The head of Ontario’s public health agency is stepping aside temporarily for personal medical reasons in the midst of the fight against COVID-19 — a second shakeup in recent days for the provincial pandemic hierarchy.

Dr. Peter Donnelly, the president and chief executive of Public Health Ontario, wasn’t a public figure until last Friday when he did a live televised briefing on an anticipated surge of cases and deaths from the novel coronavirus.

He earned plaudits for detailing a series of sobering numbers in a calming tone with candour and confidence.

“I think Dr. Donnelly’s an absolute champion. He’s amazing,” Premier Doug Ford said Thursday, a day after going public with concerns that Ontario is testing far below its laboratory capacity to process potential COVID-19 samples and get a better picture of the virus.

“Unfortunately he had to step aside for medical reasons but I can’t wait to have Dr. Donnelly back and have him part of the team.”

Public Health Ontario spokeswoman Janet Wong said Donnelly is “ill and on medical leave which is not related to COVID-19.” It’s not known how long the doctor — a cross-country skier, cyclist and runner whose research has included the impact of violence on public health — will be away.

Ford told reporters he didn’t mean to point fingers out with his critical remarks about the provincial testing effort, which came as the Star revealed former Toronto public health chief Dr. David McKeown has come aboard to lead a table of experts scrutinizing major public health measures to fight the virus.

“There’s no doubt I was frustrated. Let’s make it clear. I’m not frustrated at any individual or any group, I’m frustrated at the system,” said Ford.

His government has been under pressure to fix critical shortages of masks, face shields, gloves and gowns for health-care workers to protect themselves from the highly contagious virus, along with an anticipated shortage of ventilators to keep COVID-19 patients alive when they can no longer breathe on their own.

“When a crisis happens, you see where a lot of systems are broken down or systems where there hasn’t been a playbook to get through a crisis like this,” Ford added.

“I believe in our people, I believe in the Ontario Public Service, every single person. But we’re going to get through it and we’re going to have better systems moving forward.”

As first reported on thestar.com, Donnelly will be replaced on an acting basis by Colleen Geiger, who is Public Health Ontario’s chief of strategy, stakeholder relations, information and knowledge.

Two other executives — Dr. Vanessa Allen, chief of medical microbiology, and Dr. Shelley Deeks, chief health protection officer — will have larger roles at the agency during Donnelly’s absence, the government source said.

In the early days of the COVID-19 scare, when the virus was limited to China, Allen was called upon to give briefings to the media with Dr. David Williams, Ontario’s chief medical officer, on how testing was conducted.

Details on a new testing regime will be revealed Friday.

Williams cautioned that testing will not be population-wide because there is not enough lab capacity for that. Rather, it will be aimed selectively at nursing-home residents and staff, health-care workers and other priority or high-risk groups.

Ford signalled that his “patience has worn thin” after the province cleared its testing backlog COVID-19 last Friday but failed to take advantage of the unused capacity to test more people, particularly nursing-home residents, front-line health-care workers and first responders.

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Ontario can now process 13,000 samples a day but on several days has done just one-third or one-quarter that number, leaving health experts puzzled at the missed opportunity to get a better sense of how the new coronavirus is spreading.

As well, tests being completed lately have been revealing a larger percentage of positives in the past, indicating the virus is taking a broader hold, making the importance of testing even more crucial.

Ford said he called Ontario Health chief executive Matt Anderson to talk about the issue, which insiders said is a signal that Anderson is now a go-to person for the premier as the province’s case load has topped 6,000 and the death toll has surpassed 200. Ontario Health is the umbrella agency in charge of all elements in the provincial health system.

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