A rise in Covid cases in U.S. signals end of Omicron’s reprieve

as the Omicron wave subsided in the United States earlier this year, many experts anticipated a sort of reprieve† We certainly weren’t done with Covid, but perhaps we would get a well-deserved rest.

That break seems to be over.

An increase in infections that began in places including the Northeast and Puerto Rico is now being seen in other parts of the country. Cases will rise and fall going forward, but more worryingly, hospitalizations have started to increase as well — up 20% in two weeks. The decline in deaths has bottomed out at some 350 a day.


Epidemiologist David Dowdy of Johns Hopkins’ Bloomberg School of Public Health said that, despite the case increases, hospitalization and death rates overall remain relatively low compared with earlier periods in the pandemic — a reflection of how much immunity there is in the population.

“In some ways, this is encouraging, in that we’re starting to see a divergence between the number of cases and the number of hospitalizations and deaths,” Dowdy said. “But it’s also a little bit discouraging that we’ve been through all this and we’re still seeing a flat line and an uptick in the number of people getting admitted to the hospital and in people dying.”


To be sure, the US is at a dramatically different point now in the pandemic than in earlier periods. Even as cases have increased — to 80,000 a day, up from less than 30,000 in late March — they’re still far below the heights of earlier this year, and started rising from very low levels. Vaccinations, and particularly booster shots, are continuing to provide broad protection against the worst outcomes of Covid-19, even as the virus keeps evolving. The growing availability of the antiviral Paxlovid is helping keep at-risk people from getting so sick they need to be hospitalized. The majority of people have at least some level of protection against Covid-19 — from vaccination, past infection, or both — meaning that cases, as Dowdy noted, are increasingly less likely to result in severe outcomes.

And yet if there are more cases overall, some will still result in hospitalizations and deaths, even if at lower rates than earlier.

There are a range of factors that contribute to cases rising and falling — climate, behavior, and mitigation efforts (or lack thereof) among them. Scientists are trying to zero in on what the latest increase in cases says about the durability of protection and the ongoing evolution of the virus.

People can become susceptible to infection again if their immunity wanes or if the virus mutates in ways that allow it to sneak past the body’s defensive recognition systems. Experts analyzing current outbreak patterns think both factors could be at play: It seems that while protection against severe disease is holding up well, the ability to block an infection wanes in a matter of months. And while the first Omicron wave was driven by the BA.1 sublineage, the current spike in cases is largely BA.2, and increasingly, a spinoff called BA.2.12.1. These variants are not only more efficient spreaders than BA.1, but they could also look distinct enough from past forms of the virus that they can evade people’s immunity and trigger infections.

“Why is this happening?” said Jacob Lemieux, an infectious diseases physician at Massachusetts General Hospital, who’s been tracking variants. Is it that the novel variants are that different, or is it that immunity is that transient? “We don’t know, but it’s raising a lot of really important scientific questions,” Lemieux said.

Answering such questions could help shape our understanding of what our relationship with the SARS-CoV-2 virus will look like going forward. Could this mean, for example, that communities become susceptible to new outbreaks after just a few months, particularly with the emergence of even a further mutated virus?

Evidence for that hypothesis isn’t just emerging from the United States. South Africa suffered a major BA.1 wave, and is now seeing another surge of cases (and to a much smaller extent, hospitalizations) from other Omicron sublineages, BA.4 and BA.5.

The current infection spikes are different in other ways from previous waves. While those were driven by entirely new variants that emerged from distant points on SARS-2’s family tree, now different Omicron branches are igniting new outbreaks. This “genetic drift” is closer to how flu strains evolve

“Perhaps what we might see will be these waves of subvariants,” said Jonathan Abraham, an assistant professor of microbiology at Harvard Medical School.

Complicating the matter is that the data scientists rely on to analyze outbreaks are growing messier. Official case counts are missing more infections, as testing programs are rolled back, people rely on at-home tests, or they have such mild cases they don’t bother getting tested.

Even hospitalization data have some fuzziness. As the prevalence of the virus increases in communities, some people who go to the hospital for, say, surgery, might test positive for SARS-2 and make it into official counts. Some states are tracking who is hospitalized for Covid-19, versus who happens to be hospitalized with COVID-19. the Massachusetts dashboard, for example, notes that about 1 in 3 counted patients were “hospitalized primarily for Covid-19 related illness.” (One extra wrinkle: Even if someone is hospitalized because of complications from a chronic illness, it’s possible that Covid exacerbated it to the point they needed to be admitted.)

Global health officials are also warning about the risk of curtailed surveillance efforts. Some of the systems that were built up to test for and sequence the virus have started to wind down, which scientists say leaves the world with a poorer understanding of how the virus is mutating and what threats those changes might pose.

“Our ability to detect this is being substantially hindered because testing rates have plummeted, and in doing so, our sequencing rates have plummeted as well,” Maria Van Kerkhove, the World Health Organization’s technical lead for Covid-19, said Tuesday about BA. 4 and BA.5, noting that only a few hundred sequences of each have been shared.

It seems, Van Kerkhove said, that BA.4 and BA.5 are able to outcompete BA.2, but it’s not clear if countries that have BA.2 waves will be vulnerable to waves of BA.4 and BA.4. So far, it doesn’t appear that any of the Omicron lineages cause more severe disease on average than BA.1.

One reason why experts anticipated a break this spring was because so many millions of people in the United States were infected during its BA.1 wave. but recent studies in South Africa and elsewhere have found that a BA.1 infection alone does not provide much cross-protection from other variants — meaning people might not be able to withstand an infection from another Omicron sublineage. The combination of vaccination and BA.1 infection, however, provided broader, more robust protection.

Melanie Ott, a virologist at the Gladstone Institutes, said what’s happening now could be a preview of what’s to come. A variant begins to circulate, causes some increase in cases, and then gets overtaken by another variant that can outcompete it, likely because it is better at causing infections in people with protection. Such a pattern could look different from place to place.

“The virus is doing what viruses do, and it adapts to a changing immune landscape,” Ott said.

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