Omicron first appeared on my radar on Thanksgiving Day 2021.
I remember reading worried tweets from virologists about a new, wildly different variant that was more transmissible than delta and better at evading existing immune defenses. I ate Thanksgiving dinner — my first with family since the start of the pandemic — uneasy about what might come. That worry was borne out as omicron soon drove massive surges in infections and death around the globe. Since then, covid has claimed about 300,000 lives in the U.S. alone.
But much has changed over the last year. Many new flavors of omicron have emerged, rendering some once-effective treatments useless. Vaccines got their first update to keep pace, but too few people have gotten the reformulated booster shot. Federal officials have continually signaled a shift toward normalcy — despite persistently high levels of illness and death — by emphasizing individual protections over collective ones. Many Americans have followed suit this year, ditching masks and living lives closer to the pre-pandemic norm.
But the coronavirus is still here, killing nearly 300 people each day in the U.S. alone and infecting tens of thousands more. Grid takes stock of developments in key areas — from variants, vaccines and treatments to covid fatigue in Washington — and what those changes might mean as we approach the fourth year of the pandemic.
Before omicron, the coronavirus’ global evolution was wild and unexpected. Cycling through Greek letters — alpha, beta, epsilon, delta — new variants popped up on very different parts of the tree. Each new major variant largely displaced the old one as the virus found new ways of infecting humans and dodging defenses.
Omicron changed that story. Its descendants have remained on top all year; the big question now is how long that will continue. “The evolution of omicron itself isn’t that different from how delta evolved from the time of its emergence to omicron,” said Stephen Goldstein, a virologist at the University of Utah. “The only difference is that there hasn’t been a new, out-of-the-blue variant that’s come out and displaced omicron.”
In the absence of new competition, omicron’s branch of the tree has become a thicket of letters and numbers — BA.1, BA.2, BA.5, XE, XBB, BQ.1. So far, these subvariants haven’t made giant leaps in transmissibility, like delta or the original omicron. But they have become more adept at evading existing immunity.
“The immunity landscape is obviously very complicated now because we’ve had people infected with different versions of the virus and vaccinated different numbers of times,” said Goldstein. Those factors may explain why we’re seeing a variant soup, instead of a single dominant variant, he said.
In the U.S., BQ.1 and BQ.1.1 are now the most common subvariants, with BA.5 on the decline. BQ1.1 is one of the most antibody-evasive variants yet, according to laboratory studies, driving fear that it could fuel large spikes in infection and hospitalizations.
But that hasn’t happened yet. That’s likely because of built-up immunity through complicated histories of vaccination and infection, Goldstein said: “I think immune systems have been educated in a way that probably provides a lot of protection against serious disease.” That protection is especially robust after getting the updated bivalent booster, he added, even though it’s based on the fading BA.5 variant.
Scientists cannot say how long the omicron phase of SARS-CoV-2 evolution will persist. “Right now, we’re seeing more of a stepwise pattern of evolution, like we see with flu,” said Goldstein. “Whether that’s going to hold permanently, or whether we’ll have another burst of evolution, I honestly don’t know,” he said. “I think it’s possible we’ll see another leap down the road, but maybe not one every few months.”
Omicron’s rise has shrunk clinicians’ toolbox of treatments.
Antiviral drugs are still working as imperfectly as ever. But antibody therapies, once remarkably effective at reducing risk of hospitalization, are losing their luster as the coronavirus evolves around them.
The antivirals — Paxlovid, molnupiravir and remdesivir — target parts of the virus that change more slowly, and so their effectiveness hasn’t changed much (though that could change). Molnupiravir remains largely a dud. Remdesivir is more helpful, but the hassle of administering via infusion over several days lessens its real-world impact. Paxlovid is still the star, but even it has a mixed record.
The drug protects those at highest risk of serious illness from the worst outcomes if taken early enough, reducing risk of death by nearly 80 percent for people 65 and older. But Paxlovid can have annoying side effects, including a persistent metallic taste, and interacts with a long list of other commonly taken medications.
“Those interactions make it really impossible to use for specific kinds of immunocompromised patients like organ or stem cell transplant recipients [on certain drugs],” said Ghady Haidar, an infectious diseases physician at the University of Pittsburgh Medical Center who specializes in treating people with immunocompromising conditions. Earlier in the pandemic, such patients could take antibody therapies, which flood a patient’s system with virus-thwarting proteins.
“They work really well, especially if given early,” and have fewer side effects, said Haidar. “Unfortunately, they work by targeting a part of the virus called the spike protein, which is the part of the virus that unfortunately mutates the most quickly.” Omicron’s surprising evolution left many of these therapies in the dust. A few — bamlanivimab/etesevimab, REGEN-COV and sotrovimab — have already been pulled from the market.
The days of the remaining two — bebtelovimab and Evusheld — may be numbered as the most immune-evasive variants yet take hold in the U.S. The Food and Drug Administration has already warned that bebtelovimab likely won’t help those infected with the latest subvariants. Evusheld — which acts to prevent, not treat, infection in immunocompromised people for whom vaccination provides less benefit — may also soon be outmatched by omicron. Several companies are reportedly working on newer antibody treatments to match omicron or target more stable parts of the virus, but none are yet available.
“The pool for people needing treatment may be shrinking,” Haidar said, as vaccination and infection bolster population immunity. “Unfortunately, that pool bill includes immunocompromised patients who are kind of still drowning and floundering in that pool.”
And there are still no proven treatments for the millions of Americans suffering from long covid. Scientists have chipped away at understanding what might be causing such debilitating symptoms, including brain fog and profound fatigue. Immune dysfunction, lingering virus and micro blood clots are all leading contenders, but many questions remain. Some hopeful news arrived this fall, however, when a preliminary study found that a course of Paxlovid reduced risk of developing long covid by 25 percent.
Testing and tracking cases
The official picture of the state of the pandemic is messier, with more gaps, than it was a year ago.
Many states and the Centers for Disease Control and Prevention have scaled back their reporting procedures from daily reports to weekly updates, further splintering the national picture of cases. That shift from lab-based PCR tests toward at-home tests, whose results are often not reported to authorities, has further muddied that picture.
“Rapid at-home tests are the predominant way testing is being done today,” said Mara Aspinall, a professor of practice and biomedical diagnostics at Arizona State University. Availability of tests has improved significantly too since last year. More companies make tests, and manufacturing capacity has stayed more constant than it did in 2021, she said.
“There are a lot of positives to more at-home testing, like convenience and privacy, but it’s also led to a dramatic undercounting of cases, at least by a factor of five or six,” she said. Other estimates put the undercounting closer to 20, meaning the official case count grossly misrepresents the actual burden.
An incomplete national picture makes it harder for state and local public health officials to respond to upticks in cases. It also makes it harder for those individuals who still base their behavior in public on transmission levels to navigate the pandemic. But there are some other data sources that have improved over the past year.
Wastewater surveillance provides a birds-eye view of transmission looking for SARS-CoV-2 genetic material in sewage. Since it’s sampling wastewater — something to which everyone contributes — it can provide a more complete, albeit less detailed, look at how much virus is out there. CDC wastewater surveillance has grown significantly over the past year, from less than 300 sites to nearly 800 across all 50 states, and private companies have also expanded. Still, coverage varies from region to region.
Vaccinations and immunity
Progress in getting people vaccinated and boosted this year has been mixed.
A year ago, about 200 million Americans had completed their primary doses of the covid vaccine, roughly 60 percent of the eligible population. But only 27 million more have completed their first two doses since then. That figure includes children aged 6 months to 5 years, who became eligible in June. Overall, roughly 30 percent of the U.S. population is unvaccinated.
Those two primary doses pack less of a punch now, since the virus has evolved to get around immunity from the original vaccines and from infections with prior variants. Booster doses of vaccines became available to those 18 and older just before omicron took off last year, and evidence suggests they helped keep patients out of the hospital during last winter’s surge. Still, they arrived too late to prevent many hospitals from being overwhelmed.
A bigger problem is that booster uptake has lagged. Only 34 percent of the population has gotten a single booster, and even fewer — 11 percent — have gotten the updated bivalent booster that became available this fall and which targets the omicron variant. That leaves most Americans more vulnerable to severe illness this winter, as highly immune-evasive variants take hold. On Tuesday, the Biden administration announced a six week “sprint” to accelerate uptake of the booster through targeted ad campaigns and outreach.
Still, vaccinations aren’t the only way to build up immunity in the broader population. Over the past year, millions of people have been infected, or reinfected, with some version of omicron. One recent estimate suggests about 94 percent of the population has been infected at least once, compared with about 70 percent last December.
That wall of built-up immunity, both via infection and vaccination, should, over time, lessen the impact of the average covid case. That wall may explain why some surges of highly immune-evasive variants in Europe and other regions didn’t translate to massive waves of hospitalizations. Still, the coronavirus may throw the globe another omicron-like curveball, especially since we’re giving it ample opportunity to spread and evolve.
2022 might best be characterized as the year as many Americans decided to move on from the pandemic, despite its significant ongoing toll.
Last year, about 78 percent of Americans were at least somewhat concerned about covid, according to an Ipsos poll. That dropped to 57 percent this fall. And while only 18 percent of people said they’d returned to their pre-pandemic life a year ago, now nearly half have, the poll found.
The decline of masking is perhaps the most visible sign of this shift. Last fall, 50 to 60 percent of people reported regularly wearing masks. That’s dropped to slightly less than 30 percent, according to one survey.
“For a while, you positioned yourself with the majority; when you wore the mask, it was normal, everyone was doing it, and you looked at people without masks as renegades, as selfish people,” said Markus Kemmelmeier, a social psychologist at the University of Nevada at Reno. “But now, a sense of normalcy has flipped the situation.”
That sense has come from the top. In February, the CDC drastically relaxed its covid guidelines, raising the bar for when to advise indoor masking. Practically overnight, the CDC went from advising masking in nearly all counties to only about 30 percent of counties, signaling a shift away from a collective pandemic response toward an individualized one.
President Joe Biden underlined that shift in September, calling the pandemic “over” in an interview with “60 Minutes,” even as 400 to 500 people still died of covid each day. Still, the Biden administration is asking Congress for about $10 billion in new covid funding to help prepare for a possible winter surge and develop new tests and vaccines. The funding could also bolster programs that provided free tests and N95 masks, which are out of money. But Congress hasn’t approved new covid funding in months, and some lawmakers have pointed to Biden’s September comments as reason to deny the request. With Republicans set to take control of the House in early January, additional covid funds seem even less likely.
Thanks to Lillian Barkley for copy editing this article.