells. By picking apart the infection process, they hope to find better ways to interrupt it through improved treatments and vaccines, and learn why the latest strains, such as the Delta variant, are more transmissible.

What has emerged from 19 months of work, backed by decades of coronavirus research, is a blow-by-blow account of how SARS-CoV-2 invades human cells (see ‘Life cycle of the pandemic coronavirus’). Scientists have discovered key adaptations that help the virus to grab on to human cells with surprising strength and then hide itself once inside. Later, as it leaves cells, SARS-CoV-2 executes a crucial processing step to prepare its particles for infecting even more human cells. These are some of the tools that have enabled the virus to spread so quickly and claim millions of lives. “That’s why it’s so difficult to control,” says Wendy Barclay, a virologist at Imperial College London.

Source: Hui (Ann) Liu, Univ. Utah; Graphic: Nik Spencer/Nature 

• NEWS FEATURE
• 28 July 2021

How the coronavirus infects cells — and why Delta is so dangerous

Scientists are unpicking the life cycle of SARS-CoV-2 and how the virus uses tricks to evade detection.

• Megan Scudellari

• Twitter 
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A computer simulation of the structure of the coronavirus SARS-CoV-2.Credit: Janet Iwasa, University of Utah

The coronavirus sports a luxurious sugar coat. “It’s striking,” thought Rommie Amaro, staring at her computer simulation of one of the trademark spike proteins of SARS-CoV-2, which stick out from the virus’s surface. It was swathed in sugar molecules, known as glycans.

“When you see it with all the glycans, it’s almost unrecognizable,” says Amaro, a computational biophysical chemist at the University of California, San Diego.

Many viruses have glycans covering their outer proteins, camouflaging them from the human immune system like a wolf in sheep’s clothing. But last year, Amaro’s laboratory group and collaborators created the most detailed visualization yet of this coat, based on structural and genetic data and rendered atom-by-atom by a supercomputer. On 22 March 2020, she posted the simulation to Twitter. Within an hour, one researcher asked in a comment: what was the naked, uncoated loop sticking out of the top of the protein?

Amaro had no idea. But ten minutes later, structural biologist Jason McLellan at the University of Texas at Austin chimed in: the uncoated loop was a receptor binding domain (RBD), one of three sections of the spike that bind to receptors on human cells (see ‘A hidden spike’).

Better late than never! A Promisory Abstract from Nature..

1. nature  
2. letters  
3. article

• Letter
• Published: 11 July 2018

Reprogramming human T cell function and specificity with         non-viral genome targeting

• Theodore L. Roth, 
• Cristina Puig-Saus, 
• […]
• Alexander Marson 

Nature volume 559, pages 405–409 (2018)Cite this article

• 71k Accesses

• 292 Citations

• 589 Altmetric

• Metrics details

Abstract

Decades of work have aimed to genetically reprogram T cells for therapeutic  purposes1,2using recombinant viral vectors, which do not target transgenes to                     specific genomic sites3,4.                                                                                                                           

The need for viral vectors has slowed down research and clinical use as their                                         manufacturing and testing is lengthy and expensive.                                                                

Genome editing brought the promise of specific and efficient insertion of large            transgenes into target cells using homology-directed repair5,6.  

 Here we developed a CRISPR–Cas9 genome-targeting system that does not                        require viral vectors, allowing rapid and efficient insertion of large DNA                      sequences (greater than one kilobase) at specific sites in the genomes of                                                    primary human T cells, while preserving cell viability and function.                                             This permits individual or multiplexed modification of endogenous genes.                               

First, we applied this strategy to correct a pathogenic IL2RA mutation in cells                                          from patients with monogenic autoimmune disease, and demonstrate improved                                    signalling function. Second, we replaced the endogenous T cell receptor                                (TCR) locus with a new TCR that redirected T cells to a cancer antigen.                                        The resulting TCR-engineered T cells specifically recognized tumour antigens                                   and mounted productive anti-tumour cell responses in vitro and in vivo.                                  

Together, these studies provide preclinical evidence that non-viral genome                        targeting can enable rapid and flexible experimental manipulation and                               therapeutic engineering of primary human immune cells.

 

I WAS WRONG!

 I was wrong! I though the Chinese government was finally doing an exemplary public service  when they released science based Covid-19 information to the United Nations and to the World. 

 Today, November 5, I learned that I was wrong! It was a brave young Chinese journalist who released the information to the world and she is now paying the price. Today, Zhang Zhan is dying in a Chinese prison because she released the Covid-19 information to the United Nations. The Chinese government accused her of provoking trouble and disturbing the public order.

 As a journalist myself who discovered years ago that journalistic objectivity does not exist, my blood is boiling! I am angry for believing the Chinese government was anything but a callous group of old farts without humanitarian ethics. I am angry at myself for crediting a cruel Communist dictatorship with the decency to inform the world of a deadly pandemic creating virus. A government punishing the one journalist in China with the self sacrificing courage to speak up.

 The Chinese government would have allowed millions of people to die if it were not for the courage of Zhang Zhan. Today, I ask for her immediate release and for her hospitalization, preferably in some other country. She is an international heroine!

 Today, I am disturbing the world order by accusing the Chinese leaders of cruelty, stupidity and ridiculous politics. Zhang Zhan is being punished for telling the truth and saving millions of lives. If the Chinese leaders want to save face, I recommend they move their collective butts quickly to save Zhang Zhan or I will call for an international boycott of Chinese products and BEJING CAN GO BACK TO THE STONE AGE! 

How is this for disturbing the public order?

Signed: Nelson Joseph Raglione

International Journalist.

“Anywhere you look, you’re able to find pretty objective measures of bad things happening. It’s clear climate change impacts are arriving faster than anticipated and worse than anticipated.”

Julio Friedmann

Senior Research Scholar at the Center on Global Energy Policy at Columbia University

" California, the US state with arguably the country’s most determined climate agenda, battled more than 9,500 wildfires last year, which consumed some
4.2 million acres of forest.  Similarly, 2019 was Australia’s hottest summer on record and resulted in bushfires burning an estimated 32 million acres. Satellite data revealed in September 2020 that the year’s Arctic sea ice cover shrank to the second-lowest level ever recorded, nearly 2.5 million square kilometers less than the average of the last four decades. And data from the Brazilian National Institute of Space Research estimated there was a 9.5% increase in Amazon deforestation in the year up to July 2020 over the previous year. The economic cost of the damage is mounting; the world’s 10 costliest weather disasters of 2020 saw insured damages worth $140 billion in 2020, according to a report by Christian Aid.

“Anywhere you look, you’re able to find pretty objective measures of bad things happening. It’s clear climate change impacts are arriving faster than anticipated and worse than anticipated,” says Julio Friedmann, senior research scholar at the Center on Global Energy Policy at Columbia University. “This means that climate change is not an acute problem like a storm you clean up after,

it’s a chronic problem, like having diabetes and having to manage your health continuously.”

If the planet was managing (badly) with diabetes, it took 2020’s metaphorical heart attack for the world to really grasp the state of its health. This is not to say that prior to covid there was complete inaction. The International Energy Institute estimates that energy-related CO2 emissions in 2019, at roughly 33 gigatons, were the same as 2018, and energy emissions in advanced economies (roughly a third of the world’s total) actually dropped 4% last year.

Prospect of a green recovery

Having wiped an estimated 4.4% off the world’s GDP this year, covid-19 has put humanity’s impact on the environment back in the spotlight. First, it showed how changes in human activity can significantly reduce carbon emissions. Analysis of electricity production, air travel, and other fuel consumption data in the first half of 2020 found that CO2 emissions were 8.8% lower globally than the same period in 2019, a far greater decline than in any previous period of economic contraction.

Second, policymakers realized that the massive stimulus packages ($12.6 trillion globally) earmarked for pandemic recovery could be directed into infrastructure, innovation, and programs that will build economic and environmental resilience for the long term. Germany, the world’s “pandemic green leader,” is spending over a third of recovery stimulus on transportation transition, renewable energy capability building, and other projects that will serve as a cornerstone of the EU’s attempt to make Europe the first carbon-neutral continent. China is using its central planning prowess to develop the world’s largest comprehensive decarbonization plan, even though less than $1.5 billion of its post-covid recovery stimulus spending is specifically targeted at green projects. Even in the US, where the past four years have seen a systematic reversing of emission-capping regulations, $26 billion in stimulus is being aimed at sustainability and emissions reduction programs, providing a platform for President Joe Biden to “build back better” and fulfill his promise to rejoin the Paris Accord.

Yet there is a tension for governments around the world as they allocate the economic “pain relief” in balancing short- and long-term objectives. Many are being criticized for not using the crisis as enough of an opportunity to make hard choices and pivot away from fossil fuel- intensive sectors. Claire Healy, program director for climate diplomacy at climate advocacy group E3G, says that covid provided “a pivotal moment—a window into a decade of decarbonization, where decision-makers in government, in banks, in businesses, have to decide how we build back. It’s about competitiveness in the future; the promise of green jobs and technologies drives further action and ambition.” The Green Future Index benchmarks the progress and commitment that countries are making toward becoming future green leaders. "

Why we can never go back to the past.     

  The past is dissipated energy. Moments in the past were captured by: photographs, film and

video recordings and human memory, which today help us remember the past.

 The past can be simulated and copied in the present but never regained. The present, for better or

for worse, has new moments of changing energy which can be shaped and defined to create future energy patterns depending on how you feel and act and what choices you make. With present moments, you can prepare for the future and even though the present is continually changing, we as human beings can alter our present energy patterns to affect the future. In other words, we do not have to accept a future filled with pollution and devastating global warming.  We can alter the present to create a nurturing and sustaining future for all life on Earth but remember, we are late, very late!

 

N. J.R.

P.S. 

 Here is an interesting thought! Why not reverse the economic mind set of governments and companies by tearing down old buildings and replacing them with Trees and Flower gardens and with a vegetable garden or Two for effect? That is a hundred times better than what is happening now! Today we have Scrooge controlled money hungry companies destroying forests and woodlots in order to plant Condos and Office towers and industrial parks everywhere? We have old growth forests being massacred by quick profit timber companies and these companies need to be stopped and bloody fast!

WHAT IS GLOBAL WARMING? IT IS DEADLY!

Håkan Jansson/Alamy 

Q: What is global warming?

A: Since the Industrial Revolution, the global annual temperature has increased in total by a little more than 1 degree Celsius, or about 2 degrees Fahrenheit. Between 1880—the year that accurate recordkeeping began—and 1980, it rose on average by 0.07 degrees Celsius (0.13 degrees Fahrenheit) every 10 years. Since 1981, however, the rate of increase has more than doubled: For the last 40 years, we’ve seen the global annual temperature rise by 0.18 degrees Celsius, or 0.32 degrees Fahrenheit, per decade.

The result? A planet that has never been hotter. Nine of the 10 warmest years since 1880 have occurred since 2005—and the 5 warmest years on record have all occurred since 2015. Climate change deniers have argued that there has been a “pause” or a “slowdown” in rising global temperatures, but numerous studies, including a 2018 paper published in the journal Environmental Research Letters, have disproved this claim. The impacts of global warming are already harming peoplearound the world.

Now climate scientists have concluded that we must limit global warming to 1.5 degrees Celsius by 2040 if we are to avoid a future in which everyday life around the world is marked by its worst, most devastating effects: the extreme droughts, wildfires, floods, tropical storms, and other disasters that we refer to collectively as climate change. These effects are felt by all people in one way or another but are experienced most acutely by the underprivileged, the economically marginalized, and people of color, for whom climate change is often a key driver of poverty, displacement, hunger, and social unrest.

Q: What causes global warming?

A: Global warming occurs when carbon dioxide (CO2) and other air pollutants collect in the atmosphere and absorb sunlight and solar radiation that have bounced off the earth’s surface. Normally this radiation would escape into space, but these pollutants, which can last for years to centuries in the atmosphere, trap the heat and cause the planet to get hotter. These heat-trapping pollutants—specifically carbon dioxide, methane, nitrous oxide, water vapor, and synthetic fluorinated gases—are known as greenhouse gases, and their impact is called the greenhouse effect.

Though natural cycles and fluctuations have caused the earth’s climate to change several times over the last 800,000 years, our current era of global warming is directly attributable to human activity—specifically to our burning of fossil fuels such as coal, oil, gasoline, and natural gas, which results in the greenhouse effect. In the United States, the largest source of greenhouse gases is transportation (29 percent), followed closely by electricity production (28 percent) and industrial activity (22 percent).

Curbing dangerous climate change requires very deep cuts in emissions, as well as the use of alternatives to fossil fuels worldwide. The good news is that countries around the globe have formally committed—as part of the 2015 Paris Climate Agreement—to lower their emissions by setting new standards and crafting new policies to meet or even exceed those standards. The not-so-good news is that we’re not working fast enough. To avoid the worst impacts of climate change, scientists tell us that we need to reduce global carbon emissions by as much as 40 percent by 2030. For that to happen, the global community must take immediate, concrete steps: to decarbonize electricity generation by equitably transitioning from fossil fuel–based production to renewable energy sources like wind and solar; to electrify our cars and trucks; and to maximize energy efficiency in our buildings, appliances, and industries.

Q: How is global warming linked to extreme weather?

A: Scientists agree that the earth’s rising temperatures are fueling longer and hotter heat waves, more frequent droughts, heavier rainfall, and more powerful hurricanes.

In 2015, for example, scientists concluded that a lengthy drought in California—the state’s worst water shortage in 1,200 years—had been intensified by 15 to 20 percent by global warming. They also said the odds of similar droughts happening in the future had roughly doubled over the past century. And in 2016, the National Academies of Science, Engineering, and Medicine announced that we can now confidently attribute some extreme weather events, like heat waves, droughts, and heavy precipitation, directly to climate change.

The earth’s ocean temperatures are getting warmer, too—which means that tropical storms can pick up more energy. In other words, global warming has the ability to turn a category 3 storm into a more dangerous category 4 storm. In fact, scientists have found that the frequency of North Atlantic hurricanes has increased since the early 1980s, as has the number of storms that reach categories 4 and 5. The 2020 Atlantic hurricane season included a record-breaking 30 tropical storms, 6 major hurricanes, and 13 hurricanes altogether. With increased intensity come increased damage and death. The United States saw an unprecedented 22 weather and climate disastersthat caused at least a billion dollars’ worth of damage in 2020, but 2017 was the costliest on record and among the deadliest as well: Taken together, that year's tropical storms (including Hurricanes Harvey, Irma, and Maria) caused nearly $300 billion in damage and led to more than 3,300 fatalities.

The impacts of global warming are being felt everywhere. Extreme heat waves have caused tens of thousands of deaths around the world in recent years. And in an alarming sign of events to come, Antarctica has lost nearly four trillion metric tons of ice since the 1990s. The rate of loss could speed up if we keep burning fossil fuels at our current pace, some experts say, causing sea levels to rise several meters in the next 50 to 150 years and wreaking havoc on coastal communities worldwide.

The Pfizer vaccines worked for me!

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The mRNA

Pfizer’s vaccine is the first on the market that consists of actual genetic information from a virus in the form of messenger RNA, or mRNA, a type of molecule whose usual job is to transport copies of genetic instructions around a cell to guide the assembly of proteins. Imagine an mRNA as a long ticker tape carrying instructions. It's fairly delicate stuff, and that's why Pfizer's vaccine needs to be kept at around -100 °F (-73 °C) until it's used.

The new vaccine, delivered as a shot in the arm muscle, contains an RNA sequence taken from the virus itself; it causes cells to manufacture the big “spike” protein of the coronavirus, which the pathogen uses to glom onto a person’s cells and gain entry. On its own, without the rest of the virus, the spike is pretty harmless. But your body still reacts to it. This is what leaves you immunized and ready to repel the real virus if it turns up.

The mRNA in the vaccine, to be sure, isn’t quite the same as the stuff in your body. That’s good, because a cell is full of defenses ready to chop up RNA, especially any that doesn’t belong there. To avoid that, what’s known as “modified nucleosides” have been substituted for some of the mRNA building blocks.

But Pfizer is holding back a little. The spike gene sequence can be tweaked in small ways for better performance, by means that include swapping letters. We don’t think Pfizer has said exactly what sequence it is using, or what modified nucleosides. That means the content of the shot may not be 100% public.

The lipids

The Pfizer vaccine, like one from Moderna, uses lipid nanoparticles to encase the RNA. The nanoparticles are, basically, tiny greasy spheres that protect the mRNA and help it slide inside cells.

These particles are probably around 100 nanometers across. Curiously, that’s about the same size as the coronavirus itself.

Pfizer says it uses four different lipids in a “defined ratio.” The lipid ALC-0315 is the primary ingredient in the formulation. That’s because it’s ionizable—it can be given a positive charge, and since the RNA has a negative one, they stick together. It's also a component that can cause side-effects or allergic reactions. The other lipids, one of which is the familiar molecule cholesterol, are “helpers” that give structural integrity to the nanoparticles or stop them from clumping. During manufacturing, the RNA and the lipids are stirred into a bubbly mix to form what the FDA describes as a “white to off-white” frozen liquid.

Salts

The Pfizer vaccine contains four salts, one of which is ordinary table salt. Together, these salts are better known as phosphate-buffered saline, or PBS, a very common ingredient that keeps the pH, or acidity, of the vaccine close to that of a person’s body. You’ll understand how important that is if you’ve ever squeezed lemon juice on a cut. Substances with the wrong acidity can injure cells or get quickly degraded.

Sugar

The vaccine includes plain old sugar, also called sucrose. It’s acting here as a cryoprotectant to safeguard the nanoparticles when they’re frozen and stop them from sticking together.

Saline solution

Before injection, the vaccine is mixed with water containing sodium chloride, or ordinary salt, just as many intravenously delivered drugs are. Again, the idea is that the injection should more or less match the salt content of the blood.

No preservatives

Pfizer makes a point of saying its mixture of lipid nanoparticles and mRNA is “preservative-free.” That’s because a preservative that’s been used in other vaccines, thimerosal (which contains mercury and is there to kill any bacteria that might contaminate a vial), has been at the center of worries around over whether vaccines cause autism. The US Centers for Disease Control says thimerosal is safe; despite that, its use is being phased out. There is no thimerosal—or any other preservative—in the Pfizer vaccine. No microchips, either.

The vaccine is still known by the code name BNT162b, but once it’s authorized, expect Pfizer to give it a new, commercial name that conveys something about what’s in it and what it promises for the world.

We thank the following people for explaining the vaccine ingredients: Jacob Becraft and Aalok Shah, Strand Therapeutics; Yizhou Dong, Ohio State University; Jason Underwood, Pacific Biosciences; Andrey Zarur, Greenlight Biosciences; Charles L. Cooney, MIT; and the communications staffs of Pfizer and Moderna Therapeutics.

By Antonio Regalato

by Antonio Regalado