TRACING PANDEMIC ORIGINS: The secret life of a coronavirus

Last spring, coyotes strolled down the streets of San Francisco in broad daylight. Pods of rarely seen pink dolphins cavorted in the waters around Hong Kong. In Tel Aviv, jackals wandered a city park, a herd of mountain goats took over a town in Wales, and porcupines ambled through Rome’s ancient ruins. As the canals in Venice turned strangely clear, cormorants started diving for fish, and Canada geese escorted their goslings down the middle of Las Vegas Boulevard, passing empty shops displaying Montblanc pens and Fendi handbags. Nature was expanding as billions of people were retreating from the COVID-19 pandemic. The change was so swift, so striking that scientists needed a new name for it: the anthropause.

But the anthropause did more than reconfigure the animal kingdom. It also altered the planet’s chemistry. As factories grew quiet and traffic dropped, ozone levels fell by 7 percent across the Northern Hemisphere. As air pollution across India dropped by a third, mountain snowpacks in the Indus Basin grew brighter. With less haze in the atmosphere, the sky let more sunlight through. The planet’s temperature temporarily jumped between a fifth and half of a degree.

At the same time, the pandemic etched a scar across humanity that will endure for decades. More than 2.4 million people have died so far from COVID-19, and millions more have suffered severe illness. In the United States, life expectancy fell by a full year in the first six months of 2020; for Black Americans, the drop was 2.7 years. The International Monetary Fund predicts that the global economy will lose over $22 trillion between 2020 and 2025. UNICEF is warning that the pandemic could produce a “lost generation.”

At the center of these vast shocks is an oily bubble of genes just about 100 nanometres in diameter. Coronaviruses are so small that 10 trillion of them weigh less than a raindrop.

Since the discovery of SARS-CoV-2 last January, the scientific world has scrutinized it to figure out how something so small could wreak so much havoc. They have mapped the spike proteins the coronavirus uses to latch onto cells. They have uncovered the tricks it plays on our immune system. They have reconstructed how an infected cell creates millions of coronaviruses.

That frenzy of research has revealed a lot about SARS-CoV-2, but huge questions remain. Looming over them is the biggest question of all: Is the coronavirus alive? Scientists have been arguing over whether viruses are alive for about a century, ever since the pathogens came to light. Writing last month in the journal Frontiers in Microbiology, two microbiologists at University College Cork named Hugh Harris and Colin Hill took stock of the debate. They could see no end to it. “The scientific community will never fully agree on the living nature of viruses,” they declared.

The question is hard to settle, in part because viruses are deeply weird. But it’s also hard because scientists can’t agree on what it means to be alive. Life may seem like one of the most obvious features of the universe, but it turns out to be remarkably hard to draw sharp lines dividing it from the rest of existence. The mystery extends far beyond viruses. By some popular definitions, it’s hard to say that a rabbit is alive. If we look at our own genome, we can find life’s paradox lurking there as well. For thousands of years, people knew of viruses only through the illnesses they caused. Doctors gave these diseases names like smallpox, rabies and influenza. When Antonie van Leeuwenhoek peered at drops of water with his microscope in the late 1600s, he discovered bacteria and other minuscule wonders, but he could not see the even tinier viruses. When scientists finally discovered viruses two centuries later, they still hid from sight.

The discovery came in the late 1800s, as scientists puzzled over a strange disease called tobacco mosaic disease. It stunted plants and covered their leaves with spots, but scientists could not pin the cause on any type of bacterium or fungus. Yet when they injected sap from an infected leaf into a healthy plant, it grew sick as well. Passing the sap through a porcelain filter, scientists could produce a clear liquid, free of cells. But it still spread disease. A Dutch scientist, Martinus Beijerinck, called it “a contagious living fluid.”

Carrying out more experiments, Beijerinck became convinced the fluid contained some kind of contagion, but one unlike anything yet found. He borrowed a Latin word for “poison” to give the contagion a name: virus.

At the dawn of the 20th century, other scientists began finding viruses that infected humans, rather than plants. They found viruses infecting every form of cellular life they studied. There are even viruses that infect only bacteria, called phages. For decades, the viruses remained invisible in contagious living fluids. But in the 1930s, physicists and engineers invented electron microscopes powerful enough to bring the viral world into focus.

Tobacco mosaic viruses came to light in 1941, looking like a pile of pipes. Phages squatted atop bacteria, resembling lunar landing modules. Other viruses turned out to have the shape of writhing serpents. Some looked like microscopic soccer balls. SARS-CoV-2 belongs to the coronaviruses, which June Almeida named in 1967 for their halo of spike proteins. They reminded her of a solar eclipse, during which the sun’s corona of gas streams becomes visible.

As scientists like Almeida began seeing viruses in their electron microscopes, biochemists were breaking them down into their parts. It wasn’t just their size that set them apart from life as we knew it. They didn’t play by the same rules as cellular life. Viruses are largely made of proteins, as are we. And yet they don’t carry the factories for building proteins. They don’t have the enzymes required to turn food to fuel, or to break down waste. The bizarre nature of viruses came to light just as scientists were rewriting their definition of life in the new language of biochemistry. Viruses straddled their definitions. They multiplied, but not by eating, growing, or even reproducing. They simply invaded cells and forced them to do all the work of making new viruses.

In 1935 a scientist named Wendell Stanley showed the world just how hard it was to make sense of viruses. He dried tobacco mosaic viruses down to crystals, which he could store like table salt. Months later, he doused the crystals with water, and they changed from crystals back to familiar viruses, able to make tobacco plants sick once more. When Stanley announced his viral resurrection, this newspaper went agog. “Enough is known about matter, organized and unorganised, to assure us that there may be things ’twixt heaven and earth which are not so alive as an eel or so dead as a rock,” The Times wrote. “In the light of Dr. Stanley’s discovery the old distinction between death and life loses some of its validity.”

Carl Zimmer writes the “Matter” column for NYT