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Will Delta Survive the Omicron Wave?

Pour one out for Delta, the SARS-CoV-2 variant that Season 3 of the pandemic seems intent on killing off. After holding star billing through the summer and fall of 2021, Delta’s spent the past several weeks getting absolutely walloped by its feistier cousin Omicron—a virus that’s adept at both blitzing in and out of airways and dodging the antibodies that vaccines and other variants raise. In late November, Delta made up essentially all the SARS-CoV-2 infections that researchers were sequencing in the United States. Now it’s a measly 0.1 percent. As for the rest? It’s an Omicron show.

The global portrait’s a bit patchier, but by and large, “Delta won’t be able to compete,” Karthik Gangavarapu, a computational biologist at UCLA, told me. “My suspicion is that Omicron will take over.” It’s a fair shift from the tune many experts were singing just weeks ago, when they wondered whether Delta and Omicron might co-circulate in a vicious variant one-two punch. Katia Koelle, an evolutionary virologist at Emory University, told me she used to worry about that possibility when the world knew little about Omicron’s competitive edge, but “less so now.” Katie Gostic, an infectious-disease modeler at the University of Chicago, agrees that Delta doom is probably nigh. And if so, “good riddance,” she told me.

But Gostic and other experts are not quite ready to officially sound Delta’s death knell. As unlikely as it’s looking, a persistent, low-level Delta simmer—perhaps even a resurgence—is not off the table yet. Delta is still Top Variant in some parts of the world. Should it hold its own at any level, it will continue to pose a threat to us. After Omicron caught the world so off guard, “I would certainly not bet on Delta disappearing,” Lisa Gralinski, a coronavirologist at the University of North Carolina at Chapel Hill, told me.

To be clear, Delta is being dwarfed by Omicron right now, in the United States and in many places abroad. Although the older variant is clinging on for dear life in a few pockets, its grasp will likely continue to slacken and slip under the weight of its craftier cousin. The main difference, Gangavarapu said, seems to be about how well each variant skirts some of the immune defenses laid down by vaccines and prior encounters with the virus; on this count, Delta’s an amateur, and the highly mutated Omicron is an A-list pro. Our repertoire of shots is still staving off severe disease and death caused by any version of SARS-CoV-2. But the antibodies that reliably keep Delta from colonizing vaccinated hosts struggle to get a grip on Omicron, which means more people are vulnerable to infection with the newcomer. (The experts I spoke with were less certain that Omicron is, particle for particle, inherently more transmissible than Delta; those data are hard to come by when so many of us carry a degree of immunity.)

Omicron may also be reinforcing its own success. Delta-induced immunity doesn’t do a great job of protecting people from Omicron. But when Omicron infects people who have been vaccinated, it seems to shore up anti-Delta defenses too. (This effect is weaker in unvaccinated people, though, and it’s unclear how long the effects of these juice-ups last). That might mean that the more immunized people Omicron infects, the fewer hospitable hosts Delta will have. The new variants we get from here on out could continue to follow this pattern, displacing the morphs that came before them year after year after year.

Then again, maybe not. That this competition is blatantly favoring Omicron so far does not necessarily tell us where Delta will end up. All infections are interactions between pathogen and host, which means Delta could hold its own, or make a comeback, for a bunch of reasons that aren’t just about the virus itself. Some people could, for instance, be more biologically primed to foster a Delta infection than an Omicron one. Or Delta could exploit the vagaries of geography, taking stubborn root in an isolated population without much immunity of any kind, in which case Omicron’s advantage may be moot. Or it could find shelter in a little community where few Omicron-infected people have yet to tread—or, perhaps more concerningly, in an immunocompromised person, infected months ago, who has so far struggled to purge the virus.

Variants in this way are like pickles: They have a way of sticking around past their anticipated expiration date. Even Alpha (remember Alpha?) still occasionally blips back onto the map, though recorded instances remain quite rare. These cases can be hard to catch; researchers don’t have the capacity to detect, let alone sequence, every SARS-CoV-2 infection out there. That means the proportions of variants in the genomes researchers report aren’t necessarily representative of their proportions in the wild. “The world is a very big place, and it’s all a numbers game,” Benhur Lee, a virologist at Mount Sinai’s Icahn School of Medicine, told me.

And the longer Delta is able to bide its time, the more easily it might be able to engineer its own revival. As the world builds immunity to Omicron, the variant will have a harder time infecting new hosts; at the same time, the protective effects of vaccination and past infection that might have blocked Delta will wear off in people whom Omicron has not touched.

Even now, Delta has more than its fair share of opportunities to infect new people, replicate, and rejigger its genome. That is very much not what we want: Delta is thought to be the deadliest SARS-CoV-2 variant identified to date, and its descendants could very well preserve or even build upon its very lethal bite while picking up new tricks that bamboozle our immune systems. Those modifications wouldn’t have to happen in humans, either. Delta could seek temporary asylum in another amenable animal species and tweak its appearance before jumping back into us. That’s actually one origin hypothesis for Omicron, which traces its roots back to a 2020 branch of the SARS-CoV-2 family tree.

In a “worst-case scenario,” Gostic said, Delta could transform into something capable of catching up with Omicron, and the two would tag-team. Dual circulation doesn’t just double the number of variants we have to deal with; it “leaves open the possibility for recombination,” a phenomenon in which two coronavirus flavors can swap bits of their genomes to form a nasty hybrid offspring, Ajay Sethi, an epidemiologist at the University of Wisconsin at Madison, told me. (Delta’s brutality + Omicron’s stealth = bad-news bears.) Alternatively, a daughter of Delta may totally overtake Omicron, exacting its ancestor’s sweet, sweet revenge. Or maybe the next variant that usurps the global throne will be a bizarro spawn of Alpha … or something else entirely. In the same way that Omicron was not a descendent of Delta, the next variant we tussle with won’t necessarily sprout from Omicron.

The landscape for Delta is shifting by the day. Already, researchers are investigating an Omicron offshoot, BA.2, that’s surging in countries such as Denmark at surprising speed; too little is known to say anything for sure about how it changes Delta’s chances. That means none of the hypothetical paths to Delta re-domination necessarily represents the most likely future. But they all remain possible, especially with a large fraction of the world’s population still unvaccinated, which means it’s worth preparing for them. We can’t guarantee what hijinks the virus will pull next.

Even if Delta does vanish in short order, its legacy won’t go poof quite as quickly. During its tenure, Delta has infected countless people around the world, leaving behind debilitating illness and death. It is still tripping coronavirus tests. It is still filling hospital beds. It is still straining society’s capacity to care for the sick. A declining threat is not a nonexistent one. And until Delta is gone, truly gone, we’d be premature to bid it a full-throated adieu.




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