The Washington PostDemocracy Dies in Darkness

Latest version of omicron accounts for most new infections in many parts of the U.S., genomics testing shows

Denmark, a country of 5.8 million people, has surpassed 1 million infected citizens as the omicron variant has accelerated the spread of the virus. (Carsten Snejbjerg/Bloomberg)

The recently emerged version of the coronavirus called BA.2 that has driven a wave of cases in Europe now accounts for as much as 70 percent of new infections in many parts of the United States, according to an estimate from the genomics company Helix that could signal a new chapter in the third year of the pandemic.

The estimate from Helix, which conducts genomic sequencing on virus samples, comes amid concerns that Europe’s surge in infections will be replicated in coming weeks in the United States, where caseloads have often trailed those in Europe by roughly a month.

It’s clear BA.2, officially considered a subvariant of omicron, is gaining traction as the previously dominant lineage of omicron subsides. In two or three weeks, “everything in the Northeast is going to be BA.2,” predicted Jeremy Luban, a virologist at the University of Massachusetts Medical School.

Europe is experiencing a spike in coronavirus infections due to BA.2, a new version of the omicron variant. Health reporter Lenny Bernstein explains more. (Video: Casey Silvestri/The Washington Post)

Natalie Dean, a biostatistics expert at Emory University, noted that Britain had only a brief lull between its omicron wave and a surge from BA.2. That surprised her, and she suspects it could be repeated in the United States.

“I would have expected a longer lag period,” Dean said. “It tells me something could pick up here again, too, sooner than I would have guessed.”

The Centers for Disease Control and Prevention on Tuesday reported that BA.2 accounts for 35 percent of coronavirus infections nationally, up from 22 percent a week ago. In New England, the CDC reported, BA.2 accounts for 55 percent of new infections, compared with 39 percent last week. The Helix data is more up to date and includes samples from many states, including California, Florida, Pennsylvania, Massachusetts, Michigan and Texas, Helix chief scientist Will Lee said.

“I think cases are going to start going up again. I think I’m not going out on a limb too much in saying that,” Lee said.

Tracking the spread of omicron BA.2.

So far, no broad surge of new cases has emerged in the United States. There are so many variables at work when it comes to coronavirus transmission — including human behavior, perhaps the hardest factor to predict or measure — that disease experts cannot say with confidence whether and when a new wave will materialize. A wave of significant magnitude would be the sixth since the virus arrived in early 2020.

Another surge probably would not be as intense as what was seen in the depths of winter, when omicron sickened tens of millions of people and killed tens of thousands in a matter of weeks. Nor is it obvious that a new wave of cases would shift dramatically the policies of the Biden administration and those of institutions and private businesses that are calling staffers back to the office.

Downtowns are busy again, and students have dropped masks in schools. A federal mask mandate for air travel remains in effect until April 18 but could be lifted at that point. More than 2 million people have gone through airport security checkpoints each of the past five days, according to Transportation Security Administration data, and although the numbers are not quite back to pre-pandemic levels, they are inching in that direction. Even the CDC is tentatively planning for employees to return to its Atlanta campus in mid-April.

As the country has moved firmly into a fully reopened position, the CDC has issued guidelines that make masking no longer recommended in 99 percent of the nation’s counties. If there is a surge, the response appears likely to be governed at the personal level, as people decide whether and when to resume masking and social distancing.

“It would take a catastrophic event before we would see major restrictions put back in place,” said Michael T. Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota.

Two years-plus into the pandemic, the United States is in a particularly uncertain situation because of a long list of unknowns that can dial up or dial down the number and severity of covid-19 cases. At the top of that list is genetic mutation: Disease experts remain wary about the virus’s propensity to evolve in ways that boost transmission or evade immunity.

“We still don’t have any clue where these variants come from,” Jacob Lemieux, an infectious-disease doctor at Massachusetts General Hospital, said Monday in a Harvard Medical School media briefing. “I think the bottom line is that we are living next to this volcano. And the volcano has not erupted recently, and that’s great. But we still don’t know when the volcano erupts, why the volcano erupts and whether the next eruption is going to be bigger or less big than the last one.”

But BA.2 is clearly a handful already. Whether it can drive a new wave of cases in the United States the way it has in many countries overseas is unclear. Scientists point out that although it has been described as a “subvariant” of omicron, BA.2 is quite different — as different from omicron as the delta variant is from the alpha variant, Luban said.

There is no evidence that BA.2 makes people sicker than its omicron progenitor, and experts believe that vaccines will continue to protect against severe outcomes from BA.2 as they have in cases involving other variants.

The level of immunity stockpiled in the population is not known precisely, and that’s another variable in any forecast for the weeks and months ahead. Immunity, whether acquired through vaccines or natural infection, wanes naturally over time.

Vaccine makers have asked the Food and Drug Administration to give the go-ahead for a fourth shot for people who have received the initial series of two shots and a booster, with Pfizer-BioNTech seeking a fourth shot for people 65 and older, and Moderna for all eligible adults. Millions of adults, meanwhile, have never had a single shot, and millions more are vaccinated but have not availed themselves of a booster.

So that makes for a complex immunological landscape — explored anew by an evolving virus. Disease experts say that places that had low levels of natural infection, or have experienced low rates of vaccination and boosting, are particularly vulnerable to a new wave of infections.

Behavior is another factor. The virus leverages the social nature of human beings. Although BA.2 appears to be roughly 30 percent more transmissible than omicron, what may be even more significant is that it is spreading at a time when people are coming into contact with many more people.

“If you are beginning to make 10 times as many contacts as you were,” that will prove more significant than any transmission advantage BA.2 may have because of its mutations, said William Hanage, an epidemiologist at the Harvard T.H. Chan School of Public Health.

Although many experts anticipate a surge at some point, there is not a consensus on that. A new model from the University of Washington’s Institute for Health Metrics and Evaluation forecasts no surge in the near term.

Ali H. Mokdad, an epidemiologist at the institute, said he expects another rise in cases late in the year, when cold weather returns in parts of the nation and people gather inside. But he believes there is a huge amount of immunity in the U.S. population following previous waves of infection, including the massive omicron-driven spike that ravaged workforces in the midst of this winter.

“People are ready to go into a bunker, saying what is happening in Europe will happen here. We don’t see it,” Mokdad said. “We see a slight bump but nothing big.”

Wastewater monitoring for the presence of the virus serves as an early-warning system, and there are signs of increased virus in some areas. That data remains spotty, however, and there is not yet a clear connection between wastewater data and caseloads in those locations.

Dean, of Emory, has been closely following the pandemic for more than two years and expects to see another rise in cases.

“Right now in the U.S., we’re past the big omicron wave, and we’re at a point where case levels are relatively low,” she said. “But we should expect oscillations in the future. Unfortunately, it’s just going to be a thing that we battle with for a while.”

Hanage said the virus has shown no sign it has stopped mutating and producing new variants: “It’s only wise to assume there’s going to be another one coming along. What the consequences of that will be is very difficult to say.”

Osterholm also thinks another wave is likely at some point, but he emphasizes the uncertainties, noting that the pattern of waves in the past has been quirky, with some regions of the United States hit hard even as others were spared.

“There’s a very high likelihood that we’re going to see increased cases in the United States. Whether you call it a wave — I’m not sure it will be uniform across the country,” Osterholm said. “This one could be different from the original omicron surge — what I call the viral blizzard — where basically it had impact everywhere. I don’t think it’s clear yet that this is going to happen with this one.”

He added that humility is absolutely essential because of the unpredictability of the coronavirus.

“This virus has continued to throw us 210-mile-an-hour curveballs,” he said.

Lena H. Sun contributed to this report.

Coronavirus: What you need to know

Vaccines: The CDC recommends that everyone age 5 and older get an updated covid booster shot designed to target both the original virus and the omicron variant. Here’s some guidance on when you should get the omicron booster and how vaccine efficacy could be affected by your prior infections.

Variants: Instead of a single new Greek letter variant, a group of immune-evading omicron spinoffs are popping up all over the world. Any dominant variant will likely knock out monoclonal antibodies, targeted drugs that can be used as a treatment or to protect immunocompromised people.

Tripledemic: Hospitals are overwhelmed by a combination of respiratory illnesses, staffing shortages and nursing home closures. And experts believe the problem will deteriorate further in coming months. Here’s how to tell the difference between RSV, the flu and covid-19.

Guidance: CDC guidelines have been confusing — if you get covid, here’s how to tell when you’re no longer contagious. We’ve also created a guide to help you decide when to keep wearing face coverings.

Where do things stand? See the latest coronavirus numbers in the U.S. and across the world. In the U.S., pandemic trends have shifted and now White people are more likely to die from covid than Black people. Nearly nine out of 10 covid deaths are people over the age 65.

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