Vaccine Information for Primary Care

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 COVID-19 Vaccines

Select populations are now eligible for a fourth or booster dose of the COVID-19 vaccine. Providers are encouraged to order Moderna and /or Pfizer to provide third doses/boosters in your practice. For more information, please refer to the ministry guidance Document, COVID-19 Vaccine Third Dose and Booster Recommendations. Physicians can now order the Novavax (Nuvaxovid) and the Janssen COVID-19 vaccines through Public Health, using their current vaccine ordering process.

Onboarding process

As more primary care locations offer COVID-19 vaccines, the Waterloo Region COVID-19 Vaccine Distribution Task Force gets closer to reaching their goals of enough immunization coverage, working together to increase health system capacity, and ensuring equitable coverage with reduced barriers to access. Collaboration is imperative to ensure ongoing protection against COVID-19. 

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

Please email Stephanie Duench  and Sree Nair to start the onboarding process or to attend an in-person or virtual 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. 

COVID-19 vaccine resources

General resources 

Please email Sree Nair 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 COVID-19 Vaccines for Children and COVID-19 Vaccine General Information pages.

Please note that the Pediatric Pfizer-BioNTech Comirnaty COVID-19 Vaccine is a separate product from the Adult formulation. The pediatric formulation has an orange vial cap, while the adult formulation has a purple vial cap. Health Canada has not approved the Adult formulation for pediatric (5-11 years) use.


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 setup 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 or 519-514-1488, available Sunday to Saturday 8:30 a.m. - 8 p.m.

Please refer to the Simplified Vaccination Flow COVaxON Job Aid for information on full clinical flow COVaxON processes including check-in, dose administration, and check out.   

Ordering 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 Sree Nair at

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.

To order any ancillary supplies, please complete and submit the vaccine clinic supply form. Please email Sree Nair at to receive a copy of the supply form.


Your practice will be responsible for identifying and booking eligible patients to receive the vaccine. Your practice may provide first, second, or third doses to those eligible. All second and third dose information for the Region can be found here: Second and Third Dose Information

To learn more about the COVID-19 vaccines authorized by Health Canada, and who should get the COVID-19 vaccine, check our COVID-19 Vaccine webpage.

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. 
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 

Quarterly, you will be able to invoice the Region up to $500 per month of replacement/additional supplies as needed to continue COVID-19 vaccinations. As part of the onboarding process, you will be required to sign a purchase order agreement.

You can also bill codes for COVID-19 vaccines in office using codes G593+Q593. Please see the following resources for additional information:

Vaccine exemption

The Ontario Ministry of Health requires all Public Health units to upload medical exemptions to the COVID-19 vaccine database, COVAX, 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.

Public Health will verify exemption letters and/or forms in person only at the following two locations:

  • 99 Regina Street South, Waterloo
  • 150 Main Street, Cambridge

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 COVAX 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.

Immunization Schedule

The Ministry of Health’s publicly funded immunization schedule for Ontario provides a list of vaccines and the recommended vaccine schedule.

Publicly Funded Immunization Schedule

Influenza Vaccine

The implementation package can be found at The Ministry of Health’s 2021/2022 Universal Influenza Immunization Program (UIIP). The UIIP offers influenza vaccine free of charge each year to all individuals six months of age and older who live, work or go to school in Ontario. For questions/concerns regarding the 2021/2022 UIIP, email the ministry at

The following vaccines are available this season:

  • Quadrivalent Inactivated Vaccine (QIV) (6 months of age and older)
    • FluLaval Tetra, Fluzone Quadrivalent
  • Quadrivalent Inactivated Vaccine (QIV) (2 years of age and older)
    • Flucelvax Quad
  • Adjuvanted Trivalent Inactivated Vaccine (TIV-adj) (65 years of age and older)
    • Fluad
  • Fluzone High Dose (QIV-HD) will be available to health care providers the week of October 25
  • Flumist will not be available in Ontario this flu season

A friendly reminder that health care providers and individuals at high-risk of complications or hospitalization due to influenza should be prioritized for vaccination. Large-scale community clinics for the general population should be scheduled in November.

NACI Statement on Seasonal Influenza Vaccine 2021-22

Influenza immunization toolkit 

The toolkit provides a collection of resources that can be used to promote annual influenza immunization amongst health care workers and facility staff.

Adverse Events After Immunization (AEFI)

If a patient/client experiences an adverse event after immunization, Waterloo Region health care providers are required to report an adverse event following an immunization.

  • Report adverse events using the Adverse Event Following Immunization Form and fax it to Region of Waterloo Public Health at 519-883-2248 or submit online through the Ocean platform integrated with your EMR. The AEFI reporting form has been updated to include adverse events of special interest for COVID-19 vaccine.
  • Please do not direct your patient/client to call Region of Waterloo Public Health. We are not currently accepting self-referred AEFI reports.

Adverse Event Following Immunization Reporting For Health Care Providers In Ontario Fact Sheet (Public Health Ontario)

Vaccine Fact Sheets

Vaccine Forms

  • Biological Returns Form
  • Child Care Centres Pre-Employment Health Form
  • Contingency Plan for Planned or Unexpected Electricity Disruption
  • Hepatitis A High Risk Vaccine Order Form
  • Hepatitis B High Risk Vaccine Order Form
  • HPV High Risk Vaccine Order Form
  • Immunization Assessment Plan
  • Incident Assessment Form for Designated Officers
  • Influenza Immunization Decision Making Tool
  • Meningococcal High Risk Vaccine Order Form
  • Min/Max Thermometer Order Form 
  • Report of Positive Tuberculosis (TB) Skin Test 
  • Request for Immunization Schedule Assessment and Plan
  • Routine Vaccine Order Form
  • School Program Vaccine Order Form
  • TB Physician Referral Form
  • Vaccine Storage and Handling Form
  • Varicella Immunity Confirmation Form 

To access any of the forms listed above, please use our Request a form tool. 

Vaccine Information

Vaccine Toolkit

Resources to assist with assessing records:

Resources to assist with vaccine storage and handling:

Presentations that can be provided by Public Health staff:

  • Assessing and Administering Immunization Schedule
    • Topics include: review of eligibility, immunization schedules, dosing, intervals and antigens
  • Vaccine Administration Practices
    • Topics include: client assessment, rights of immunization, immunization sites, client positioning, pain management techniques, vaccine preparation, administration, and disposal and adverse events following immunization
  • Vaccine Storage and Handling for Health Care Providers
    • Topics include: cold chain responsibilities, temperature monitoring, equipment, cold chain incidents, contingency planning

Please contact us at 519-575-4400 ext 5505 for further information about these presentations.


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