A penetrating new audit of the Health Department’s pandemic response makes clear that problems at the agency run much deeper than its misreporting of nursing home deaths.

The audit released Tuesday by Comptroller Tom DiNapoli examines in detail what the department knew during the early weeks of the COVID-19 outbreak – and provides further confirmation that officials were aware of thousands more deaths than they shared with the public.

Just as importantly, however, the audit explores what the department didn’t know, due to long-standing flaws in its early-warning system for nursing home outbreaks and shortcomings in its data analysis capabilities.

The report further documents that New York was slower than many states to inspect nursing homes for their infection control procedures even as the state was suffering one of the deadliest outbreaks in the world.

Also concerning was the department’s handling of the 18-month audit process, as explained in an unusually stern statement from the comptroller’s office: “DOH imposed impediments on the audit, including delaying requested data, limiting auditors’ contact with program staff, not addressing auditors’ questions during meetings, and not providing supporting documentation. These are not routine actions by state agencies undergoing an Office of the State Comptroller audit and raise serious concerns about the control environment at DOH.”

While there is room for debate about some of the comptroller’s conclusions, the audit raises questions that deserve open and honest discussion – and reform – not defensiveness and stonewalling.

Here are some of the noteworthy findings: 

Officials distorted the timeline of events. Former Governor Cuomo claimed in his book that his March 13, 2020, order banning most visitors from nursing homes came “even before New York had a single COVID death.” In fact, Health Department data reviewed by auditors shows that the first reported COVID death in a nursing home occurred on March 3, and nine residents had died by March 13.

Similarly, a Health Department report originally published in July 2020 – which was heavily edited by the governor’s office – said the first employee infection “known at the time” was March 5, and the first resident infection “known at the time” was March 11. This is one of many uncorrected errors and falsehoods in the report, which is still posted in updated form on the department’s website.

Officials used these timelines to argue that they had moved promptly to protect residents – and to deny that a March 25 order sending infected people into nursing homes had made things worse. By the time that report and governor’s book were written, officials would have known those dates were wrong.

An early-warning system was undermined by widespread non-compliance. Nursing homes are supposed to alert the Health Department about infectious diseases spreading among their residents through a program known as Nosocomial Outbreak Reporting Application, or NORA.

Auditors found, however, that some facilities had not notified this system of a single sick patient in as many as three years. 

Throughout March 2020, facilities reported just 176 cases of COVID to the NORA system – even as the department separately documented 705 deaths at 160 facilities.

As auditors noted: “The Department has been aware that certain facilities were failing to report incidents through NORA at least since 2015 but has not followed through on plans to address the issues.”

DOH was relatively slow to conduct infection-control inspections. On March 4, 2020, the federal Centers for Medicare & Medicaid Services directed states to suspend their routine inspections of nursing homes and focus instead on infection-control surveys, intended to assure facilities were taking proper precautions to minimize the spread of COVID.

Citing a federal inspector general’s report, auditors found that New York had completed inspections for only 20 percent of homes by May 30, compared to 50 percent for Florida and Texas and 90 percent for California.

It further faulted the agency for not making better use of data collected through NORA and other systems to prioritize higher-risk homes for attention – not to mention detecting patterns and trends, such as outbreaks of unknown diseases.

“Based on prior audit findings, we have discerned a pattern by the Department of focusing on meeting minimum standards rather than ensuring that programs’ objectives are met,” the report said. 

The auditors suggested that “persistent underinvestment in public health over the last decade may have limited the Department’s ability to prepare and respond in the most effective way.”

A lack of communication left local public health agencies in the dark. Echoing media accounts, officials from the New York City Department of Health and Mental Hygiene and other local public health agencies reported what auditors described as “serious communication deficiencies” in the state Health Department. 

When local officials called the Department for information, the few contacts who would speak to them would “backchannel” information as they were not allowed to officially speak to them. County officials also stated that the Department would arrive on site at the county departments but would not share information on their activities – even to those county officials responsible for administering policy at the local level. …

Outside of advisories and alerts via the Health Commerce System, the Department did not provide guidance on data collection and reporting, and through the pandemic, DOHMH and the Department did not have matching data for the same metrics. In addition, many of these advisories and alerts were received after New York City was already experiencing and dealing with the issue on the ground in real time.

Officials noted that routine, staff-level communications with the Department were not helpful as they were not able to answer questions about the guidance, solicit or incorporate feedback from the local level, or give them advance notice prior to the public release of information.”

Top management created an unhealthy work environment. The audit emphasized that many of the department’s problems were linked to a “negative control environment,” an accounting term for organization’s overall management and culture.

As our audit evolved, the control environment was identified as a common denominator across our findings – a negative control environment that spawned systemic internal control deficiencies, thwarted transparency and accountability, and undermined the Department’s mission and responsibility to the public. As supported by prior audits and various investigative reports, the Department was plagued by a threatening environment of intimidation, closed ranks, and lack of commitment to openness – at the expense of the public’s trust.

In a response appended to the audit report, Kathryn Garcia, Governor Hochul’s director of state operations, contended that the new administration has tried to improve the control environment in the Health Department and elsewhere: “We want to assure [the comptroller’s office] that upon taking office, Governor Kathy Hochul directed her administration to dramatically change course and prioritize transparency, including cooperation and communication with oversight agencies on all levels.”

But the Health Department’s own response – delivered by Acting Executive Deputy Commission Kristin Proud, a longtime Cuomo appointee – suggested that not everything has changed.

Addressing the under-reporting of nursing home deaths, department said:

Whatever criticisms may now be directed at the prior Administration relating to issues of transparency, or the particular categories of information that were publicly disclosed, those ultimately were matters for the Executive Chamber of the prior Administration and not Department personnel. The Department’s use and analysis of available data for public health purposes was not affected or constrained in any way by the prior administration’s public reporting determinations …

To the contrary, the department’s former highest-ranking official, former Commissioner Howard Zucker, repeatedly echoed Cuomo’s distorted claims, failed to set the record straight and resisted requests for complete and accurate information.

And the department’s use and analysis of data was clearly constrained when it came to the July 2020 report, which was replete with errors, omissions and dubious analysis. Those flaws may have been added by Cuomo and his aides, but the report was published in the department’s name, and remains posted, uncorrected, on the department’s website.

In her personal response to the audit, Hochul set a more constructive tone: “I do want to look back,” she told reporters on Wednesday. “I want to continue working with the comptroller and find out every aspect of the pandemic — what was done right, what was done wrong, should we be in that same situation again.”

Although Cuomo and Zucker bear responsibility for many of the failings of the state’s pandemic response, their departure alone does not assure the state’s readiness for the next virus. That requires an in-depth, systematic review of policies, procedures and performance – and DiNapoli and his auditors have provided a model for how it should be done.