A chaotic vaccine rollout and allegations of a cover-up threaten Cuomo’s perch.Mr. Cuomo conceded that his administration’s lack of transparency about how it counted coronavirus-related deaths in the state’s nursing homes had been a mistake.By Bryan Pietsch, Jesse McKinley and Ron DePasquale

Gov. Andrew M. Cuomo of New York wrote the book on pandemic leadership, literally. He won an International Emmy for his TV briefings during the outbreak’s early months. Now, his self-created image as America’s Covid-19 governor may be threatened by his efforts to protect it.

Mr. Cuomo conceded on Monday that his administration’s lack of transparency about how it counted coronavirus-related deaths in the state’s nursing homes had been a mistake.

The pandemic has ravaged nursing homes across the country. But as recently as late January, New York was reporting only about 8,500 nursing-home fatalities, excluding virus-related deaths that occurred outside those facilities, such as in hospitals. Now, with those included, more than 15,000 residents of New York’s nursing homes and long-term care facilities are known to have died from Covid-19.

The spike came after the state’s attorney general, Letitia James, accused the Cuomo administration of severely undercounting deaths connected to nursing homes. The state quickly updated those numbers, adding thousands. A court order has since led to more updates and an even higher number.

Speaking Monday in the State Capitol, Mr. Cuomo made his first remarks since a top aide to the governor, Melissa DeRosa, privately told some state lawmakers last week that the state had withheld data from the Legislature. She said it had feared that the Trump administration would use the information to begin a federal investigation into the state’s handling of nursing homes.

The governor echoed Ms. DeRosa’s comments and acknowledged that by failing to answer questions from state lawmakers, the public and the news media, the state created a void that was “filled with skepticism, cynicism and conspiracy theories which furthered confusion.”

The revelation that data was withheld from lawmakers has prompted accusations of a cover-up and calls from lawmakers in both parties for the Democratic governor to be investigated and stripped of the emergency powers that he has exercised during the pandemic.

President Trump’s Justice Department never formally opened an investigation. But the episode has cast a shadow on the governor’s record on nursing homes, darkening his carefully cultivated image as a competent executive beholden to facts. In October, Mr. Cuomo published a memoir, “American Crisis,” offering “leadership lessons” from his approach to the pandemic, which has killed more than 45,000 people in New York.

The nursing-home revelations are “really potentially politically problematic” for Mr. Cuomo, who plans to run for a fourth term in 2022, said Patrick Egan, a political-science professor at New York University. But he added that if the governor successfully pushes for the vaccinations of large numbers of New Yorkers, his transgression “may be long forgotten.”

New York ranks 38th among states in vaccinating its population with at least one shot, according to a New York Times database.

The governor has been eager to expand vaccine access, most recently to millions of New Yorkers with chronic health conditions. He has done so even as demand outstrips supply by far.

New Yorkers lined up to receive the vaccine at sites around the city on Monday, a day after people inundated a state website and call center and found a shortage of appointments.

Last month, state officials scrambled to loosen vaccine eligibility restrictions after medical providers said they had to throw out vaccine doses because they were struggling to find patients who fit the guidelines.

Vaccination bottlenecks “could very quickly resolve themselves,” Dr. Egan said, but Mr. Cuomo’s reputation as a pandemic leader could lose its luster if investigations brought damaging revelations.

“We just don’t know if it’s going to metastasize into a bigger problem,” he said. “Are there more things that the government withheld?”

The governor echoed Ms. DeRosa’s comments and acknowledged that by failing to answer questions from state lawmakers, the public and the news media, the state created a void that was “filled with skepticism, cynicism and conspiracy theories which furthered confusion.”

The revelation that data was withheld from lawmakers has prompted accusations of a cover-up and calls from lawmakers in both parties for the Democratic governor to be investigated and stripped of the emergency powers that he has exercised during the pandemic.

President Trump’s Justice Department never formally opened an investigation. But the episode has cast a shadow on the governor’s record on nursing homes, darkening his carefully cultivated image as a competent executive beholden to facts. In October, Mr. Cuomo published a memoir, “American Crisis,” offering “leadership lessons” from his approach to the pandemic, which has killed more than 45,000 people in New York.

The nursing-home revelations are “really potentially politically problematic” for Mr. Cuomo, who plans to run for a fourth term in 2022, said Patrick Egan, a political-science professor at New York University. But he added that if the governor successfully pushes for the vaccinations of large numbers of New Yorkers, his transgression “may be long forgotten.”

“We just don’t know if it’s going to metastasize into a bigger problem,” he said. “Are there more things that the government withheld?”

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