In 2009, Deeks joined Public Health Ontario, where she served as the Medical Director of Immunization and Vaccine-Preventable Diseases, and later, as Chief of Communicable Diseases, Emergency Preparedness and Response.[5][6][7] She participated as a member of the Ontario Vaccine Safety Surveillance Working Group.[8] She also contributed to a presentation on increasing uptake of adult immunizations presented by Immunize Canada in 2015.[9] At some time prior to 2020, Deeks was appointed chief health protection officer of Ontario.[2][10]
Deeks delivered several presentations at the 2018 Canadian Immunization Conference in Ottawa, on subjects including vaccine development, adverse events following immunization, HPV vaccination for gay men, risks of un-immunized Ontario children, non-medical exemptions to vaccination, and MMR vaccines.[1][11] The same year, she also presented at the Ontario Public Health Convention on the topics of the epidemiology of varicella, waning measles immunity in infants, and mumps activity in Ontario.[1]
In 2020, Deeks left Public Health Ontario one month after she "revealed that the government ignored Public Health Ontario's recommendations on COVID-19."[2] In reality, she was not consulted in November 2020 "on colour-coded COVID restrictions", and two days after the revelations the Ford government moved to bring the colour codes into line with PHO's recommendations.[5][6] Later that month, she delivered a virtual presentation to health care providers on the safety and efficacy of the then newly-authorized Moderna COVID-19 vaccine.[13][14]
In February 2021, Deeks was appointed the inaugural public health surveillance medical officer of Nova Scotia.[2] The press release said she would "lead Public Health surveillance, support epidemiologists and support Nova Scotia's publicly funded immunization program".[6]
On 29 March 2021, as vice-chair of NACI, Deeks said that "There is substantial uncertainty about the benefit of providing AstraZenecaCOVID-19 vaccines to adults under 55 given the potential risks." She said that the risk of a cerebral venous sinus thrombosis blood clot was "potentially as high as one in 100,000, much higher than the one in one million risk believed before... Most of the patients in Europe who developed a rare blood clot after vaccination with AstraZeneca were women under age 55, and the fatality rate among those who develop clots is as high as 40%."[15] In June 2021, Deeks delivered a presentation for CANVax outlining NACI's recommendations regarding "mixing and matching" of COVID-19 vaccines.[16] She assisted the Nova Scotia Department of Health and Wellness in a promotion campaign for the vaccine program, including encouraging second doses to protect against new variants of COVID-19 and reassuring viewers that side effects are rare and well-tolerated.[17][18][19] She later participated in Q&A-style videos answering common questions about COVID-19 vaccines for ages 5–11.[20]
In October 2021, Deeks and Nova Scotia’s Chief Medical Officer of Health Dr. Robert Strang criticized media allegations that healthcare providers were failing to identify and report adverse reactions to the COVID-19 vaccines, asserting that the risk of a serious adverse event was "about seven for every 100,000".[21] Deeks was among the public health experts invited to a public debate during the Freedom Convoy by a group including anti-mandate doctors Paul E. Alexander, Roger Hodkinson and Byram Bridle.[22]
She collaborated in 2015 with the founders of Sigvaria Mobile Technologies Inc. on a paper exploring the benefits and challenges of using mobile devices as a method of centralizing storage and access to individual vaccination information, as well as for use in cross-border travel.[24] Sigvaria developed ImmunizeCA, a smartphone application with various vaccine-related capabilities resembling an early version of a digital vaccine passport.[25][26]
^"Meeting with Dr. Shelley Deeks"(PDF). Ontario's Long-Term Care COVID-19 Commission. 8 January 2021. Archived(PDF) from the original on 10 August 2021. Retrieved 20 March 2022.
^"ACIP Current Membership Roster". U.S. Centers for Disease Control and Prevention. 12 January 2022. Archived from the original on 19 April 2022. Retrieved 19 April 2022.
^Government of Canada, Canadian Institutes of Health Research (17 February 2022). "Is Ontario prepared for the return of measles?". Funding Decisions Database. Archived from the original on 20 March 2022. Retrieved 20 March 2022.