Vehicles are lined up at a drive-in Covid-19 testing center at Charles R. Drew University of Medicine and Science in South Los Angeles. | Mario Tama/Getty Images

OAKLAND — California's top health official said Friday the state has identified why its infectious disease reporting system failed and is working through a backlog of 250,000 to 300,000 records — a glitch that has stymied decision-making at the state's highest levels.

“Bottom line, our data system failed,” said Mark Ghaly, secretary of the California Health and Human Services Agency, offering an apology to residents for the blunder.

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County officials across California this week have flagged problems with the state's data reporting system, saying it has resulted in an undercount of Covid-19 cases. That has made it difficult to determine case trends and has affected whether counties can allow certain sectors to move forward — most notably in-person instruction, right as the school year begins.

California has had more than 524,000 cases, the most of any state in the nation, as well as 10,000 deaths. Despite the data issues, Ghaly said he still believes California is seeing cases decline and a lower positivity rate, while hospitalizations are also falling.

“We do feel confident in the trend … and believe the trend has been stabilizing and coming down,” he said.

Ghaly said the data problem started July 25 and was centered on a server outage that created delays in lab results coming into the California Reportable Disease Information Exchange, known as CalREDIE.

At the same time, he said, a certificate involving one the state’s largest commercial labs, Quest Diagnostics, wasn’t renewed at the end of the month, preventing lab results from flowing into the system for four to five days. He said the state has since renewed the certificate, which was required by an intermediary that Quest uses to route results to the state.

Ghaly said the state has resolved the issues with the CalREDIE system, but acknowledged that it wasn’t built to handle the volume of lab results created by the pandemic. He said the state is looking to develop a new lab system specifically for Covid-19.

Not all of the 250,000 to 300,000 records are coronavirus cases, Ghaly said, since the system handles results for all reportable infectious diseases.

The state health leader said Friday for the first time that the state froze its watch list a week ago due to a separate issue — transitioning to new federal reporting requirements for hospital data. The state relies on those metrics to help determine whether a county must remain on a watch list and impose stricter requirements on businesses and activities.

Thirty-eight of California's 58 counties are on that list, representing nearly all of the state's population, and many are tracking their status by the day, if not the hour. The CalREDIE problem has led counties and the state to halt waivers for elementary schools that want to open in-person instruction, a process Gov. Gavin Newsom just announced Monday.

The state first revealed Tuesday that technical glitches in the CalREDIE system were likely leading to a “significant” undercount in the number of cases — but only after counties began going public.

County health officials expressed frustration, saying that the glitch has crippled their ability to assess the epidemic in their communities.

The data issue has revealed internal communications problems within the state Health and Human Services Agency. Ghaly said he was not aware of the CalREDIE issue until Monday afternoon — after Newsom went public with a rare bit of “good news” that the state's seven-day average daily case count had dropped 21 percent.

Ghaly was forced to acknowledge Tuesday that the governor's figure was likely wrong due to the case undercount. He said Friday that some state health officials were aware of data problems prior to Monday and that his office was examining their internal processes.

Meanwhile, the California Department of Public Health on Wednesday told POLITICO that it was still collecting hospitalization data and suggested it was still using that information as criteria to determine county watch list status. While going through the transition to the federal data system, “CDPH is in continuous communication with counties to understand the conditions and data to determine if a county is still outside of threshold,” the department said.

But Friday, Ghaly announced that the watch list of 38 counties was actually frozen in place because of the hospital data transition five days before CDPH's statement to POLITICO.

Alexander Nieves contributed to this report.

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