Tag: SARS-CoV-2 infections

How Bad Are America’s COVID-Vaccination Rates?

Relatively speaking, 2023 has been the least dramatic year of COVID living to date. It kicked off with the mildest pandemic winter on record, followed by more than seven months of quietude. Before hospitalizations started to climb toward their September mini-spike, the country was in “the longest period we’ve had without a peak during the entire pandemic,” Shaun Truelove, an infectious-disease modeler at Johns Hopkins University, told me. So maybe it’s no surprise that, after a year of feeling normalish, most American adults simply aren’t that worried about getting seriously sick this coming winter.

They also are not particularly eager to get this year’s COVID shot. According to a recent CDC survey, just 7 percent of adults and 2 percent of kids have received the fall’s updated shot, as of October 14; at least another 25 percent intends to nab a shot for themselves or their children but haven’t yet. And even those lackluster stats could be an overestimate, because they’re drawn from the National Immunization Surveys, which is done by phone and so reflects the answers of people willing to take federal surveyors’ calls. Separate data collected by the CDC, current as of October 24, suggest that only 12 million Americans—less than 4 percent of the population—have gotten the new vaccine, according to Dave Daigle, the associate director for communications at the CDC’s Center for Global Health.

CDC Director Mandy Cohen still seems optimistic that the country will come close to the uptake rates of last autumn, when 17 percent of Americans received the updated bivalent vaccine. But for that to happen, Americans would have to maintain or exceed their current immunization clip—which Gregory Poland, a vaccine expert at Mayo Clinic, told me he isn’t betting on. (Already, he’s worried about the possible dampening effect of new data suggesting that getting flu and COVID shots simultaneously might slightly elevate the risk of stroke for older people.) As things stand, the United States could be heading into the winter with the fewest people recently vaccinated against COVID-19 since the end of 2020, when most people didn’t yet have the option to sign up at all.

This winter is highly unlikely to reprise that first one, when most of the population had no immunity, tests and good antivirals were scarce, and hospitals were overrun. It’s more likely to be an encore of this most recent winter, with its relative calm. But that’s not necessarily a comfort. If that winter was a kind of uncontrolled experiment in the damage COVID could do when unchecked, this one could codify that experiment into a too-complacent routine that cements our tolerance for suffering—and leaves us vulnerable to more.

To be fair, this year’s COVID vaccines have much been harder to get. With the end of the public-health emergency, the private sector is handling most distribution—a transition that’s made for a more uneven, chaotic rollout. In the weeks after the updated shot was cleared for use, many pharmacies were forced to cancel vaccination appointments or turn people away because of inadequate supply. At one point, Jacinda Abdul-Mutakabbir, an infectious-disease pharmacist at UC San Diego, who’s been running COVID and flu vaccination in her local community, was emailing her county’s office three times a week, trying to get vaccine vials. Even when vaccines have been available, many people have been dismayed to find they need to pay out of pocket for the cost. (Most people, regardless of insurance status, are supposed to be able to receive a free COVID-19 vaccine.)

[Read: Fall’s vaccine routine didn’t have to be this hard]

The vaccine is now easier to find, in many places; insurance companies, too, seem to be fixing the kinks in compensation. But Abdul-Mutakabbir told me she worries that many of the people who were initially turned away may simply never come back. “You lose that window of opportunity,” she told me. Even people who haven’t gotten their autumn shot may be hesitating to try if they expect access to be difficult, as the emergency physician Jeremy Faust points out in his Inside Medicine newsletter.

Plus, because the rollout started later this year than in 2022, many people ended up infected before they could get vaccinated and may now be holding off on the shot—or skipping it entirely. And some Americans have simply decided against getting the shot. The CDC reported that 38 percent don’t plan to vaccinate themselves or their children; earlier this fall, more than half of respondents in a Kaiser Family Foundation poll said they probably or definitely wouldn’t be signing up themselves or their kids. More than 40 percent of those polled by KFF remain doubtful, too, that COVID shots are safe—dwarfing the numbers of people worried about flu shots, and even about RSV shots, which are newer than their COVID counterparts.

The consequences of low COVID-vaccine uptake are hard to parse. This year, like last year, most Americans have been vaccinated, infected, or both, many of them quite recently. COVID’s average severity has, for many months, been at a relatively consistent low. The last catastrophic SARS-CoV-2 variant—one immune-evasive enough to spark a massive wave of sickness, death, and long COVID—arrived two years ago. Barring another feat of viral evolution, perhaps these dynamics have reached something like a stable state, Justin Lessler, an infectious-disease modeler at the University of North Carolina at Chapel Hill, told me. So maybe the most likely scenario is a close repeat of last winter: a rise in hospitalizations and deaths that’s ultimately far more muted than any earlier in the outbreak. And the COVID-19 Scenario Modeling Hub, which Lessler co-leads alongside Truelove and a large cohort of other researchers, projects that “next year will look a lot like this year, whatever this year ends up looking like,” Lessler said.

But predictability is distinct from peace. COVID has still been producing roughly twice the annual mortality that flu does; roughly 17,000 people are being hospitalized for the disease each week. SARS-CoV-2 infections also still carry a risk, far higher than flu’s, of debilitating some people for years. “And I do think we’re going to experience a winter increase,” Truelove told me. Even if this year’s COVID-vaccine uptake were to climb above 30 percent, models suggest that January hospitalizations could rival numbers from early 2023. Go much lower than that, and several scenarios point to outcomes being worse.

Based on the limited data available, at least one trend is mildly encouraging: Adults 75 and older, the age demographic most vulnerable to COVID and that stands to benefit most from annual shots, also have the highest vaccine uptake so far, at about 20 percent. At the same time, Katelyn Jetelina, the epidemiologist who writes the popular Your Local Epidemiologist newsletter, points out that CDC data suggest that only 8 percent of nursing-home residents are up to date on their COVID shots. “That is what keeps me up at night,” Jetelina told me. Early National Immunization Surveys data also suggest that uptake is lagging among other groups that might fare less well against COVID—among them, rural populations, Hispanic people, American Indians and Alaskan Natives, the uninsured, and people living below the poverty line.

Last winter was widely considered to be a bullet dodged, and the reactions to the coming months may be similar: At least it’s no longer that bad. Since the winter of Omicron, the country has been living with lower vaccine uptake while experiencing lower COVID peaks. But those lower peaks shouldn’t undermine the importance of vaccines. Infection-induced immunity, past vaccinations, improvements in treatments, and other factors have combined to make COVID look like a gentler disease. Add more recent vaccination to that mix, and many of those gains would likely be enhanced, keeping immunity levels up without the risks of illness or passing the virus to someone else.

[Read: The one thing everyone should know about fall COVID vaccines]

As relatively “okay” as this past year-plus has been, it could have been better. Missed vaccinations still translate into more days spent suffering, more chronic illnesses, more total lives lost—an enormous burden to put on an already stressed health-care system, Jetelina told me. For the flu, more Americans act as if they understand this relationship: This year, as of November 1, nearly 25 percent of American adults, and more than 20 percent of American kids, have gotten their fall flu shot. Most of the experts I spoke with would be surprised to see such rates for COVID vaccines even at the end of this rollout.

If last winter was a preview of future COVID winters, our behaviors, too, could predict the patterns we’ll follow going forward. We may not be slammed with the next terrible variant this year, or the next, or the next. When one does arrive, though, as chances are it will, the precedent we’re setting now may leave us particularly unprepared. At that point, people may be years out from their most recent COVID shot; whole swaths of babies and toddlers may have yet to receive their first dose. Some of us may still have some immunity from recent infections, sure—but it won’t be the same as dosing up right before respiratory-virus season with protection that’s both reliable and safe. Systems once poised to deliver COVID vaccines en masse may struggle to meet demand. Or maybe the public will be slow to react to the new emergency at all. Our choices now “will be self-reinforcing,” Poland told me. We still won’t be doomed to repeat our first full COVID winter. But we may get closer than anyone cares to endure.

Katherine J. Wu

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November 2, 2023
Pandemic Babies’ Microbiomes Are Bound to Be Different

In the spring of 2021, Brett Finlay, a microbiologist at the University of British Columbia, offered the world a bold and worrying prediction. “My guess is that five years from now we are going to see a bolus of kids with asthma and obesity,” he told Wired. Those children, he said, would be “the COVID kids”: those born just before or during the height of the crisis, when the coronavirus was everywhere, and we cleaned everything because we didn’t want it to be.

Finlay’s forecast isn’t unfounded. As James Hamblin wrote in The Atlantic last year, our health relies on a constant discourse with trillions of microbes that live on or inside our bodies. The members of the so-called microbiome are crucial for digesting our food, training the immune system, even greasing the wheels of cognitive function; there does not seem to be a bodily system that these tiny tenants do not in some way affect. These microbe-human dialogues begin in infancy, and the first three or so years of life are absolutely pivotal: Bacteria must colonize babies, then the two parties need to get into physiological sync. Major disruptions during this time “can throw the system out of whack,” says Katherine Amato, a biological anthropologist at Northwestern University, and raise a kid’s risk of developing allergies, asthma, obesity, and other chronic conditions later in life.

The earlier, more intense, and more prolonged the interruptions, the worse. Infants who receive heavy courses of antibiotics—which can nuke microbial diversity—are at greater risk of developing such problems; the same is roughly true for babies who are born by C-section, who formula feed, or who grow up in nature-poor environments. If pandemic-era mitigations re-create even an echo of those effects, that could spell trouble for a whole lot of little kids who may have lost out on beneficial microbes in the ongoing effort to keep nasty ones at bay.

More than a year and a half after Finlay’s original prediction, children are back in day care and school. People no longer keep their distance or avoid big crowds. Even hygiene theater is (mostly) on the wane. And if the wave of respiratory viral illness now slamming much of the Northern Hemisphere is any indication, microbes are once again swirling between tiny hands and mouths. But for the circa-COVID kids, the specter of 2026 and Finlay’s anticipated chronic-illness “bump” still looms—and it’ll be a good while yet before researchers have clarity on just how much of a difference those months of relative microbial emptiness truly made.

Read: A year without germs

For now, “we are in the realm of speculation,” says Maria Gloria Dominguez Bello, a microbiologist at Rutgers. Scientists don’t understand how, or even which, behaviors may affect the composition of our inner flora throughout our life span. Chronic illnesses such as obesity and asthma also take time to manifest. There’s not yet evidence that they’re on the rise among children, and even if they were, researchers wouldn’t expect to see the signal for at least a couple of years, perhaps more.

Finlay, for one, stands by his original prediction that the pandemic will bring a net microbiome negative. “We underwent a massive societal shift,” he told me. “I am sure we will see an effect.” And he is not the only one who thinks so. “I think it’s almost inevitable that there has been an impact,” says Graham Rook, a medical microbiologist at University College London. If the middle of this decade passes without incident, Rook told me, “I would be very surprised.” Other researchers, though, aren’t so sure. “I don’t think we have doomed a generation of kids,” says Melissa Manus, an anthropologist and microbiome researcher at the University of Manitoba. A few scientists are even pondering whether the pandemic’s ripple effects may have buoyed the microbiomes of the COVID kids. Martin Blaser, a microbiologist at Rutgers University, told me that, “with any luck,” rates of asthma and obesity might even dip in the next few years.

When it comes to the pandemic’s potential fallout, researchers agree on just one thing: COVID babies undoubtedly had an unusual infancy; on average, their microbiomes are bound to look quite different. Different, though, isn’t necessarily bad. “It’s not like there is one golden microbiome,” says Efrem Lim, a microbiologist at Arizona State University. Take Liz Johnson’s sons, born in March 2018, August 2020, and March 2022. All three were born vaginally, in the same hospital, with the assistance of the same midwife; all of them then breastfed; and none of them has undergone an early, concerning antibiotic course. And still, “they all started off with different microbiomes,” she told me. (As a microbiome researcher at Cornell focused on infant nutrition, Johnson can check.)

That’s probably totally fine. Across the human population, microbiomes are known to vary wildly: People can carry hundreds of bacterial species on and inside their bodies, with potentially zero overlap from one individual to the next. Bacterial communities aren’t unlike recipes—if you don’t have one ingredient on hand, another can usually take its place.

Johnson’s middle son, Lucas, had a starkly different birth experience from that of his older brother—even, in many ways, from that of his younger brother. Lucas was born into a delivery room full of masked faces. In the days after his arrival, no family members came to visit him in the hospital. And although his brothers spent several of their early months jet-setting all around the world with their mother for work trips, Lucas stayed put. “Hardly anybody even knew he was born,” Johnson told me. But throughout his first two years, Lucas still breastfed and had plenty of contact with his family at home, as well as with other kids at day care; he romped in green spaces galore. Yet Johnson and others can’t say, precisely, whether all of that outweighs the sanitariness and the uncrowdedness of Lucas’s earliest days. There would have been a cost to both overcaution and under-caution, “so we just tried to balance everything,” Johnson said. When it comes down to it, scientists just don’t know how much microbial exposure constitutes enough.

Read: Pregnant? Breastfeeding? The vaccine might protect you and your baby

Among COVID babies, microbiome mileage will probably vary, depending on what decisions their parents made at the height of the pandemic—which itself hinges on the sorts of financial and social resources they had. Amato worries most about the families that may have packaged a bunch of sanitizing behaviors together with more established cullers of microbiome diversity: C-sections, formula-feeding, and antibiotic use. Meghan Azad, an infant-health researcher at the University of Manitoba, told me that some new parents might have found it far tougher to breastfeed during the pandemic’s worst—a time when in-person counseling resources were harder to access, and employment was in flux. Chronically poor diets and stress, which many people experienced these past few years, can also chip away at microbiome health.

Part of the problem is that many of these risk factors, Rook told me, will disproportionately coalesce among people of lower socioeconomic status, who already tend to have less diverse microbiomes. “I worry this will further increase the health disparity between the rich and the poor,” he said. Even SARS-CoV-2 infections themselves, which have continued to concentrate among essential workers and in crowded living settings, appear to alter the microbiome—a shift that may be temporary in adults, but potentially less so in infants, whose microbiomes haven’t yet matured into a stable state.

Many families exist in a gray zone. Maybe they bleached their households often, but found it easier to breastfeed and cook healthful meals while working from home. Maybe their kids weren’t mingling with tons of other toddlers at day care, but they spent much more time rolling around in the backyard, coated in their pandemic puppy’s drool. If all of those factors feed into an equation that sums up to healthy or not, scientists can’t yet do the math. They’re still figuring out how to appropriately weigh each component, and how to identify others they’ve missed.

Even in the absence of extra outdoorsiness or dog slobber, Lim isn’t very concerned about the behavioral mitigations people picked up. We’re all “exposed to thousands of microbes all the time,” Lim, who has a 1-and-a-half-year-old daughter, told me. Some extra hand-washing, masking, and time at home is nothing compared with, say, an antibiotic blitzkrieg. Even kids who stayed pretty cloistered “were not living in a bubble.” Some of the social sacrifices kids made may even have strange silver linings. Children no longer attending day care or preschool might have skirted a whole slew of other viral infections that would otherwise have gotten them inappropriate and microbiome-damaging antibiotics prescriptions. Antibiotic use in outpatient settings dropped substantially in 2020, compared with the prior year. Stacked up against the relatively minor toll of pandemic mitigations, Blaser told me, the plus of avoiding antibiotics might just win out. When antibiotic use declines, for example, so do asthma rates.

Finlay and others are still keeping an eye out for signals that might start to appear in the next few years. Perhaps most at risk are kids whose families went into “hyper-hygiene mode” in the first couple months of their life, when microbes are crucial for properly calibrating the immune system’s anti-pathogen alarms. Miss out on those opportunities, and our body’s defensive cells might end up mistaking enemies for allies, or vice versa, sparking particularly severe infections or autoimmune disease. Once wired into a developing child, Finlay said, such changes might be difficult to reverse, especially for the youngest of the COVID cohort. But other experts are hopeful that certain microbial losses can still be recouped through some combination of diet, outdoor play, and socialization (with people who aren’t sick)—restorative interventions that, ideally, happen as early as possible. “The sooner we fix it, the better,” Blaser said.

Read: The pandemic broke the flu … again

No one can choose precisely which microbes to be exposed to: Tactics that halt the transmission of known pathogens have a way of halting the transmission of benign bugs too. But context matters. It’s possible for microbe-inviting behaviors, such as outdoor play, to coexist alongside microbe-shunning tactics, such as ventilating indoor spaces when there’s a massive respiratory outbreak. The fact that we can influence microbial colonization at all is powerful. During the pandemic, mitigations that kept COVID at bay also cratered rates of flu and RSV. Now that those viruses are back, experts are pointing out that we already know how they can once again be stopped. And the choices that people made, and continue to make, to protect their families from pathogens shouldn’t be viewed as some harmful mistake, says Ariangela Kozik, a microbiologist at the University of Michigan.

Pandemic kids can get on board with that concept too. Kozik’s now-7-year-old son was a toddler when the pandemic began; even amid society’s hygiene craze, he learned the joys of tumbling around in the dirt and playing with the family’s two dogs. “We talk about how not all germs are the same,” Kozik told me. Her son also picked up and maintained an infection-quashing habit that makes his mom proud: Every day, when he comes home from school, he makes a beeline for the sink to wash his hands. “It’s the first thing he does,” Kozik told me, “even without being asked.”

Katherine J. Wu

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December 5, 2022
Will We Get Omicron’d Again?

In COVID terms, the middle of last autumn looked a lot like this one. After a rough summer, SARS-CoV-2 infections were down; hospitalizations and deaths were in a relative trough. Kids and workers were back in schools and offices, and another round of COVID shots was rolling out. Things weren’t great … but they weren’t the most terrible they’d ever been. There were vaccines; there were tests; there were drugs. The worst winter development the virus might produce, some experts thought, might involve the spawning of some nasty Delta offshoot.

Then, one year ago this week, Omicron appeared. The first documented infection with the variant was identified from a specimen collected in South Africa on November 9, 2021; by December 1, public-health officials had detected cases in countries all around the globe, including the United States. Twenty days later, Omicron had unseated Delta as America’s dominant SARS-CoV-2 morph. The new, highly mutated variant could infect just about anyone it encountered—even if they’d already caught a previous version of the virus or gotten several shots of a vaccine. At the beginning of December, and nearly two years into the pandemic, researchers estimated that roughly one-third of Americans had contracted SARS-CoV-2. By the middle of February this year, that proportion had nearly doubled.

Omicron’s arrival and rapid spread around the world was, and remains, this crisis’s largest inflection point to date. The variant upended scientists’ expectations about SARS-CoV-2’s evolution; it turned having COVID into a horrific norm. Now, as the U.S. approaches its Omicronniversary, conditions may seem ripe for an encore. Some experts worry that the emergence of another Greek-letter variant is overdue. “I’m at a loss as to why we haven’t seen Pi yet,” says Salim Abdool Karim, an epidemiologist at the Centre for the AIDS Programme of Research in South Africa. “I think there’s a chance we still will.”

A repeat of last winter seems pretty unlikely, experts told me. But with a virus this unpredictable, there’s no guarantee that we won’t see disaster unspool again.

Read: The worst pediatric care crisis in decades

A lot has changed since last year. For one thing, population immunity to SARS-CoV-2 is higher. Far more people have received additional doses of vaccine, many of them quite recently, with an updated formula that’s better tailored to the variants du jour. Plus, at this point, nearly every American has been infected at least once—and most of them with at least some subvariant of Omicron, says Shaun Truelove, an epidemiologist and a modeler at Johns Hopkins University. These multiple layers of protection make it more challenging for the average SARS-CoV-2 spin-off to severely sicken people. They also raise transmission obstacles for the coronavirus in whatever form it takes.

Omicron does seem to have ushered in “a different phase of the pandemic,” says Verity Hill, an evolutionary virologist at Yale. The variants that took over different parts of the world in 2021 rose in a rapid succession of monarchies: Alpha, Beta, Gamma, Delta. But in the U.S. and elsewhere, 2022 has so far been an oligarchy of Omicron offshoots. Perhaps the members of the Omicron lineage are already so good at moving among hosts that the virus hasn’t needed a major upgrade since.

If that’s the case, SARS-CoV-2 may end up a victim of its own success. The Omicron subvariants BQ.1 and BQ1.1 appear capable of spreading up to twice as fast as BA.5, according to laboratory data. But their takeover in the U.S. has been slow and halting, perhaps because they’re slogging through a morass of immunity to the Omicron family. That alone makes it less likely that any single Omicron subvariant will re-create the sudden surge of late 2021 anytime soon. In South Africa and the United Kingdom, for instance, different iterations of Omicron seem to have triggered just modest bumps in sickness in recent months. (That said, those countries—with their distinct demographics and vaccination and infection histories—aren’t a perfect bellwether for the U.S.)

For an Omicron 2021 redux to happen, SARS-CoV-2 might need to undergo a substantial genetic makeover—which Abdool Karim thinks would be very difficult for the virus to manage. In theory, there are only so many ways that SARS-CoV-2 can scramble its appearance while retaining its ability to latch onto our cells; by now, its options should be somewhat slimmed. And the longer the Omicron line of succession persists, the tougher it may be to upend. “It’s just getting harder to compete,” Hill told me.

But the world has gotten overconfident before. Even if SARS-CoV-2 doesn’t produce a brand-new version of itself, low uptake of the bivalent vaccine could allow our defenses to wither, driving a surge all the same, Truelove told me. Our transmission-dampening behaviors too are slacker than they’ve been since the pandemic’s start. This time last year, 50 to 60 percent of Americans were regularly wearing masks. The latest figures, many of them several months old, are closer to 30 percent. “The more opportunities you give the virus to get into somebody,” Hill said, “the more chances you give it to get the group of mutations that could help it take off.” Immunocompromised people who remain chronically infected with older variants, such as Alpha or Delta, could also become the sites of new viral offshoots. (That may be how the world got Omicron to begin with.)

Going on probability alone, “it seems more likely that we’ll keep going with these subvariants of Omicron rather than dealing with something wholly brand-new,” says Maia Majumder, an epidemiologist at Boston Children’s Hospital. But Lauren Ancel Meyers, an infectious-disease modeler at the University of Texas at Austin, warns that plenty of uncertainty remains. “What we don’t have is a really data-driven model right now that tells us if, when, where, and what kind of variants will be emerging in the coming months and years,” she told me. Our window into the future is only getting foggier too as fewer people submit their test results—or take any test at all—and surveillance systems continue to go offline.

It wouldn’t take another Omicron-type event to hurl us into disarray. Maybe none of the Omicron subvariants currently jockeying for control will surge ahead of the pack. But several of them might yet drive regional epidemics, Majumder told me, depending on the local nitty-gritty of who’s susceptible to what. And as winter looms, some of the biggest holes in our COVID shield remain unpatched. People who are immunocompromised are losing their last monoclonal-antibody treatments, and although powerful drugs exist to slash the risk of severe disease and death, useful preventives and treatments for long COVID remain sparse.

Read: The end of Evusheld

Our nation’s capacity to handle new COVID cases is also low, Majumder said. Already, hospitals around the country are being inundated with other respiratory viruses—RSV, flu, rhinovirus, enterovirus—all while COVID is still kicking in the background. “If flu has taken over hospital beds,” says Srini Venkatramanan, an infectious-disease modeler at the University of Virginia, even a low-key wave will “feel like it’s having a much bigger impact.”

As the country approaches its second holiday season with Omicron on deck, this version of the virus may “feel familiar,” Majumder pointed out. “I think people perceive the current circumstances to be safer than they were last year,” she said—and certainly, some of them are. But the fact that Omicron has lingered is not entirely a comfort. It is also, in its way, a reminder of how bad things once were, and how bad they could still get.

Katherine J. Wu

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November 10, 2022