Buffeted by covid-19, struggling with crumbling finances, one of America’s largest nursing home chains gave its CEO a $5.2 million “retention payment” in late October, just as the second big wave of the pandemic was rising.

On Jan. 5, nonetheless, George Hager Jr. retired as head of Genesis HealthCare.

He will have to pay an unspecified amount of the money back, to avoid certain tax liabilities, according to an SEC filing by the company, but he will apparently be reimbursed over the next two years. The Genesis board also agreed to give him an immediate $650,000 bonus and a $300,000 consulting contract, according to the filing. The company would not elaborate on the arrangement.

Under Hager’s leadership the more than 300 Genesis nursing homes experienced 14,352 confirmed cases of covid-19 through mid-December, according to reports the company made to Medicare officials. The total number of residents who died of the disease was 2,812, as of Dec. 20. Both figures are higher than in comparable nursing home chains.

Nearly all of the company’s nursing homes reported continuing shortages of personal protective equipment through the months of the pandemic, according to a Washington Post analysis of Medicare data, with the situation easing only toward the end of November — after Hager’s big payout was approved.

Since last summer, Genesis, which has been signaling a financial squeeze since 2017 in its reports to the SEC, has been warning investors it may not be able to continue as a going concern because of high costs and low occupancy rates exacerbated by the pandemic.

“5.2 million is a lot of money given that nursing homes have been squawking about a lack of cash,” said Brian Lee, executive director of an advocacy group called Families for Better Care. “Yet they can take care of those they love best — those at the top.”

The company noted Hager’s base salary of $900,000 had not been increased since 2017. He also received a $935,000 annual bonus in 2020.

In a November conference call, the company’s chief financial officer, Tom DiVittorio, said, “We are more dedicated than ever to providing the highest quality care possible.”

The American Health Care Association, which represents for-profit nursing home chains such as Genesis and other health-care providers, has been vigorously lobbying for more federal assistance to meet the costs of the pandemic, on top of the more than $10 billion that the federal government has already committed to nursing homes for emergency aid.

“Our nursing home providers are facing the worst financial crisis in the history of the industry due to increased costs related to covid,” said the head of the association, Mark Parkinson. “Without adequate resources, the U.S. will repeat the same mistakes made during the initial outbreak last spring.”

A survey of its members, the association reported, found that 86 percent of nursing homes are operating at a profit margin of 3 percent or less.

Critics point out, however, that some nursing home operators have become adept at funneling profits to affiliated companies, from which they buy a variety of services. A Washington Post investigation found the California-based Brius chain has become a leader in this field. A Post analysis found Genesis is within the top five chains nationally in the amount of money each nursing home pays to affiliated entities. As income streams are dispersed, care suffers.

For-profit chains, which control about 70 percent of American nursing homes, have made the most use of this practice. “The residents are wasting away in soaked diapers and bowel movements for hours because the nursing homes are too cheap to do anything about it,” Lee said. “They’re concerned about padding the bottom line at the expense of our loved ones.”

Genesis is in worse financial shape than most, despite considerable government assistance.

Through the first three quarters of 2020, the company said it received $254 million in federal relief tied to the pandemic, and pledges of $85 million from several of the states where it operates. An additional $90 million in payroll taxes was deferred. Medicare prepaid $157 million this year, as well — effectively providing an interest-free loan, but one that must be paid back starting this spring unless the terms are changed.

Yet it still reported a loss of $96 million for its 360 nursing homes and assisted-living centers during that period. (Fourth-quarter figures have yet to be reported.)

The company is based in Kennett Square, Pa., and its nursing homes in Connecticut, Massachusetts, New Jersey, Maryland and Pennsylvania were especially hard hit by the coronavirus when it erupted last spring. In Windsor, Conn., 47 residents died at Kimberly Hall North; 42 died at St. Joseph’s, in Trumbull; at Chapel Manor, in Philadelphia, 38 died, and at Voorhees Center in New Jersey, 42 died.

The chain’s overall covid death rate was higher than among some of its major competitors. One way to assess the rate is to compare deaths with the number of beds (though that does not take into account occupancy figures or turnover among residents). By that measure, Genesis nursing homes had 1 death for every 12.5 beds. Signature Healthcare had 1 death for every 14.3 beds; Consulate Health Care, 1 death for every 20 beds; and Life Care Centers of America was at about the national average of 1 death for every 16.7 beds.

“CEO compensation is determined by the compensation committee of our board of directors, composed entirely of three independent directors,” DiVittorio said in a statement provided to The Post after Hager retired. “The compensation committee works closely with an independent consultant to examine the effectiveness and reasonableness of our executive compensation program. The CEO base salary has remained unchanged since 2017 with 75 percent of comparable CEOs paid more.”

DiVittorio defended the company’s handling of the pandemic.

“Genesis has been not only fully operational on the frontlines of this virus — our leadership and employees have been working around the clock to keep our patients, residents and staff members as safe as possible,” he said. “Genesis has paid out tens of millions of additional ‘hero’ dollars to our staff and support staff on the frontlines of this battle. We thank them for their dedication and support. They are true heroes.”

In addition to approving the retention payment for Hager, the Genesis board also decided in October to put aside $2.1 million in a trust the company described as beyond the reach of creditors, to be used for bonuses for seven of the company’s high-ranking officers.

Through the spring, summer and early fall, most Genesis nursing homes reported shortages every week of masks and protective eye gear. Unlike some other chains, the company has not reported significant staff shortages. In the November conference call with analysts, Hager said the company had been seeing sharp increases in overtime pay and wages for temporary workers. In New Jersey, second quarter labor costs were up 65 percent over the same period in 2019, he said.

“There is no question Genesis will need ongoing support from the federal government and our capital partners to sustain operations,” Hager said in that call. “We are aggressively managing liquidity at every turn. That being said, we are still burning cash.”

Genesis shares, which traded at $1.77 in February, hit a low of 48 cents in late December, but have been volatile so far this year following Hager’s retirement, rising since states have begun to administer the coronavirus vaccines.

Part of Genesis’ business is providing rehabilitation services to other nursing home chains. Hager said that sector has been “resilient throughout the pandemic.”

Hager had been CEO since 2003, guiding the company out of a 2000 bankruptcy. In 2017, Genesis agreed to pay a $53 million settlement in a federal false claims case. The government alleged companies later acquired by Genesis had submitted “false claims to government health care programs for medically unnecessary therapy and hospice services” and provided “grossly substandard nursing care.” In paying the settlement, Genesis did not acknowledge wrongdoing.

Genesis has been hobbled by some of the highest rental and lease costs of any major chain. Its nursing home real estate is typically owned by other investors, and the leases often contain mandated annual increases. Except for some loans guaranteed by the Department of Housing and Urban Development, most of the loans taken out by Genesis have interest rates of between 6.5 percent and 14 percent, according to its SEC filings — far higher than a typical home mortgage, for instance.

The company’s real estate costs are especially high in Virginia and West Virginia, a Post analysis of cost data reported to the Centers for Medicare and Medicaid Services found. DiVittorio declined to comment on those expenses.

Genesis said it is working with its creditors in a bid to restructure its $1.5 billion long-term debt.

While Hager is staying on as a consultant, the Genesis board chairman, Robert Fish, will take over as CEO. “I am pleased to become Genesis’s chief executive officer and am excited to lead the company as we look to emerge from the pandemic and navigate to recovery,” Fish said in a prepared statement.

Fish’s base salary is $1,150,000. The board gave him a $350,000 signing bonus and promised $1 million more if he meets certain goals by the end of June. He is also eligible for a $1.3 million annual bonus.

Joel Jacobs contributed reporting.