The new variant seems to be our quickest one yet. That makes it harder to catch with the tests we have.
https://www.theatlantic.com-By Katherine J. Wu
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It certainly might not seem like it given the pandemic mayhem we’ve had, but the original form of SARS-CoV-2 was a bit of a slowpoke. After infiltrating our bodies, the virus would typically brew for about five or six days before symptoms kicked in. In the many months since that now-defunct version of the virus emerged, new variants have arrived to speed the timeline up. Estimates for this exposure-to-symptom gap, called the incubation period, clocked in at about five days for Alpha and four days for Delta. Now word has it that the newest kid on the pandemic block, Omicron, may have ratcheted it down to as little as three.
If that number holds, it’s probably bad news. These trimmed-down cook times are thought to play a major part in helping coronavirus variants spread: In all likelihood, the shorter the incubation period, the faster someone becomes contagious—and the quicker an outbreak spreads. A truncated incubation “makes a virus much, much, much harder to control,” Jennifer Nuzzo, an epidemiologist at the Johns Hopkins Center for Health Security, told me.
Already, that’s what this variant seems to be. In less than a month, Omicron has blazed into dozens of countries, sending case rates to record-breaking heights. If, as some scientists suspect, this variant is so primed to xerox itself more quickly inside us—including, it seems, in many people with at least some immunity—that leaves punishingly little time in which to detect the virus, intervene with antivirals, and hamper its spread.
A pause here. We are still just weeks into our fight against Omicron, and it’s not easy to gather data on incubation periods, which might differ among populations, or suss out exactly how the virus is tangoing with our cells. But the early warning signs are here—and as my colleague Sarah Zhang has reported, we know enough to act.
All of this, then, ups the urgency on having tests that can quickly and reliably pinpoint Omicron. “If Omicron has a shorter incubation period, that’s going to wreak havoc on how we test for it and deal with it,” Omai Garner, a clinical microbiologist in the UCLA Health system, told me. But testing in the United States remains slow, expensive, and, for many, infuriatingly out of reach. We’re ill-prepared for the incoming Omicron surge not just because it’s a new version of the coronavirus, but because it’s poised to exploit one of the greatest vulnerabilities in our infection-prevention toolkit. The coronavirus is getting faster, which means it’s also getting harder to catch.
Since the World Health Organization designated Omicron as a variant of concern at the end of November, the virus seems to have popped up just about everywhere. Researchers are tracing cases of it back to schools, child-care centers, hotels, universities, weddings, and bars. And they’re finding it at office holiday parties, like the one at a restaurant in Oslo, Norway, where about 80 people may have caught or transmitted Omicron.
In a research paper describing the Oslo outbreak, scientists noted that, after the event, symptoms seemed to come on quickly—typically in about three days. More troubling, nearly every person who reported catching Omicron said that they were vaccinated, and had received a negative antigen-test result sometime in the two days prior to the party. It was a clue that perhaps the microbe had multiplied inside of people so briskly that rapid-test results had rapidly been rendered obsolete.
The time lines described by the Norwegian researchers are preliminary, and might not be representative of the rest of us. But they appear to match up with early, sometimes-anecdotal reports, including some out of South Africa, one of the first countries to detect and report Omicron’s existence. Shorter incubation periods generally lead to more infections happening in less time, because people are becoming more contagious sooner, making onward transmission harder to prevent. Ajay Sethi, an epidemiologist at the University of Wisconsin at Madison, told me he still wants more data on Omicron before he touts a trim incubation. But “it does make sense,” he said, considering the variant’s explosive growth in pretty much every country it’s collided with. In many places, Omicron cases are doubling every two to three days.
Nailing the incubation interval really is tough. Researchers have to track down sizable outbreaks, such as the Oslo Christmas party; try to figure out who infected whom; wait for people to report when they start feeling sick—always a fickle thing, because symptoms are subjective—then, ideally, track whether the newly infected are spreading the virus too. The numbers will vary depending on who was involved: SARS-CoV-2-incubation periods could differ by vaccination status, underlying health conditions, infection history, age, and even the dose of the virus people get blasted with. To complicate things further, the start of symptoms tends to lag behind the start of contagiousness by, on average, a couple of days; when symptoms begin earlier, transmission might not follow to exactly the same degree.
If Omicron’s incubation period turns out to be conclusively shorter, we would still have to figure out how it got winnowed down. Some of it could be inherent to the virus itself. Omicron’s spike protein is freckled with more than 30 mutations, some of which, based on previous variants, could help it grip more tightly onto cells and wriggle more efficiently into their interiors. Two recent laboratory studies, neither yet published in scientific journals, may be hinting at these trends. One, from a team at Harvard University, showed that a harmless virus, engineered to display Omicron’s spike on its surface, more easily penetrated human cells in a dish; another, out of Hong Kong University, found that Omicron multiplied dozens of times faster than Delta in tissue extracted from the upper airway. The findings won’t necessarily translate into what goes on in actual bodies, but they support the idea that Omicron is turbocharging the rate at which it accumulates to contagiousness. The faster that happens, the more quickly the virus can spill out of one person and into the next. If the data pan out, “this could go a long way in explaining the rapid transmission,” Lisa Gralinski, a virologist at the University of North Carolina at Chapel Hill, told me.
The unvaccinated remain most at risk, but this trend would have troubling consequences for the vaccinated and previously infected too, especially if they’re unboosted. Many of the antibodies we marshaled against previous versions of the coronavirus don’t recognize Omicron very well, and won’t be able to sequester it before it foists itself into cells. Eventually, a vaccine- or infection-trained immune system will “catch up,” Ryan McNamara, a virologist at Harvard Medical School, told me, churning out more antibodies and launching an army of T cells that can quell the virus before it begets serious disease. But those defenses take a few days to kick in and might not arrive in time to forestall the early, and often most potent, stages of transmission. The faster Omicron sprints, the more of a head start it gets against the body’s defenses.
The picture on Omicron is coalescing both microscopically within us and broadly in communities—steep, steep, steep slopes in growth. The two phenomena are linked: A shorter incubation period means there’s less time to pinpoint an infection before it becomes infectious. With Omicron, people who think they’ve been exposed may need to test themselves sooner, and more often, to catch a virus on the upswing. And the negative results they get might have even less longevity than they did with other variants, Melissa Miller, a clinical microbiologist at UNC, told me. Tests offer just a snapshot of the past, not a forecast of the future; a fast-replicating virus can go from not detectable to very, very detectable in a matter of hours—morning to evening, negatives may not hold.
This, especially, could be bad news for PCR tests, which have been the gold standard throughout the pandemic and essential for diagnosing the very sick. (Thankfully, most PCR tests do seem to be detecting Omicron well.) These tests have to be processed in a laboratory before they can ping back results—a process that usually takes at least a few hours but, when resources are stretched thin as they are now, can balloon out to many days. In that time, Omicron could have hopped out of one person’s body and into the next, and into the next. It’s a particular gamble for people who don’t have symptoms and who are still out and about while they await their results. The more swiftly the virus becomes infectious, the more important testing speed becomes too.
Rapid at-home antigen tests—which can be purchased over the counter, and can return results in about 15 minutes—could fill some of the gaps. Their results would also come with quick expiration dates, but they’d also manifest faster, and, potentially, offer a better representation of what’s happening in the body right now.
But rapid antigen tests aren’t a perfect solution. Compared with PCR tests, they are less able to pick up on the virus when it’s present at pretty low levels—which means they might have a harder time homing in on the virus while it’s simmering early in infection, or might even fail to detect it in people who are already contagious. A few experts told me that they’re worried some antigen tests will struggle to pinpoint the highly mutated Omicron at all, something still being monitored by the FDA.
People could test themselves repeatedly to lower the chances that they miss the microbe, but a strategy like that quickly starts to verge on impractical. You can’t reasonably ask people to test themselves every 12 hours, Nuzzo said. And the products still aren’t available in high enough numbers to meet anywhere near that kind of demand. They’re also wildly expensive, keeping them out of the hands of many of the vulnerable communities that need them most. Some states are passing out rapid tests for free, but they’re still in the minority. And the Biden administration’s limited reimbursement plan won’t take effect until next year. On grand scales, American supply is still massively, massively falling short. That fact, married with Omicron’s probable pace, means “we’re not going to catch everybody who has it,” Nuzzo said.
The variant’s fleet-footedness is likely to have big ripple effects in clinical settings too. Garner and Miller, who both run clinical labs, are worried that the coming testing surge will delay results for patients who have to be screened before going into surgery, or who need a diagnosis for treatment. That could be especially problematic for doling out the much-anticipated antiviral pills to treat COVID, which need to be taken very early in the course of illness to effectively halt the progression of disease. Stretched laboratory capacity could also compromise testing for other pathogens, including the flu, which is creeping back into the population just as health-care systems are starting to buckle once more. Nationwide, Garner said, “we are as unprepared for a surge as we were a year ago.”
People shouldn’t give up on tests, experts told me; they’ll still make a big difference when and where they’re used, especially for diagnosing the sick. But Omicron’s speed is a sharp reminder of humanity’s own sluggishness during this pandemic. Until now, tests offered only a porous safety net; in the era of Omicron, the holes are even wider. We’ll need to close the gaps by doubling down further on preventive measures: masking, vaccination, ventilation, and, unfortunately, cutting back on travel and socializing. Viruses don’t actually move that fast on their own—they need human hosts to carry them. If things stay as they are, though, we’ll keep giving this one the ride of a lifetime.
The Atlantic’s COVID-19 coverage is supported by grants from the Chan Zuckerberg Initiative and the Robert Wood Johnson Foundation.
Katherine J. Wu is a staff writer at The Atlantic, where she covers science.