Why the coronavirus’s delta variant dominated 2021

2021 was a year of coronavirus variants.

Alpha and beta kicked off the year, and several worrisome variants later, omicron is closing it out. How omicron may come to define the pandemic’s future remains uncertain. But even as omicron comes on strong, one variant, which rose to global dominance midyear in a way variants like alpha and beta never did, continues to largely define the pandemic right now: delta.

Things had actually seemed to be looking up in some parts of the world in the late spring and early summer of 2021, a year and a half into the COVID-19 pandemic. In the United States, for instance, millions of people were vaccinated, cases of the disease were falling, and people were beginning to socialize and resume normal activities.

But then delta hit hard. First spotted in India in October 2020, this variant of SARS-CoV-2, the coronavirus that causes COVID-19, quickly swept around the world, supplanting other versions of the virus in 2021 (SN: 7/2/21). Delta overwhelmed health care systems, tore through unvaccinated populations and showed that even the vaccinated were vulnerable, causing some breakthrough cases.
It soon became clear why delta wreaks so much havoc. People infected with delta make more of the virus and spread it for longer than people infected with other variants, researchers reported in Clinical Infectious Diseases in August. As a result, delta infections are more contagious. Consider two scenarios in a community where no one has immunity to the coronavirus: A person infected with an earlier version of the virus — the one first identified in Wuhan, China, that set off the pandemic — might spread it to two or three others. But a person infected with delta may transmit it to five or six people.

Delta owes its success to mutations in some of its proteins. Take, for instance, a mutation called R203M in the coronavirus’s nucleocapsid, or N protein, located inside the virus. This mutation may increase the amount of viral RNA that can be made or make it easier for the N protein to do its job, packing RNA into newly assembled viral particles, researchers reported in Science in November.
Mutations similar to delta’s have appeared here and there in other variants that proved themselves capable of spreading more easily or better evading the body’s immune defenses than the original virus. That includes alpha, first spotted in the United Kingdom; beta, first characterized in South Africa; and gamma, first noted in Brazil. The recently discovered omicron variant, first described in South Africa and Botswana, also shares some of the same mutations (SN: 12/1/21).

Some of delta’s grab bag of mutations are identical to those found in other variants, while others change the same protein building block, or amino acid, in a different way or pop up in the same part of the virus. For instance, alpha and omicron also have the same mutation of the 203rd amino acid in the N protein, but it is a different amino acid change than seen in delta. And some mutations are entirely new to delta.
Scientists don’t yet know the effect that all those changes have on delta’s ability to replicate or spread to others. What’s more, delta continues to evolve, picking up additional changes over time. But studies have zeroed in on the unique constellation of mutations decorating the virus’ spike protein. It’s the knobby protein studding each coronavirus that helps the virus latch onto and invade human cells. What looks like an individual knob is in fact composed of three identical pieces that fit together, each carrying the same set of mutations.

Some of delta’s spike protein mutations may help the virus more easily break into cells, where it turns cell machinery into virus-making factories. Two of those, dubbed T478K and L452R, are advantageously located on the receptor-binding domain. This is the part of the spike protein that attaches to ACE2, a protein on the surface of host cells.

Other mutations show up in a region of the spike protein called the N-terminal domain, which is a known target of the immune system’s neutralizing antibodies. These mutations may help the virus evade those antibodies, which can stop the virus from infecting cells.

And yet two other mutations, P681R and D614G, may help prep newly made viruses to go out and conquer. Those mutations are nestled near the dividing line for two parts of the spike protein, S1 and S2. Those parts need to be split apart to allow the coronavirus to engage in the gymnastics needed to help it fuse with the membrane of its prospective human host cell.
Human cells actually aid in this process: Inside infected cells a human protein called furin nicks the spike protein between the S1 and S2 segments, opening the receptor-binding domain so it can better grab ACE2. The P681R and D614G mutations may make the spike protein easier for furin to cut. Once snipped, newly-made viruses are primed to infect other cells.

Taken together, these mutations help delta break into cells more quickly and perform several tasks better than other variants do. As a result, in 2021, delta was able to become the dominant variant in the world.

Here’s how specific delta spike protein mutations may aid in a cell take-over:

  1. Some mutations allow the spike protein to get a better grip on cells.
    The coronavirus begins its cellular break-in by latching onto a protein called ACE2 that studs the surface of many types of human cells. Three mutations may make delta grabbier than other variants.

D614G interrupts some molecular interactions in the spike protein near a hinge that controls whether the receptor binding domain is in a closed position where it is protected from antibodies, or in an open position so that it can grab ACE2. With the D614G mutation, it’s more likely that one or more of ACE2-snagging portions of the protein will be open for action.

L452R may strengthen the interaction between ACE2 and the spike protein, making the virus more likely to infect cells. The change switches the charge on a protein building block in a key part of the spike protein from neutral to positive. So, like a magnet attracted to metal, the mutation seems to make the spike protein bind more tightly to a part of ACE2 that has a negative charge.

T478K is unique to the delta variant. It’s so far unclear what it does, but like L452R, it may also help strengthen the spike protein’s hold on ACE2.

  1. Some mutations allow delta to better fuse with the cell’s membrane, paving the way for the coronavirus to dump its genetic material into the cell.
    Once delta latches onto ACE2, a human protein called TMPRSS2 cuts away a part of the spike protein. As a result, the S1 portion of the protein is discarded, freeing up the S2 portion of the protein to twist into shape for the next step in the process: fusing to the cell. Some evidence suggests delta may be better at letting go of S1, making breaking into cells easier.

L452R may help the virus fuse with the membrane on the outside of the cell it’s trying to infect. That allows the virus to release its genetic material and begin hijacking the cell’s machinery to begin making more copies of itself.

P681R may create a stretch of basic amino acids that could help the virus fuse better with the cell membrane, helping more viruses get inside more cells.

As a result of these and other changes, delta can fuse with cells faster and can enter cells that have lower levels of ACE2 studding their surfaces than other variants can, researchers reported in Science in October.

After the virus fuses to the cell, it sets loose its RNA and turns its new lair into a virus factory: Viral RNA is copied, human ribosomes make viral proteins and the cell churns out nearly identical copies of the coronavirus. As the virus makes copies of its RNA, it can make typos. Sometimes, the genetic errors help the virus, which can give rise to variants like delta. But not all changes are good for the virus. Some genetic typos cause damage to viral proteins, meaning the viruses with those mutations can’t infect new cells. Other changes don’t have any effect on the virus at all.

  1. Some delta mutations may better prime newly made viruses to more easily infect cells.
    Before newly made viruses are released from the cell, the human protein furin snips the spike protein between S1 and S2. That lets the spike protein adopt the right shape to snag human cells and sets the protein up to allow for better membrane fusion.

Delta may be snippier than other variants.

Mutations D614G and P681R may increase the number of spike proteins cut by furin on each newly made virus, better prepping the viruses to enter other cells.

D614G makes it easier for furin to make its snips. This preliminary cut happens in a different location than the TMPRSS2 cut. The mutation may also increase the number of spike proteins on each copy of the virus.

Like D614G, P681R may also boost the number of spike proteins cut by the human cell protein furin, priming the newly made viruses to infect new cells.

  1. Some mutations may help newly released viruses evade antibodies as the viruses seek out other cells to infect.
    The immune systems of people who have recovered from an infection or those who got vaccinated make antibodies to the coronavirus. Several of delta’s mutations may help the virus evade these antibodies, which would otherwise block viral entry into other cells.

T19R, G142D, R158G and two spots — called E156del and F157del — where amino acids are missing from the protein may hide parts of the virus from antibodies, helping it slip past those immune system defenses.

T478K, the mutation unique to the delta variant, is close to the same spot as E484K, a mutation that was implicated in the antibody-evasion tactics of the beta variant.

Barnacles are famed for not budging. But one species roams its sea turtle hosts

Barnacles aren’t exactly renowned for their athleticism, staying glued in place for much of their lives. But turtle-riding barnacles are fidgety travelers.

As adults, the turtle barnacles (Chelonibia testudinaria) can move about 1.4 millimeters a week across turtle shells, researchers report October 6 in Proceedings of the Royal Society B. Previous observations of barnacles stuck on green sea turtles suggested that the creatures were somehow mobile, propelled by either outside forces or their own actions. But this is the first experimental confirmation that they embark on self-directed treks.

Barnacles start life as free-swimming larvae, eventually settling and adhering to rocks, ship hulls or even the skin of marine mammals (SN: 9/27/16). Some species have been known to rotate on their base or even scooch a smidge when nudged by a too-close neighbor. But once settled in, they live and grow, eating particles of food drifting by what was long considered their permanent address.
Now it turns out some may need forwarding addresses. Benny K.K. Chan, a marine ecologist at Academia Sinica in Taipei, Taiwan, decided to test C. testudinaria’s mobility experimentally when one of his students successfully transferred turtle barnacles from crabs to an acrylic plate. The team followed 15 transferred barnacles with time-series photography over a year.

Chan’s team also collaborated with researchers in Spain to track the movement of barnacles on the shells of five captive loggerhead sea turtles over a few months and with citizen scientist divers who gathered photos of wild green sea turtles in Taiwan. The team logged the positions of the green turtles’ barnacles over 16 weeks.
Turtle-riding barnacles moved as much as 54 millimeters — a little less than the length of an adult human’s thumb — during this time. Laboratory barnacles moved too, leaving trails of pale cement in layered, crescent-shaped patterns. “We were amazed,” says Chan.

How the barnacles move is still a mystery, but researchers think the crustaceans may partially dissolve their own cement and lift their soft base slightly off the surface. “Then the barnacle can secrete a new cement layer and probably surf on the cement,” says Chan.

The barnacles mostly traveled against the flow of any currents, showing that they weren’t just moving from the pressure of flowing water. They also didn’t get closer together, suggesting that the barnacles are seeking better locations to filter food out of the water rather than mating opportunities.
“This is rock-solid proof of something that is otherwise anecdotal,” says marine biologist Henrik Glenner at the University of Bergen in Norway , who was not involved with this study.

Barnacles typically exemplify biological competition for space and resources, because after settling they must compete in that spot for the rest of their lives, Glenner says. But being mobile upends this dynamic.

And it raises new questions. Glenner wonders if any barnacles in crowded, intertidal environments might also be capable of movement. And Tara Essock-Burns, a marine ecologist at the University of Hawaii at Manoa, wants to learn more about the cement itself and its flexible properties. “It is possible that turtle barnacle cement has a very different biochemistry than other barnacles that permanently adhere to [surfaces],” she says. This is precisely what Chan and his team plan on investigating next.

“There is a reason that Darwin was so captivated by barnacles,” says Essock-Burns. “They never cease to amaze us.”

Here’s the physics of why ducklings swim in a row behind their mother

There’s physics to having your ducklings in a row.

By paddling in an orderly line behind their mother, baby ducks can take a ride on the waves in her wake. That boost saves the ducklings energy, researchers report in the Dec. 10 issue of the Journal of Fluid Mechanics.

Earlier measurements of duckling metabolism showed that the youngsters saved energy when swimming behind a leader, but the physics behind that savings wasn’t known. Using computer simulations of waterfowl waves, naval architect Zhiming Yuan of the University of Strathclyde in Glasgow, Scotland, and colleagues calculated that a duckling cruising in just the right spot behind its mother gets an assist.

When a duckling swims on its own, it kicks up waves in its wake, using up some energy that would otherwise send it surging ahead. That wave drag resists the duckling’s motion. But ducklings in the sweet spot experience 158 percent less wave drag than when swimming alone, the researchers calculated, meaning the duckling gets a push instead.

Like good siblings, the ducklings share with one another. Each duckling in the line passes along waves to those behind, so the whole brood gets a free ride.

But to reap the benefits, the youngsters need to keep up with their mom. If they fall out of position, swimming gets harder. That’s fair punishment for ducklings that dawdle.

How radio astronomy put new eyes on the cosmos

ne can only imagine what Grote Reber’s neighbors thought when, in 1937, the amateur radio enthusiast erected in his yard a nearly 10-meter-wide shallow bowl of sheet metal, perched atop an adjustable scaffold and topped by an open pyramid of gangly towers. Little could his neighbors have known that they were witnessing the birth of a new way of looking at the cosmos.

Reber was building the world’s first dedicated radio telescope. Unlike traditional telescopes, which use lenses or mirrors to focus visible light, this contraption used metal and circuitry to collect interstellar radio waves, low frequency ripples of electromagnetic radiation. With his homemade device, Reber made the first map of the sky as seen with radio-sensitive eyes and kicked off the field of radio astronomy.
“Radio astronomy is as fundamental to our understanding of the universe as … optical astronomy,” says Karen O’Neil, site director at Green Bank Observatory in West Virginia. “If we want to understand the universe, we really need to make sure we have as many different types of eyes on the universe as we possibly can.”

When astronomers talk about radio waves from space, they aren’t (necessarily) referring to alien broadcasts. More often, they are interested in low-energy light that can emerge when molecules change up their rotation, for example, or when electrons twirl within a magnetic field. Tuning in to interstellar radio waves for the first time was akin to Galileo pointing a modified spyglass at the stars centuries earlier — we could see things in the sky we’d never seen before.

Today, radio astronomy is a global enterprise. More than 100 radio telescopes — from spidery antennas hunkered low to the ground to supersized versions of Reber’s dish that span hundreds of meters — dot the globe. These eyes on the sky have been so game-changing that they’ve been at the center of no fewer than three Nobel Prizes.

Not bad for a field that got started by accident.

In the early 1930s, an engineer at Bell Telephone Laboratories named Karl Jansky was tracking down sources of radio waves that interfered with wireless communication. He stumbled upon a hiss coming from somewhere in the constellation Sagittarius, in the direction of the center of the galaxy.

“The basic discovery that there was radio radiation coming from interstellar space confounded theory,” says astronomer Jay Lockman, also of Green Bank. “There was no known way of getting that.”

Bell Labs moved Jansky on to other, more Earthly pursuits. But Reber, a fan of all things radio, read about Jansky’s discovery and wanted to know more. No one had ever built a radio telescope before, so Reber figured it out himself, basing his design on principles used to focus visible light in optical scopes. He improved upon Jansky’s antenna — a bunch of metal tubes held up by a pivoting wooden trestle — and fashioned a parabolic metal dish for focusing incoming radio waves to a point, where an amplifier boosted the feeble signal. The whole contraption sat atop a tilting wooden base that let him scan the sky by swinging the telescope up and down. The same basic design is used today for radio telescopes around the world.

For nearly a decade — thanks partly to the Great Depression and World War II — Reber was largely alone. The field didn’t flourish until after the war, with a crop of scientists brimming with new radio expertise from designing radar systems. Surprises have been coming ever since.
“The discovery of interstellar molecules, that’s a big one,” says Lisa Young, an astronomer at New Mexico Tech in Socorro. Radio telescopes are well suited to peering into the dense, cold clouds where molecules reside and sensing radiation emitted when they lose rotational energy. Today, the list of identified interstellar molecules includes many complex organics, including some thought to be precursors for life.

Radio telescopes also turned up objects previously unimagined. Quasars, the blazing cores of remote galaxies powered by behemoth black holes, first showed up in detailed radio maps from the late 1950s. Pulsars, the ultradense spinning cores of dead stars, made themselves known in 1967 when Jocelyn Bell Burnell noticed that the radio antenna array she helped build was picking up a steady beep … beep … beep from deep space every 1.3 seconds. (She was passed over when the 1974 Nobel Prize in physics honored this discovery — her adviser got the recognition. But an accolade came in 2018, when she was awarded a Special Breakthrough Prize in Fundamental Physics.)

Pulsars are “not only interesting for being a discovery in themselves,” Lockman says. They “are being used now to make tests of general relativity and detect gravitational waves.” That’s because anything that nudges a pulsar — say, a passing ripple in spacetime — alters when its ultraprecise radio beats arrive at Earth. In the early 1990s, such timing variations from one pulsar led to the first confirmed discovery of planets outside the solar system.

More recently, brief blasts of radio energy primarily from other galaxies have captured astronomers’ attention. Discovered in 2007, the causes of these “fast radio bursts” are still unknown. But they are already useful probes of the stuff between galaxies. The light from these eruptions encodes signatures of the atoms encountered while en route to Earth, allowing astronomers to track down lots of matter they thought should be out in the cosmos but hadn’t found yet. “That was the thing that allowed us to weigh the universe and understand where the missing matter is,” says Dan Werthimer, an astronomer at the University of California, Berkeley.
And it was a radio antenna that, in 1964, gave the biggest boost to the then-fledgling Big Bang theory. Arno Penzias and Robert Wilson, engineers at Bell Labs, were stymied by a persistent hiss in the house-sized, horn-like antenna they were repurposing for radio astronomy. The culprit was radiation that permeates all of space, left behind from a time when the universe was much hotter and denser than it is today. This “cosmic microwave background,” named for the relatively high frequencies at which it is strongest, is still the clearest window that astronomers have into the very early universe.

Radio telescopes have another superpower. Multiple radio dishes linked together across continents can act as one enormous observatory, with the ability to see details much finer than any of those dishes acting alone. Building a radio eye as wide as the planet — the Event Horizon Telescope — led to the first picture of a black hole.

“Not that anybody needed proof of the existence [of black holes],” Young says, “but there’s something so marvelous about actually being able to see it.”

The list of discoveries goes on: Galaxies from the early universe that are completely shrouded in dust and so emit no starlight still glow bright in radio images. Rings of gas and dust encircling young stars are providing details about planet formation. Intel on asteroids and planets in our solar system can be gleaned by bouncing radio waves off their surfaces.

And, of course, there’s the search for extraterrestrial intelligence, or SETI. “Radio is probably the most likely place where we will answer the question: ‘Are we alone?’” Werthimer says.
That sentiment goes back more than a century. In 1899, inventor Nikola Tesla picked up radio signals that he thought were coming from folks on another planet. And for 36 hours in August 1924, the United States ordered all radio transmitters silent for five minutes every hour to listen for transmissions from Mars as Earth lapped the Red Planet at a relatively close distance. The field got a more official kickoff in 1960 when astronomer Frank Drake pointed Green Bank’s original radio telescope at the stars Tau Ceti and Epsilon Eridani, just in case anyone there was broadcasting.

While SETI has had its ups and downs, “there’s kind of a renaissance,” Werthimer says. “There’s a lot of new, young people going into SETI … and there’s new money.” In 2015, entrepreneur Yuri Milner pledged $100 million over 10 years to the search for other residents of our universe.

Though the collapse of the giant Arecibo Observatory in 2020 — at 305 meters across, it was the largest single dish radio telescope for most of its lifetime — was tragic and unexpected, radio astronomers have new facilities in the works. The Square Kilometer Array, which will link up small radio dishes and antennas across Australia and South Africa when complete in the late 2020s, will probe the acceleration of the universe’s expansion, seek out signs of life and explore conditions from cosmic dawn. “We’ll see the signatures of the first structures in the universe forming the first galaxies and stars,” Werthimer says.
But if the history of radio astronomy is any guide, the most remarkable discoveries yet to come will be the things no one has thought to look for. So much about the field is marked by serendipity, Werthimer notes. Even radio astronomy as a field started serendipitously. “If you just build something to look at some place that nobody’s looked before,” he says, “you’ll make interesting discoveries.”

A new map shows where carbon needs to stay in nature to avoid climate disaster

Over decades, centuries and millennia, the steady skyward climb of redwoods, the tangled march of mangroves along tropical coasts and the slow submersion of carbon-rich soil in peatlands has locked away billions of tons of carbon.

If these natural vaults get busted open, through deforestation or dredging of swamplands, it would take centuries before those redwoods or mangroves could grow back to their former fullness and reclaim all that carbon. Such carbon is “irrecoverable” on the timescale — decades, not centuries — needed to avoid the worst impacts of climate change, and keeping it locked away is crucial.

Now, through a new mapping project, scientists have estimated how much irrecoverable carbon resides in peatlands, mangroves, forests and elsewhere around the globe — and which areas need protection.

The new estimate puts the total amount of irrecoverable carbon at 139 gigatons, researchers report November 18 in Nature Sustainability. That’s equivalent to about 15 years of human carbon dioxide emissions at current levels. And if all that carbon were released, it’s almost certainly enough to push the planet past 1.5 degrees Celsius of warming above preindustrial levels.
“This is the carbon we must protect to avert climate catastrophe,” says Monica Noon, an environmental data scientist at Conservation International in Arlington, Va. Current efforts to keep global warming below the ambitious target of 1.5 degrees C require that we reach net-zero emissions by 2050, and that carbon stored in nature stays put (SN:12/17/18). But agriculture and other development pressures threaten some of these carbon stores.

To map this at-risk carbon, Noon and her colleagues combined satellite data with estimates of how much total carbon is stored in ecosystems vulnerable to human incursion. The researchers excluded areas like permafrost, which stores lots of carbon but isn’t likely to be developed (although it’s thawing due to warming), as well as tree plantations, which have already been altered (SN: 9/25/19). The researchers then calculated how much carbon would get released from land conversions, such as clearing a forest for farmland.

That land might store varying amounts of carbon, depending on whether it becomes a palm oil plantation or a parking lot. To simplify, the researchers assumed cleared land was left alone, with saplings free to grow where giants once stood. That allowed the researchers to estimate how long it might take for the released carbon to be reintegrated into the land. Much of that carbon would remain in the air by 2050, the team reports, as many of these ecosystems take centuries to return to their former glory, rendering it irrecoverable on a timescale that matters for addressing climate change.
Releasing that 139 gigatons of irrecoverable carbon could have irrevocable consequences. For comparison, the United Nations’ Intergovernmental Panel on Climate Change estimates that humans can emit only 109 more gigatons of carbon to have a two-thirds chance of keeping global warming below 1.5 degrees C. “These are the places we absolutely have to protect,” Noon says.

Approximately half of this irrecoverable carbon sits on just 3.3 percent of Earth’s total land area, equivalent to roughly the area of India and Mexico combined. Key areas are in the Amazon, the Pacific Northwest, and the tropical forests and mangroves of Borneo. “The fact that it’s so concentrated means we can protect it,” Noon says.

Roughly half of irrecoverable carbon already falls within existing protected areas or lands managed by Indigenous peoples. Adding an additional 8 million square kilometers of protected area, which is only about 5.4 percent of the planet’s land surface, would bring 75 percent of this carbon under some form of protection, Noon says.

“It’s really important to have spatially explicit maps of where these irrecoverable carbon stocks are,” says Kate Dooley, a geographer at the University of Melbourne in Australia who wasn’t involved in the study. “It’s a small percentage globally, but it’s still a lot of land.” Many of these dense stores are in places at high risk of development, she says.

“It’s so hard to stop this drive of deforestation,” she says, but these maps will help focus the efforts of governments, civil society groups and academics on the places that matter most for the climate.

What the Perseverance rover’s quiet landing reveals about meteor strikes on Mars

The lander was listening. On February 18, NASA’s InSight lander on Mars turned its attention to the landing site for another mission, Perseverance, hoping to detect its arrival on the planet.

But InSight heard nothing.

Tungsten blocks ejected by Perseverance during entry landed hard enough to create craters on the Martian surface. Collisions like these — whether from space missions or meteor strikes — send shock waves through the ground. Yet in the first experiment of its kind on another world, InSight failed to pick up any seismic waves from the blocks’ impacts, researchers report October 28 in Nature Communications.

As a result, researchers think that less than 3 percent of the energy from the impacts made its way into the Martian surface. The intensity of impact-generated rumblings varies from planet to planet and is “really important for understanding how the ground will change from a big impact event,” says Ben Fernando, a geophysicist at the University of Oxford.
But getting these measurements is tricky. Scientists need sensitive instruments placed relatively near an impact site. Knowing when and where a meteor will strike is nearly impossible, especially on another world.

Enter Perseverance: a hurtling space object set to hit Mars at an exact time and place (SN: 2/17/21). To help with its entry, Perseverance dropped about 78 kilograms of tungsten as the rover landed about 3,450 kilometers from InSight. The timing and weight of the drop provided a “once-in-a-mission opportunity” to study the immediate seismic effects of an impact from space, Fernando says.

The team had no idea whether InSight would be able to detect the blocks’ impacts or not, but the quiet arrival speaks volumes. “It lets us put an upper limit on how much energy from the tungsten blocks turned into seismic energy,” Fernando says. “We’ve never been able to get that number for Mars before.”