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Death-certificate data show the total number of U.S. Covid-19 deaths this year exceeded those in 2020, when the pandemic first altered daily life in the country and before the widespread rollout of vaccines.

States have reported at least 186,000 Covid-19 deaths since the end of July, around the time the highly transmissible Delta variant began to increase mortality numbers, Johns Hopkins data show. Delta’s emergence threw off the nation’s earlier progress against the virus, largely by exploiting the still-unvaccinated population, according to infectious-disease experts.

Public-health officials are now closely watching for any impact that may come from the new Omicron variant, which accounted for an estimated 2.9% of Covid-19 cases nationwide as of Dec. 11.

“I thought that the fall would look a lot different,” said

Ryan Demmer,

an epidemiologist and associate professor at the University of Minnesota School of Public Health. “I just hadn’t foreseen that so many different variants would be coming out and there would be so much vaccine hesitancy.”

About 64.8% of eligible Americans are fully vaccinated, according to data from the U.S. Centers for Disease Control and Prevention, including 70.4% of those aged 12 and older and 87.2% of those 65 and older. Vaccination rates vary widely across the U.S., with some communities reporting rates far above national totals and others far below them.

Infectious-disease experts say vaccination is the best defense against Covid-19. Shots available in the U.S. have proved to significantly lower the risk of hospitalization and death.

President Biden on Tuesday urged Americans to get vaccinated, as he commemorated those lost to Covid.

“I know what it’s like to stare at an empty chair around the kitchen table, especially during the holiday season, and my heart aches for every family enduring this pain,” he said. “As we head into the winter and confront a new variant, we must resolve to keep fighting this virus together.”

A report released Tuesday by the Commonwealth Fund, a healthcare research foundation, found that widely available vaccines in the U.S. prevented about 1.1 million additional deaths and more than 10.3 million additional hospitalizations. The federal government recently authorized Covid-19 boosters for adults and some teenagers to help extend protection from the virus.

“That’s what makes this continued loss of life so tragic,” said

Wafaa El-Sadr,

a professor of epidemiology and medicine at Columbia University’s Mailman School of Public Health. “We know these are preventable deaths in many ways.”

Across the U.S., the seven-day average of newly reported Covid-19 deaths sits at 1,260 a day, according to a Wall Street Journal analysis of Johns Hopkins data. In early July, that average hit as low as 223 deaths reported a day, as vaccines had become more widely available several months earlier. At the pandemic’s peak in January 2021, there was at one point an average of 3,403 new deaths reported each day, data show.

Since the start of the pandemic, states predominantly in the south—Arkansas, Louisiana, Mississippi, Alabama, Georgia and Florida—and other places including Arizona, New Jersey and New York City have reported the highest Covid-19 death rates in the country, according to the CDC.

The true number of fatalities linked to the disease is likely higher, both in the U.S. and world-wide, due to inconsistent reporting and the lack of available tests to confirm infections early in the pandemic.

Between Feb. 1, 2020, and late November, there have been more than 902,000 excess deaths in the U.S., according to the CDC, reflecting what public-health experts say are both missed Covid-19 cases and collateral damage from the pandemic, such as surging drug overdoses.

Hospitalizations linked to Covid-19 have been rising recently in cold-weather states, with the latest data reported by the Department of Health and Human Services showing 67,306 Covid-19 patients in hospitals around the U.S., compared with 47,411 a month earlier. Numbers remain down from the 105,111 hospitalizations reached at the end of August, when the Delta surge was hammering many southern states before fading in the fall.

Some northern states including Maine, New Hampshire and Michigan have recently seen record hospitalizations. Most U.S. hospitalizations are among the unvaccinated, according to the CDC.

The rise is straining hospitals yet again and worsening burnout among some staff. Minnesota hospital leaders this week urged residents to get vaccinated or receive booster shots in full-page newspaper ads describing overwhelmed emergency departments and scarce beds. “Every day we’re seeing avoidable illness and death as a direct result of COVID19,” the ad said.

The U.S. on Monday surpassed more than 50 million reported Covid-19 cases, according to Johns Hopkins data. Confirmed cases started to increase across the country again in November. Midwestern and northeastern states including Minnesota, New Hampshire, Rhode Island, Maine, Michigan, Indiana, Vermont and Massachusetts are reporting the highest rates of new Covid-19 cases in the U.S. over the past week, according to the CDC.

The rise in cases and the busy holiday season have prompted some state leaders to reimpose restrictions. California said Monday that masks would be required in all public indoor settings, regardless of vaccination status, for one month beginning Dec. 15. In New York, a mandate requiring masks in indoor public places—unless those spots required proof of vaccination—took effect Monday. It also ends Jan. 15.

—Jon Kamp contributed to this article.

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The Omicron Variant

Related coverage, selected by the editors

The New Omicron Covid-19 Variant: What to Know

Study Finds Two Pfizer Vaccine Doses Offer Less Protection Against Omicron

Omicron Accounts for 3% of U.S. Cases

Better Tests Provide Clues to Omicron’s Spread

U.S. to Tighten Rules for Travelers

What It Means for Travel

The Threat to Global Economies

Symptoms and Vaccines: What Scientists Are Saying

Write to Jennifer Calfas at Jennifer.Calfas@wsj.com