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Chief public health officer Dr. Theresa Tam is reflected in a wall as she leaves a news conference in Ottawa on Jan. 5, 2021.

Adrian Wyld/The Canadian Press

The Public Health Agency of Canada has acknowledged in newly released federal documents a critical shortage of scientific expertise to confront the pandemic, and the department has been scrambling to plug those holes as the outbreak worsened.

The admission in documents released this week follows a Globe and Mail investigation in July that reported Public Health lost much of its scientific capacity in the years before COVID-19 hit, severely hindering the country’s pandemic preparedness and response.

Doctors and epidemiologists said the agency became populated by civil servants with no background in public health. They told The Globe that important information often had to be “dumbed down” before it was moved up the chain of command, while early warnings about the urgency of the outbreak were shrugged off or ignored by directors within the department.

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Two federal probes have been launched into the allegations, including an investigation by the Auditor-General and an independent review ordered by the Health Minister. While the department has mostly remained silent about the problems, an internal audit performed in September – two months after The Globe’s investigation – acknowledged “multiple capacity and skills gaps across the agency” that have hurt Canada’s response to the pandemic.

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“It quickly became evident that the agency did not have the breadth and depth of human resources required to support an emergency response of this never-seen-before magnitude, complexity or duration,” the internal audit report says.

The document, titled “Lessons Learned,” was among hundreds of internal federal files released this week in response to a sweeping production order approved in October by the House of Commons over the objections of Liberal MPs. It shows a Public Health Agency caught flat-footed by COVID-19, scrambling to hire expertise from outside government, and scouring other departments for epidemiologists and emergency-management skills.

“Longer-term mobilization efforts have been challenged by an inability to find available staff to fill capacity gaps and, in particular, available staff with the required skills and expertise,” the internal audit says.

The Globe reported in July that the agency’s ranks swelled over the past decade with civil servants from departments such as Treasury Board and border services, while doctors and epidemiologists left in frustration. By September, the internal audit confirmed the agency was in dire need of “public health expertise, including epidemiologists, psychologists, behavioural scientists and physicians at senior levels.”

A Globe investigation in December reported that the agency in recent years stopped sending scientists to key international meetings on pandemic preparedness, instead choosing senior civil servants with no epidemiological training. The erosion of skills became worrisome enough that scientists proposed an internal crash course in public health to teach staff the basics on the fly. But it was never adopted.

Such changes have left the agency “without the needed breadth and depth of experience to lead complex files,” the internal audit says.

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It also left Canada’s Chief Public Health Officer, Theresa Tam, the public face of Ottawa’s pandemic response, without sufficient scientific backup, often dealing with slow and sometimes inaccurate information from federal officials, the report says.

“The senior medical expertise needed to support her navigating the rapidly changing science of this new virus was slow to be put in place, and most likely is still insufficient to provide the support required,” the audit report states. “[Dr. Tam’s] office noted that she often received information in the wrong format, with inaccuracies, or in an inappropriate ‘voice’ needed to convey information to a particular audience.”

The report also warns of a serious risk of burnout for Dr. Tam and others working 20-hour days, seven days a week. “This is problematic and unsustainable on multiple levels,” the audit says.

Michael Garner, a former senior science adviser at Public Health who left in 2019, said on Friday that the chief public health officer doesn’t have full decision-making power, answering instead to the agency’s president, who is responsible for ensuring the department is properly structured.

“The [audit] highlights structural flaws within the agency that have been long-standing, and the person who has to lead that change is the president,” Mr. Garner said.

“The experts, who are few and far between, will eventually burn out. They can’t keep going at this rate. And the pandemic, especially with the variants emerging, there’s a long game to this … I think somebody needs to think about what’s the three-year plan for Public Health.”

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Former National Research Council head Iain Stewart took over as Public Health president when Tina Namiesniowski stepped aside after the Globe’s July investigation, which also detailed how the agency silenced its pandemic early warning system less than eight months before the outbreak.

NDP health critic Don Davies called the internal audit report a “scathing assessment” of the agency’s problems. “One can understand a deficiency here and there, but this is a pretty comprehensive indictment of an agency that was very, very poorly prepared and, frankly, in some cases, dangerously so,” he said.

Mr. Davies said the concerns about the quality of information provided to Dr. Tam are troubling. “When one of our chief scientists is getting inaccurate information, it’s hard to see how policy can be based on science,” he said.

The Globe’s July investigation reported that epidemiologists at the agency said they included urgent details about the virus in their reports early in the pandemic, but learned that civil servants who didn’t understand the science removed information before those reports made their way up the chain of command.

The hundreds of internal documents released this week are a small portion of what the government has been ordered to produce. The Oct. 26 order called for memos, e-mails and other records related to Canada’s COVID-19 response.

The government said it gave Parliament more than 30,000 pages of material, but a disagreement with the Commons law clerk over who should translate them is slowing their release. Conservative MP Michelle Rempel Garner said the government is not living up to its obligations under the order. “There’s a lot missing,” she said.

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With a report from Janice Dickson in Ottawa

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