COVID-19 Resources for Health Professionals

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Report a suspect, probable or confirmed case of COVID-19

This form can be used by the following high-risk congregate settings to report suspected, probable or confirmed cases of COVID-19:

  • Hospitals
  • Long-term care homes
  • Retirement Homes
  • Congregate Settings
  • Emergency Shelters

COVID-19 vaccines

Select populations are eligible for a booster dose of the COVID-19 vaccine. Providers are encouraged to order Moderna and/or Pfizer to provide booster doses in their practice. For more information, please refer to the ministry guidance document, COVID-19 Vaccine Guidance.

Physicians can now order the Novavax (Nuvaxovid) vaccine through Public Health, using their current vaccine ordering process.

Primary care COVID-19 vaccine onboarding process

To be eligible to participate in the COVID-19 vaccine program, you:

Please email to start the onboarding process or to attend an in-person training on drawing-up COVID-19 vaccines or using COVaxON. OntarioMD also offers virtual COVaxON training to all primary care practice staff offering vaccination clinics. All primary care practices/offices are strongly encouraged to attend an OntarioMD COVaxON Training as part of onboarding. Register here for a training session.

Ordering COVID-19 vaccine and supplies

Orders for vaccine must be submitted using the Online Vaccine Inventory System. To access the system, staff will need to register using the unique invite code provided by Public Health. If you do not yet have an account, please email

Order requests must be submitted no later than 48 hours prior to your clinic start. For Monday delivery the order needs to be submitted by noon on Thursday and for Tuesday delivery by noon on Friday. Medical Services Courier will deliver your vaccines between the hours of 9 a.m. - 12 p.m. Deliveries will not occur on weekends.

If you find yourself in a situation where you require a last minute delivery, Public Health will try to accommodate, where possible. If last minute deliveries are needed, please email: Emails are answered Monday to Friday 8:30 a.m. - 4:30 p.m.

Orders for COVID-19 Vaccines and ancillary supplies must be submitted using the vaccine clinic supply form. Please email to receive a copy of the supply form. 

COVID-19 vaccine accountability logs

All clinics must submit an Accountability Log using the Online Vaccine Inventory System each day you administer vaccines and each day you receive a vaccine delivery. Please submit accountability logs no later than 11 p.m. the day of the clinic or delivery.  

COVaxON information

COVaxON is the provincial system used to record COVID-19 vaccinations. The COVaxON database keeps record of the doses administered to each client by date and includes information on the vaccine product. COVaxON helps Public Health track how much vaccine product is being administered in the Region to inform inventory and ordering processes. Direct clinical data entry into COVaxON at the point of care is the standard. 

Public Health will set up COVaxON accounts as well as a COVaxON Event for your practice/office. COVaxON training resources will be provided at the time of on boarding.

The link to COVaxON is

If you need more help, including help with two-factor authentication, contact Public Health at, available Monday to Friday 8:30 a.m. - 4:30 p.m.  

COVaxON aggregate primary care vaccination data reports

The COVaxON Aggregate Primary Care Vaccination Report identifies your rostered patients that have received a COVID-19 vaccine on a platform similar to the Screening Activity Report (SAR).

For detailed instructions on obtaining this report and using this information to determine which eligible patients have not yet been fully vaccinated, please visit the EMR-eReport Patient Vaccination Reconciliation Toolkit .

Adverse events following immunization (AEFI) 
  • If your patient/client experiences an adverse event following immunization:
  • If you experience an adverse event following immunization:
    • Please contact your health care provider. Do not self-report your own adverse event. Your health care provider will complete the required form and submit it to Region of Waterloo Public Health.
COVID-19 vaccine medical exemption

The Ontario Ministry of Health requires all Public Health units to upload medical exemptions to the COVID-19 vaccine database, COVaxON, for the purposes of obtaining a QR code and receipt.

Guidance is available to Physician/Specialists for evaluating contraindications or precautions to COVID-19 vaccination that may warrant a medical exemption. The Ontario Ministry of Health has also created a sample medical exemption template.

Your primary care physician, specialist or registered nurse must fax a Medical Exemption Form or letter that documents the medical exemption on your behalf to 519-883-2248.

The healthcare providers can either:

  • Prepare a letter on their office letterhead documenting the medical exemption as per the guidance provided to them; or
  • complete a Medical Exemption Form which will need to be accompanied by a logo or letterhead identifying them 

The exemption must clearly indicate the reason why the individual cannot be vaccinated against COVID-19; check the Medical Exemption Guidance for details.

Public Health will review the medical exemption. If the exemption meets all of the criteria, the exemption will be uploaded to COVaxON and a link will be emailed to the client to download their receipt with the QR code.

If Public Health staff determine the medical exemption does not meet the requirements (i.e. incomplete, not an eligible condition) they will email the client to inform them and so they can follow up with their physician/specialist.

COVID-19 vaccine resources for healthcare professionals

Please email to receive additional resources including:

  • mRNA Medical Directive
  • Pediatric Pfizer Placemat
  • Pediatric Pfizer Vaccine Dilution Syringe Setup
  • Adult Pfizer Vaccine Placemat
  • Adult Pfizer Vaccine Dilution Syringe Setup
  • Moderna Vaccine Placemat

For patient resources, please visit our COVID-19 Vaccine webpage. 

Long-term care homes, retirement homes, and congregate living settings (including group homes, emergency shelters and co-living settings)

Report all residents with COVID-19 symptoms or positive COVID-19 test results using the secure online reporting form. When your facility is in a suspect or confirmed outbreak, staff and visitors who test positive for COVID-19 should also be reported through the online reporting form.

Questions? Contact Public Health by email or call 519-575-4400 ext. 5506.

Outbreak management
Facility status 

Review current COVID-19 outbreaks via Ontario COVID-19 Data Tool or the Waterloo Region COVID-19 Summary.

Outbreak preparedness 

Public Health Ontario Resources:

Additional resources

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