Philadelphia’s child vaccination rates were wrongly inflated for weeks because the city’s health department counted thousands of vaccinated children twice, the city’s health commissioner said.

The Philadelphia Department of Public Health was wrong last week, Health Commissioner Cheryl Bettigole said Tuesday, when it blamed the error on merging data from Pennsylvania’s health department into its own records. It is the latest in a series of embarrassing gaffes plaguing the department since the start of the pandemic two years ago.

“It is deeply frustrating, and I try really hard to make sure I only say things that are true,” Bettigole said in an interview with The Inquirer. “This is an incredibly hardworking staff that made an honest mistake.”

For weeks, the city had reported a vaccination rate for children 5 to 11 of more than 50% — far higher than national and regional averages. In early March, The Inquirer identified discrepancies in the vaccination rate for those children, and a week later, the health department acknowledged the true vaccination rate was closer to a third.

The city’s analysis corrected the data, but misunderstood the cause of the error, Bettigole said. When she reviewed the data Friday, she said she realized the math still didn’t make sense if the state data were to blame. Her review came the same day The Inquirer filed a series of requests seeking details on how vaccination rates were calculated.

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The health department failed to distinguish between first and second doses when it calculated the pediatric vaccination rate for its public-facing online dashboard, so thousands of children who had completed the two-dose series were counted twice, falsely inflating the overall number to have received a shot. The health department has removed from its dashboard raw counts of child vaccinations, but last week reported about 44,000 5- to 11-year-olds had received at least one dose. The city has estimated there are about 134,000 children in that age range in Philadelphia, and 26% of them have received second doses.

The state data didn’t factor into the problem with the rate for 5- to 11-year-olds, Bettigole said, though she said it was the cause for incorrect adult vaccination rates. The rate of fully vaccinated residents 18 and older had been reported at 82%, when the correct number was just over 76%.

The U.S. Centers for Disease Control and Prevention also release data on Philly residents and their vaccination rates. Comparing the city’s rates with the numbers provided by the federal government could have — and potentially should have — shown city officials that their numbers were wrong. The CDC has access to more data than the city does — namely, the vaccinations administered by federal entities to city residents. As a result, CDC vaccination rates should always be higher than the city’s reported numbers. But the rate that Philly reported last month for first dose vaccination among children was actually higher than the CDC’s number, by more than 10 percentage points, according to an Inquirer analysis.

After the city revised its number on March 9, its rate finally fell below the CDC’s reported pediatric vaccination rate.

Bettigole was aware there were problems with the city’s vaccination rates by Feb. 16, she said, but didn’t publicly acknowledge the issues until last week to give her staff time to thoroughly analyze how the errors occurred and correct them.

“If I was going to tell Philadelphia the numbers were wrong, I wanted to make sure the new numbers were right,” she said. “I didn’t want to further undermine confidence by being wrong again.”

The errors are the third highly publicized misstep from Philadelphia’s health department during the pandemic.

  • At the beginning of 2021, the health department failed to properly vet Philly Fighting COVID, a vaccine distribution operation run by college students that allegedly mishandled vaccine doses, gave shots to the organizers’ family and friends, and changed its privacy policy to allow it to sell the personal information of people who received doses. The city’s then-deputy health commissioner, Caroline Johnson, resigned after The Inquirer obtained records showing she gave the organization an unfair advantage in the bidding process.

  • In May 2021, the then-health commissioner, Thomas Farley, resigned after he admitted he ordered the destruction of victim remains from the 1985 MOVE bombing that were in the possession of the Medical Examiner’s Office. That order was not carried out — a fact that was revealed after the remains were found in the basement of the Medical Examiner’s Office. They have since been returned to family members.

Bettigole acknowledged the credibility issues created by the repeated errors in the vaccination data.

“I don’t want the message that our team is not to be trusted or not strong,” she said. “They really are.”

» READ MORE: Philly says it found the remains of the MOVE bombing victims it thought it had cremated and discarded

The mistake in the pediatric vaccination rate, she said, was due to a staff error. Pennsylvania’s calculation of its vaccination rates suffered from the same error last year, leading to an inflated number of partially vaccinated people. The number of fully vaccinated people was also inaccurately low.

“How an individual person makes a human error is hard to say,” Bettigole said.

Vaccine providers have to specify whether each dose they administer is a first or second shot in the two-dose regimen, said Ala Stanford, a pediatric surgeon and founder of the Black Doctors COVID-19 Consortium, which is providing vaccine doses to children in city schools.

“We do a spreadsheet and they’re sent out as first and second doses, and also have to include the person’s name,” she said. “We have to send all the demographic information.”

The health department has two teams now reviewing vaccine records reported on the city’s public dashboard, Bettigole said.

“There’s just a lot more eyes on the data and a lot more cross-checking happening,” Bettigole said.

Staff writer Kasturi Pananjady contributed to this article.