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Last July, when the New York State Department of Health issued a report absolving the Cuomo administration of responsibility for the soaring number of COVID-19 deaths in the state’s nursing homes, Jim Malatras was tasked with handling what quickly became a storm of criticism.

Health care experts and lawmakers had derided the report as deeply flawed and designed to provide political cover for Gov. Andrew Cuomo. But Malatras, a former administration official who had been brought back from a job in higher education to assist Cuomo in responding to the pandemic, did not shrink from his assignment.

In an interview with ProPublica days after the report’s release, Malatras defended the integrity of the report, which he said had been developed by health department experts with data analysis help from the consulting firm McKinsey & Company.

Malatras said the report’s authors had used a sophisticated statistical model to reach a persuasive conclusion: Infected nursing home staff had been the chief driver of the spread of disease and death, not the thousands of potentially still-contagious patients transferred from hospitals to the homes under a Cuomo administration policy adopted early in the pandemic.

Malatras told ProPublica the report should silence the administration’s many critics, who he said had engaged in a cynical effort to blame Cuomo for contributing to the deaths of more than 6,000 nursing home residents by early last summer. He said he looked forward to the report’s critics doing their own studies.

“Write a public letter countering the report, run their own tests, and we’ll see what it looks like,” Maltatras said. “Let’s see their tests.”

One month after the release of the report, Malatras was appointed chancellor of the State University of New York system, one of the largest public university systems in the country, with scores of campuses and about 400,000 enrolled students. At the time, the SUNY Board of Trustees described Malatras as a “visionary” whose work with Cuomo made him uniquely qualified to run the sprawling higher education system at a critical moment in its history.

In the wake of new reporting by The New York Times and The Wall Street Journal, it is clear Malatras had not told the full story of the health department’s report. The Cuomo administration, it turned out, had removed from its analysis the state’s count of nursing home residents believed to have died of COVID-19 after being transferred from the homes to local hospitals. The administration’s changing of the report meant that the sophisticated analysis offered to the public last July had failed to account for thousands of additional COVID-19 deaths among nursing home residents, and the administration knew it.

In a statement, Malatras said he had played a role in shaping and editing the health department report, but had not been the one to remove the hospital deaths data. Beth Garvey, counsel to Cuomo, said in a statement the hospital deaths had been omitted at the time because the state was then still trying to make sure the count was accurate. The administration did not release the true total of nursing home deaths due to COVID-19 until last month, and when it did, the number grew by some 50%, from more than 8,000 to more than 12,000.

Gary Holmes, a spokesperson for the health department, said in a statement that the department in fact performed an analysis last July that included all deaths of nursing home residents — those who died in facilities and in hospitals — and the result was the same: The greatest surge in deaths at the homes resulted from infected workers and not the state’s policy requiring homes to accept potentially contagious patients who had tested positive for COVID.

Holmes offered no explanation for why the health department had not said so at the time. The department, he said, had now made public both the truncated July report and the more complete report including all nursing home deaths. He said the department stood by both reports.

Ron Kim, the Democratic chair of the State Assembly Committee on Aging, said anybody involved in the July report ought to resign from their positions.

“In my personal opinion, they conspired in a coordinated fraud,” Kim said.

In February, Kim accused Cuomo of personally threatening to ruin him over Kim’s criticism of the state’s handling of nursing home deaths. Cuomo has denied he ever threatened Kim.

ProPublica contacted Malatras again this week, and asked why he hadn’t previously disclosed the removal of the hospital deaths from last July’s report, whether he’d agreed at the time with the decision to remove the additional deaths, and whether he stood by the integrity of the health department’s work and his defense of it.

Citing ongoing federal and state investIgations into the Cuomo administration’s handling of the COVID-19 crisis in the state’s nursing homes, Malatras issued a short statement: “Thank you for your follow up. As I’m sure you can appreciate, given the nature of the various inquiries, I’m not going to respond to any questions beyond what I said the other day. My focus and my energies are on my job as Chancellor of SUNY, which I will continue to do every day.”

Malatras, who from 2017 to 2019 ran the Rockefeller Institute of Government, a SUNY-affiliated think tank, directed ProPublica to remarks he had made last week about his involvement with the health department report.

“Given my expertise in public policy including public health issues such as opioid misuse and health care, I was asked to help review feedback on the scientific language in that public report to make it more accessible for a general audience,” Malatras said on March 5 at an event in the Bronx. “That’s the exact role I played while at the Rockefeller Institute of Government on dozens of reports as they neared publication. As with many reports, there were back and forth with structure, citations and other language during the process, but to be clear, I included the fatalities data provided by the New York State Department of Health which I did not alter and change.”

ProPublica reached out to Merryl Tisch, chair of the SUNY Board of Trustees, to ask if she had any concerns about the role Malatras had played in the July report on nursing home deaths, but received no response. Cesar Perales, the board’s vice chair, would not comment when asked about Malatras.

The Cuomo administration’s official count of nursing home deaths due to COVID-19 has been a source of controversy almost from the outset of the pandemic. At first, New York state only counted confirmed cases of deaths from COVID-19, while other states reported both confirmed and presumed cases. New York eventually began to formally record both confirmed and presumed cases, but refused to include deaths of residents that occurred at hospitals in nursing home figures, record keeping that was routine in many other states.

Republican and Democratic lawmakers in both Albany and Washington hammered the administration for refusing to disclose the deaths in hospitals, and accused Cuomo of trying to hide the full scale of the state’s failures to protect the population most at risk of being killed by the virus.

For months, the Cuomo administration claimed it couldn’t release the number of additional deaths because it was struggling to make sure they were accurate, an assertion ridiculed by public health experts and nursing home industry leaders. Counting COVID-19 deaths of nursing home residents no matter where they died was not complicated, they said, especially for a health department regarded as among the best in the nation.

Questions about the true scope of nursing home deaths in the state intensified after the Cuomo administration issued a policy on March 25, 2020, stating that nursing homes had to accept patients who were released by hospitals after testing positive for COVID-19 and deemed “medically stable” enough to be transferred. The homes were barred from testing the patients to see if they were still infected.

Nursing home operators and families of residents objected to the policy, saying it needlessly put already vulnerable residents at greater risk. Republican critics of Cuomo claimed the policy led to thousands of needless deaths.

The July report issued by the Department of Health asserted that such claims were not true. It said data showed that the greatest peaks of deaths in the homes mostly followed peaks in infections of staff members, and preceded peaks in nursing home admissions from hospitals. It dismissed the idea that the March 25 policy had any strong impact on the number of deaths.

The revelations of the last week, however, make clear that the July report had omitted many deaths from its analysis. The health department indeed tracked the numbers of residents who died of COVID-19 in nursing homes and at local hospitals, and was confident enough of the accuracy of the numbers to include them in a draft of the July report, according to interviews and a review of documents by The New York Times. Those numbers showed that the true death toll was closer to 9,000 by July than the publicly acknowledged 6,000.

“The health department knew what the numbers were, and wanted them in the July report,” said Bill Hammond, a policy analyst at the Empire Center, an Albany think tank. “They were the ones with the Ph.D.s. They were the scientists. They had done the work. Taking the numbers out was simply indefensible.”

Denis Nash, an epidemiologist who is executive director of the City University of New York’s Institute for Implementation Science in Population Health, agreed.

“The original approach was flawed from an epidemiological and causal inference standpoint,” Nash said. “The missing deaths was one of several red flags. Would any study be valid if it excluded deaths known to occur in hospitals versus in a nursing home? No, that would be a fatal flaw.”

The Empire Center, which successfully sued the Cuomo administration this fall to force the release of the hospital deaths, recently issued its own study on the possible impact of the administration’s March 25 directive, which led to more than 6,000 transfers of COVID-19 patients from hospitals to nursing homes. Hammond said that while the study showed the directive had not been the primary cause of the greatest surges in nursing home deaths, there was still reason to believe it had led to as many as 1,000 additional deaths in the homes.

“The entire thrust of our report was that the health department’s claims that the March 25 directive did not have any meaningful correlation to deaths in the homes was wrong.”

The administration did not respond when told of Hammond’s assertions.

Malatras is a longtime confidante of Cuomo, having served as his chief of operations from 2014 to 2017. He rejoined Cuomo as the pandemic worsened last spring, and became one of the governor’s three or four closest advisers on the state’s response.

The New York Times reported late last week that Malatras and several other senior advisers to Cuomo reworked the health department’s July report, and that a decision was made to remove the hospital deaths for fear the complete numbers would be an embarrassment for the governor.

Garvey, Cuomo’s counsel, issued a statement after the Times’ report, saying that the ultimate decision to remove the hospital deaths was made by “the Chamber.” Hammond said he regarded “the chamber” to be a coy way of conceding without saying so directly that the governor himself made the decision. An administration spokesperson did not respond when asked what Garvey meant by “the chamber,” and about Hammond’s interpretation.

Garvey said the Cuomo administration had long acknowledged it wasn’t making public the count of deaths in hospitals, but noted that the deaths had always been included in the total figures for COVID-19 deaths in New York state.

Back in July, days after the health department report was made public, ProPublica asked Malatras about what methodology the report had used, who had written it and why the administration had claimed it was peer-reviewed. Malatras would not say who authored the report and conceded the analysis had not been peer-reviewed in the way a report in a medical journal would have been.

At the time, Malatras said nothing about the removal of hospital deaths or whether he or any other senior aide to Cuomo had played a role in reworking aspects of the report.

“Some people alleged that the spread of infection came from early cases; some people said it was due to the amount of personal protective equipment; some said it was the relative age of residents; some said it was the quality of the facilities,” he said of the questions the report tried to answer. “So we measured that. We took the independent variables and measured it against the fatalities.”

Malatras added at the time: “This is a sort of academic study. You can’t with 100% certainty say none of the cases were due to admissions or age or other things. Of course not. That’s not what an academic study does; it takes data and says what are the strongest variables. We found it was the workforce.”

ProPublica asked a McKinsey spokesperson if the firm had been aware of the removal of the hospital deaths and whether it was comfortable with that decision and with the limited report that was released last July. The firm said it could not comment.

When the SUNY Board of Trustees named Malatras as chancellor last August, the board said it had forgone a national search, instead looking only at candidates within its ranks, because of the urgency of the moment, as colleges across the country wrestled with how to deliver for their students during the pandemic. Malatras had served as chancellor at a SUNY campus, Empire State College, prior to rejoining the administration during the pandemic.

“A critical lesson learned from Covid-19 is that a pandemic demands urgent action,” board member Stanley Litow wrote after Malatras had been appointed. Of Malatras, Litow wrote, “Importantly, New York Governor Andrew Cuomo turned to him to help manage the overall effective statewide response to the pandemic where he worked closely with all agencies, especially those in health and economic development areas.”

Lawmakers from both major parties raised alarms about the appointment of Malatras, objecting to the decision not to conduct a national search and questioning whether someone so close to Cuomo could truly be an independent protector of the state university system. The Board of Trustees was unmoved.

“Covid-19 is a pandemic with no precedent,” Litow wrote. “Finding the right new leadership for SUNY required prompt and effective action. Breaking with tradition will prove to be the right decision.”

Litow did not respond to a request for comment on Malatras and his role in crafting and defending the July report.

Joaquin Sapien contributed reporting.