The Omicron BA.2 variant represents more than half of new Covid-19 cases in the U.S., the latest federal estimates show, as signs suggest infections are edging higher again in parts of the Northeast.

The region has the highest BA.2 concentrations, including more than 70% in an area including New York and New Jersey, according to estimates the Centers for Disease Control and Prevention released Tuesday. BA.2 has been moving steadily higher for more than a month and represents an estimated 55% of national cases in the week ended March 26, the CDC said.

Public-health authorities and experts are watching BA.2 closely, in part because it appears to spread more easily than the version that caused record levels of Covid-19 cases and hospitalizations in the U.S. this winter. BA.2 has fueled new surges in European countries including the U.K., where pandemic trends have often presaged events in the U.S. Parts of Asia, including Hong Kong and Shanghai, are also confronting serious Omicron surges.

“Predictions are hard, but I am expecting that the U.S. will have a surge in at least some locations,” said Aubree Gordon, an associate professor of epidemiology at the University of Michigan School of Public Health.

Covid-19 case data have become less reliable because more people are using home test kits, whose results generally aren’t captured in state tallies.

Photo: Gabby Jones for The Wall Street Journal

U.S. data remain a mix of positive signs, including counts of hospitalized patients near record lows, and some evidence of new pressure as BA.2 spreads. The dropping of precautions meant to restrain the virus, including mask mandates, is likely also playing a role, disease experts and health officials say.

Research has suggested BA.2 is similar to an earlier Omicron version when it comes to the risk of hospitalizations and developing severe disease. But research also indicates BA.2 spreads more easily.

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The Food and Drug Administration said last Friday that providers should no longer use GlaxoSmithKline PLC’s Covid-19 antibody treatment sotrovimab in Massachusetts, New York and several other states, after finding that the drug is likely ineffective against the BA.2 variant.

The agency also said it would track BA.2’s prevalence around the U.S. and might need to further limit where sotrovimab can be used.

Gilead Sciences Inc.’s remdesivir, molnupiravir from Merck & Co. and Ridgeback Biotherapeutics LP and the main component in Pfizer Inc.’s Paxlovid pill were all effective against the BA.2 variant, according to a study published this month in the New England Journal of Medicine.

Nationally, the seven-day average for newly reported cases has hovered around 30,000 for about two weeks, according to Johns Hopkins University data. This is above an all-time, post-surge low of under 12,000 reached last June.

Case data have become less reliable because more people are swabbing their noses at home with test kits whose results generally aren’t captured in state tallies. A recent report published by the CDC found that the percentage of surveyed adults with Covid-like symptoms who said that they had used at-home tests reached 20% during the winter’s Omicron wave, compared with about 6% during the earlier Delta wave.

“It does create something of a blind spot about what the true prevalence of Covid-19 is in communities,” said William Morice, president of Mayo Clinic Laboratories and chair of the Mayo Clinic’s Department of Laboratory and Medicine and Pathology.

Despite the counting challenges, the existing data show signs of rising cases in some areas, including in New York City. And New York’s state health department on Monday highlighted pressure in the central New York region, where the seven-day average for cases per 100,000 people recently reached about 46.5, compared with 14.7 statewide.

The state said local vaccination rates, mask wearing and adherence to other mitigation efforts might play a role in central New York’s rising cases. New York was among the states that maintained mask requirements through the Omicron surge, but it recently ended mandates as case and hospitalization counts fell. State health officials don’t anticipate a serious jump in cases throughout New York, the health department said.

Wastewater samples from the Deer Island treatment plant in Boston, which covers some 2.4 million people, have shown Covid-19 rates trending higher.

Photo: Vanessa Leroy for The Wall Street Journal

There are also clues suggesting higher virus levels in wastewater samples, which health experts are watching as an early warning system. The latest samples from the Deer Island treatment plant in Boston, which covers some 2.4 million people in the city and suburbs, is among those showing numbers that are starting to trend higher again from recently low levels.

Some epidemiologists are hopeful that built-up immunity in the U.S. population from that winter surge can help mute the BA.2 variant’s impact. At least one early study from Denmark, which isn’t yet published, suggests that reinfections with BA.2 shortly after an Omicron infection are possible, but they seem to be rare. Out of some 1.8 million cases from last November to February, there were just 47 such reinfections, the report found.

Public-health experts are also hopeful the U.S. will benefit from spring weather leading to less time indoors, where the virus can spread easily. The low base of transmission in the U.S. when BA.2 arrived might also be playing a role in slowing the variant’s spread, said Crystal Watson, a senior scholar at the Johns Hopkins Center for Health Security.

“Those are the things that are giving me a little hope,” she said, adding that she expects a U.S. surge but believes the country has a chance to avoid the levels seen in Europe.

The U.S. has some vulnerabilities relative to other nations, including vaccination rates that lag behind those of many European countries. The rate of people getting booster shots—which data have shown to be important in enhancing protection against Omicron—also fell as the wintertime surge faded. About half the booster-eligible population still hasn’t gotten an additional shot, CDC data show.

The CDC on Tuesday endorsed a second booster shot for people 50 years old and older.

—Jared S. Hopkins contributed to this article.

Write to Jon Kamp at jon.kamp@wsj.com and Brianna Abbott at brianna.abbott@wsj.com