Sarah Zhang

A lot is still unknown around Omicron, but a worrying trend has become clear: This variant sure is spreading fast. In South Africa, the U.K., and Denmark—countries with the best variant surveillance and high immunity against COVID—Omicron cases are growing exponentially. The variant has outcompeted the already highly transmissible Delta in South Africa and may soon do the same elsewhere. According to preliminary estimates, every person with Omicron is infecting 3–3.

No one knows exactly what endemic COVID will look like, but whatever it looks like, this—gestures at the current situation—ain’t it. COVID is not yet endemic. There is little doubt that the coronavirus will get there eventually, when almost everyone has been vaccinated or infected or both, but right now we are still living through a messy and potentially volatile transition period. Cases are ticking up again. A new variant is afoot.

Winter has a way of bringing out the worst of the coronavirus. Last year, the season saw a record surge that left nearly 250,000 Americans dead and hospitals overwhelmed around the country. This year, we are much better prepared, with effective vaccines—and, soon, powerful antivirals—that defang the coronavirus, but cases seem to be on the rise again, prompting fears of another big surge.

We know how this ends: The coronavirus becomes endemic, and we live with it forever. But what we don’t know—and what the U.S. seems to have no coherent plan for—is how we are supposed to get there.

Damian Adams grew up knowing that his parents had used an anonymous sperm donor to conceive him, and as a teen, he was even proud of this identity. He considered donating to help other families have children. Becoming a father himself, however, changed everything. When his daughter was born 18 years ago, he cradled her in his arms, and he instantly saw himself in her and her in himself. He felt a biological connection so powerful that it made him reconsider his entire life up until then.

Editor’s Note: This article is part of our coverage of The Atlantic Festival. Learn more and watch festival sessions here. The vaccine timeline for young kids is looking a little more solid. This morning, Pfizer submitted data to the FDA showing that its COVID-19 vaccine is effective and safe for children ages 5 to 11. And this afternoon, the company’s CEO, Albert Bourla, said that trial results for even younger kids, aged 2 to 4, will be available in a couple months’ time.

Updated at 3:00 p.m. ET on September 7, 2021When London vanquished cholera in the 19th century, it took not a vaccine, or a drug, but a sewage system. The city’s drinking water was intermingling with human waste, spreading bacteria in one deadly outbreak after another. A new comprehensive network of sewers separated the two. London never experienced a major cholera outbreak after 1866.

In the 1980s, doctors at an English hospital deliberately tried to infect 15 volunteers with a coronavirus. COVID-19 did not yet exist—what interested those doctors was a coronavirus in the same family called 229E, which causes the common cold. 229E is both ubiquitous and obscure. Most of us have had it, probably first as children, but the resulting colds were so mild as to be unremarkable.

When Barbara Klump ran into homeowners on trash-collection day, she would tell them that something very special was happening in their suburb of Sydney. She meant the birds. The big white ones?, the residents asked. The birds that are always opening trash cans and making a huge mess? Yes, those, the sulphur-crested cockatoos.

Kayla Fratt began preparing for her summer job in March, when a package of frozen bat carcasses arrived for her in the mail. Well, actually, the bats were for her border collies, Barley and Niffler, and it is really their summer job too. They needed to learn the scent of a dead bat, because they would be spending three months on wind farms, looking for bats killed by spinning turbines.

Nicole Lawson spent the beginning of the pandemic incredibly worried about her daughter, who has asthma. Five-year-old Scarlett’s asthma attacks were already landing her in the ER or urgent care every few months. Now a scary new virus was spreading. Respiratory viruses are known triggers of asthma attacks, and doctors also feared at the time that asthma itself could lead to more severe coronavirus infections.

Last winter, when vaccines were still incredibly scarce in the United States, Ashish Jha told The Atlantic that he was feeling optimistic about summer: By July 4, Jha, the dean of the Brown University School of Public Health, expected enough people to be vaccinated that he could host a backyard barbecue. Indeed, Jha confirmed to me this week, he will be grilling burgers and hot dogs for friends this Fourth of July.

Divers who have seen the phenomenon firsthand describe many types of underwater sea snot. There are the “stringers,” which most resemble the sticky goo that might actually come out of your nose. But there are also floating “clouds,” white and ethereal, so delicate that they break apart in your fingers.

This much is clear: The coronavirus is becoming more transmissible. Ever since the virus emerged in China, it has been gaining mutations that help it spread more easily among humans. The Alpha variant, first detected in the United Kingdom last year, is 50 percent more transmissible than the original version, and now the Delta variant, first detected in India, is at least 40 percent more transmissible than Alpha.

This much is clear: The coronavirus is becoming more transmissible. Ever since the virus emerged in China, it has been gaining mutations that help it spread more easily among humans. The Alpha variant, first detected in the United Kingdom last year, is 50 percent more transmissible than the original version, and now the Delta variant, first detected in India, is at least 40 percent more transmissible than Alpha.

Bowen the goldendoodle is never home alone. When he first came home as a puppy, last June, his parents were working remotely because of the pandemic. If they try to leave their Boston apartment for even a few minutes now, he makes his unhappiness audible. “He’s whining and barking, and we just don’t want to upset the neighbors,” Jon Canario told me. So they don’t. Wherever they go, he goes. Wherever he can’t go, they don’t go.

The three teenagers—two boys and a girl—could not have known what clues their lungs would one day yield. All they could have known, or felt, before they died in Germany in 1918 was their flu-ravaged lungs failing them, each breath getting harder and harder. Tens of millions of people like them died in the flu pandemic of 1918; they happened to be three whose lungs were preserved by a farsighted pathologist.

At its peak, in late March, the mass-vaccination site at Nashville’s Music City Center was giving out 2,100 doses a day. It was all hands on deck: Local nurses, volunteers, FEMA employees, and even U.S. Forest Service EMTs were redeployed to help give COVID-19 shots. But last week, the number of daily doses dropped to less than 1,300—about 1,100 second doses and only 190 first doses.

When Johannes Krause was a graduate student working on the Neanderthal genome in the 2000s, so much of the DNA recovered from the ancient bone fragments came from everything else: the skin cells of excavators and scientists, the bacteria on those humans, the microbes in the soil. To get to Neanderthal DNA, you had to junk the rest.

Like many parents, Jason Newland, a pediatrician at Washington University in St. Louis and a dad to three teens ages 19, 17, and 15, now lives in a mixed-vaccination household. His 19-year-old got vaccinated with Johnson & Johnson’s shot two weeks ago and the 17-year-old with Pfizer’s, which is available to teens as young as 16.The 15-year-old is still waiting for her shot, though—a bit impatiently now.

A year ago, when the United States decided to go big on vaccines, it bet on nearly every horse, investing in a spectrum of technologies. The safest bets, in a way, repurposed the technology behind existing vaccines, such as protein-based ones for tetanus or hepatitis B. The medium bets were on vaccines made by Johnson & Johnson and AstraZeneca, which use adenovirus vectors, a technology that had been tested before but not deployed on a large scale.

One of the most perplexing and enduring mysteries of the pandemic is also one of the most fundamental questions about viruses. How can the same virus that kills so many go entirely unnoticed in others?The mystery is hardly unique to COVID-19. SARS, MERS, influenza, Ebola, dengue, yellow fever, chikungunya, West Nile, Lassa, Japanese encephalitis, Epstein-Barr, and polio can all be deadly in one person but asymptomatic in the next.

It was 1996, Bill Clinton was president, and endangered bald eagles were dying in his home state of Arkansas.Twenty-nine were found dead at a man-made reservoir called DeGray Lake, before deaths spread to two other lakes. But what really puzzled scientists was how the eagles acted before they died. The stately birds were suddenly flying straight into cliff faces. They hit trees. Their wings drooped. Even on solid ground, they stumbled around as if drunk.

Ruby Martinez was eating a banana when she noticed the nothingness. She chewed but tasted no sweetness. She sniffed but got none of the fruit’s redolent musk. “I started freaking out,” she says. She smelled a bottle of perfume. Nothing. She ate a pickle. Still nothing.That was in June. Since then, her senses of smell and taste have started to come back—but intermittently and in strange ways.

In the beginning, there was one.The first genome for the virus causing a mysterious illness we had not yet named COVID-19 was shared by scientists on January 10, 2020. That single genome alerted the world to the danger of a novel coronavirus. It was the basis of new tests as countries scrambled to find the virus within their own borders. And it became the template for vaccines, the same ones now making their way to millions of people every day.

Editor’s Note: The Atlantic is making vital coverage of the coronavirus available to all readers. Find the collection here. Last spring and summer, when a COVID-19 vaccine was only a glimmer of hope on the horizon, scientists warned in their careful way that vaccines might not live up to the public’s high expectations. The FDA said a vaccine needed to be just 50 percent effective.

For most of 2020, the coronavirus that causes COVID-19 jumped from human to human, accumulating mutations at a steady rate of two per month—not especially impressive for a virus. These mutations have largely had little effect.But recently, three distinct versions of the virus seem to have independently converged on some of the same mutations, despite being thousands of miles apart in the United Kingdom, South Africa, and Brazil.

The vaccine rollout is not going as planned. Since mid-December, the U.S. has distributed 21.4 million doses of COVID-19 vaccines; less than one-third have actually made it into people’s arms. The problems have been many and varied: holiday delays, scheduling scams, long lines in some places, and not enough demand in others. These initial kinks are getting worked out, but that alone will not get us back to normal anytime soon.

In garden ponds and in oceans, in desert soil and in industrial water-cooling towers, matters of life and death are playing out unseen by the human eye. Here, giant viruses prey on single-celled hosts such as amoebas or algae. This microscopic bloodbath can happen on such a large scale that massive algae blooms visible on the ocean surface turn white, as dead algae fade to reveal their colorless skeletons.

Editor’s Note: The Atlantic is making vital coverage of the coronavirus available to all readers. Find the collection here. With the FDA’s emergency authorization of the first COVID-19 vaccine imminent, the biggest and most complex vaccination campaign in the nation’s history is gearing into action. Planes are ferrying vaccines around the country, hospitals are readying ultracold freezers, and the very first people outside of clinical trials will soon get shots in their arms.