Former Pennsylvania Health Secretary Rachel Levine faced tough questioning Thursday during a Senate confirmation hearing regarding reported discrepancies in state records on COVID-related nursing home deaths.  

Levine was nominated by President Biden to serve as assistant secretary at the Department of Health and Human Services.

"You assured me that Pennsylvania did not do what New York did, that it accurately reported," Sen. Susan Collins, R-Maine, said to LevineThursday. "However, I am told that in September of 2020, Spotlight PA reported issues with inadequate disclosure of cases and deaths in nursing homes," she continued, pointing to facilities that were found to have reported "no data" while the facilities claimed they had.

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Levine said these discrepancies could be explained because of "lag time" between when a death was reported to when it hit Pennsylvania’s electronic death reporting system (EDRS).

But the Keystone state publication -- Spotlight PA -- alleged the "lag time" explanation given by Levine Thursday, did not actually answer for the discrepancies they found.

The problem originated after nursing homes were "self-reporting" their coronavirus cases and deaths to the state health department through separate online portals, not through the state’s EDRS, as Levine alleged Thursday.

The lack of uniform reporting allegedly led to irregularities and incomplete records.

In an attempt to remedy the reporting anomalies, Pennsylvania’s health department informed nursing home administrators in a June 18 letter that they could face fines or prison time if they did not comply with the state’s reporting requirements.

Spotlight PA found that though facilities claimed they were submitting their coronavirus nursing home data through the state system, irregularities persisted. 

In addition, the facilities were either frustrated by the fact that their public-facing data were chock-full of errors, or could not explain why their data were excluded from the state’s weekly reports entirely.

But the health department told Fox News that the significant issue is still largely facilities misreporting. 

"The ongoing challenges associated with long-term care facilities self-reporting of COVID-19 cases is not an issue of inaccuracy on the part of the department, but rather of the accuracy and ability of facilities to report separately to the department amid work to keep residents safe and protected – a priority that should be first and foremost," health department spokesman Barry Ciccocioppo told Fox News. 

"Most of the facilities are reporting data, and we appreciate that," he added. "We do have some facilities that are reporting inaccurate data and we continue to work with them."

Investigative reporting by Spotlight PA found that the errors continue to plague the state’s EDRS. On Feb. 17, 139 facilities recorded "no data," followed by missing data for 145 facilities in the week following, on Feb. 23.

The Department of Health said that "lag time" is attributable to "data dumps" that have occurred during peak coronavirus cases and deaths in the state. 

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More than half of all deaths reported in Pennsylvania came from COVID-19 cases found in nursing homes.

Pennsylvania has reported nearly 923,000 cases of coronavirus since the pandemic started, with close to 24,000 deaths –12,355 of which have been reported by nursing homes.

The Department of Health made clear that all nursing home-related deaths are reported by the nursing home, not by the hospital. 

"Unlike New York, Pennsylvania does not report the death of a nursing home resident as a hospital death. Period," Ciccocioppo told Fox News. "If an individual was a nursing home resident, contracted COVID-19 and later died, whether in the nursing home, at the hospital, or even at home, it is considered a nursing home death."