COVID-19 vaccination clinical information

The information on this page will assist health professionals delivering the COVID-19 Vaccination Program in South Australia. Information contained in these documents is correct at the time of release. As information is continually evolving some documents will be updated if related information and recommendations change in the future.

Advice from ATAGI

The Australian Technical Advisory Group on Immunisation (ATAGI) advises the Minister of Health on the immunisation programs and provides clinical guidance on the vaccines available in Australia.

ATAGI advice on vaccination for people with certain conditions

ATAGI recommends vaccination with the Pfizer COVID-19 vaccine for people who have a history of the following rare conditions (advice may be updated as further information is available):

  • a history of cerebral venous sinus thrombosis (CVST)
  • a history of heparin-induced thrombocytopenia (HIT)
  • a history of idiopathic splanchnic (mesenteric, portal and splenic) venous thrombosis
  • anti-phospholipid syndrome with thrombosis
  • people with contraindications to COVID-19 Vaccine AstraZeneca:
    • anaphylactic reaction to a previous dose of COVID-19 Vaccine AstraZeneca, or to an ingredient of the vaccine
    • history of capillary leak syndrome
    • Thrombosis with thrombocytopenia after the first dose of COVID-19 Vaccine AstraZeneca
    • other serious adverse events attributed to the first dose of COVID-19 Vaccine AstraZeneca

ATAGI advice on access to a third primary COVID-19 vaccine dose for immunocompromised individuals

ATAGI recommends a third dose of COVID-19 vaccine as part of the primary course in individuals who are severely immunocompromised. This is to address the risk of suboptimal or non-response to the standard two dose schedule. The third dose is intended to maximise the level of immune response to as close as possible to the general population.

This recommendation applies to all individuals aged 12 years and over with certain conditions or on therapies leading to severe immunocompromise. An individual with an unlisted condition should only be considered for a third dose where the treating physician has assessed the patient as having a similar level of severe immunocompromise to the conditions specified in the ATAGI statement.

Eligible conditions

A third dose is recommended for people with the following immunocompromising conditions:

  • Active haematological malignancy
  • Non-haematological malignancy with current active treatment including chemotherapy, radiotherapy, and/or hormonal therapy, but excluding immunotherapy with immune checkpoint inhibitors
  • Solid organ transplant with immunosuppressive therapy
  • Haematopoietic stem cell transplant (HSCT) recipients or chimeric antigen receptor T-cell (CAR-T) therapy within 2 years of transplantation.
    • These patients require revaccination with 3 additional doses of COVID-19 vaccine, irrespective of doses given prior to transplantation, commencing generally ≥3-6 months after their transplant after discussion with their treating specialist.
    • Those beyond 2 years from transplant should discuss with their treating specialist about the need for a third dose.
  • Immunosuppressive therapies including:
    • High dose corticosteroid treatment equivalent to >20mg/day of prednisone for ≥14 days in a month, or pulse corticosteroid therapy.
    • Multiple immunosuppressants where the cumulative effect is considered to be severely immunosuppressive.
    • Selected conventional synthetic disease-modifying anti-rheumatic drugs (csDMARDS):
      • including mycophenolate, methotrexate (>0.4 mg/kg/week), leflunomide, azathioprine (>3mg/kg/day), 6-mercaptopurine (>1.5 mg/kg/day), alkylating agents (e.g. cyclophosphamide, chlorambucil), and systemic calcineurin inhibitors (e.g. cyclosporin, tacrolimus)
      • excluding hydroxychloroquine or sulfasalazine when used as monotherapy
    • Biologic and targeted therapies anticipated to reduce the immune response to COVID-19 vaccine:
      • including B cell depleting agents (e.g. anti-CD20 monoclonal antibodies, BTK inhibitors, fingolimod), anti-CD52 monoclonal antibodies (alemtuzumab), anti-complement antibodies (e.g. eculizumab), anti-thymocyte globulin (ATG) and abatacept
      • excluding agents with likely minimal effect on vaccine response such as immune checkpoint inhibitors, anti-integrins, anti-TNF-α, anti-IL1, anti-IL6, anti-IL17, anti-IL4 and anti-IL23 antibodies
  • Primary immunodeficiency including combined immunodeficiency and syndromes, major antibody deficiency (e.g., common variable immune deficiency (CVID) or agammaglobulinemia), defects of innate immunity (including phagocytic cells), defects of immune regulation, complement deficiencies and phenocopies of primary immunodeficiencies.
  • Advanced or untreated HIV with CD4 counts <250/μL or those with a higher CD4 count unable to be established on effective anti-retroviral therapy
    • a thirdprimary dose is not required for people living with HIV, receiving ART with CD4 counts ≥250/μL
  • Long term haemodialysis or peritoneal dialysis

Proof of eligibility when attending pharmacy or SA Health site

Patients attending a pharmacy or SA Health site will need to show evidence of their eligibility for a third dose as outlined in the eligibility declaration form published by the Commonwealth.

Evidence can be provided in one of the following ways:

  1. A letter from a GP or other treating specialist confirming the individual is severely immunocompromised (as per guidelines)
  2. Proof in the form of an alternative medical record that is dated within the last 5 years which shows the individual is severely immunocompromised (as per guidelines) including:
    1. a printout of the medical history (from clinical records or MyHealth Record – i.e. patient medical summary as printed out from treating GP’s practice
    2. a printout of a chronic disease care plan from the treating GP
    3. a discharge summary from a hospital or other medical facility
    4. a named script for a medication that has been prescribed to treat one or more of the relevant conditions or procedures outlined in the guideline
  3. A condition-specific identifier that the patient has been issued
  4. A completed Eligibility Declaration Form (if unable provide any of the above evidence of eligibility)
    1. Patients are NOT required to provide any medical or other details about their condition to their vaccination provider.

Further information

  • An mRNA vaccine (Pfizer or Moderna) is preferred to Vaxzevria (AstraZeneca) for this third dose.
  • The recommended interval for the third dose is two to six months after the second dose of vaccine. A minimum interval of four weeks may be considered in exceptional circumstances (e.g. anticipated intensification of immunosuppression, outbreaks). People who have had a second dose more than six months ago should receive a third dose whenever feasible.
  • Antibody testing is not recommended to assess for immunity to SARS-CoV-2 following COVID-19 vaccination, including in immunocompromised individuals after a second or third dose.

For more information see the ATAGI statement.

Booster doses

In South Australia booster doses are available to everyone 18 years and over who have completed their primary course of a COVID-19 vaccine at least 3 months ago. A booster dose will make sure the protection from the primary course is even stronger and longer lasting and should help prevent spread of the virus. Pfizer and Moderna are available for a booster dose.

ATAGI is not currently recommending booster doses for people aged 12 to 17 years.

For more information see ATAGI’s advice on COVID-19 booster doses.

Vaccinating children aged 5 to 11

Children aged 5 to 11 can now get their COVID-19 vaccine at most SA Health vaccination clinics (including some mobile clinics), and selected GPs, Respiratory Clinics and pharmacies.

Vaccinating children aged 5 to 11 against COVID-19 decreases spread of the disease to all age groups, as well as reduces the child’s risk of rare but serious adverse reactions, such as multi-system inflammatory syndrome, and long COVID-19.

The Pfizer COVID-19 vaccine is the recommended vaccine in Australia for children aged 5 to 11 and is one third of the dose given to those aged 12 and over.

The vaccine should be given in two doses at least 8 weeks apart. This can be reduced to a minimum of 3 weeks in special circumstances.

For more information, read the fact sheet Immunisation providers vaccinating children aged 5 to 11 (PDF 179KB).

For more information about the paediatric Pfizer COVID-19 vaccine compared to over COVID-19 vaccine, see the COVID-19 vaccines (MRNA) quick reference guide for clinics (PDF 200KB).

For information about vaccinating children, read the Guide to Vaccinating Young Children (PDF 684KB) and watch the training video for immunisation providers below.

Access for Pfizer vaccine for medically at risk children 5 – 15 years

Children requiring review or vaccination at the Paediatric COVID-19 Specialist Immunisation Service, WCH

Children with an underlying medical condition should first see their GP or treating specialist.
If they are assessed as medically stable, they can receive the vaccine at their most convenient clinic, which may be at a participating GP, a regional clinic or at a mass vaccination clinic.

If the GP or specialist feels the child requires further review or an appointment at the Pfizer Vaccination Clinic at the WCH or the Paediatric COVID-19 Specialist Immunisation Service at WCH, a referral will be required.

Requests can be made using the WCHN Referral Form - COVID-19 Vaccine 12-15 years (PDF 216KB).

Access to Pfizer vaccine as a mixed schedule

Requests to access the Pfizer COVD-19 vaccine can be made by GPs for patients to complete their course of COVID-19 vaccination with Pfizer (mixed schedule) for the below reasons:


  • Anaphylaxis following a previous dose of COVID Vaccine AstraZeneca.
  • Anaphylaxis to any component of the vaccine including polysorbate 80.
  • Thrombosis with thrombocytopenia syndrome (TTS) following the first dose of COVID-19 Vaccine AstraZeneca.
  • History of capillary leak syndrome.
  • Any serious vaccine-attributable adverse events after dose 1 COVID Vaccine Astra Zeneca, including: any other serious adverse event attributed to the first dose of a COVID-19 vaccine (and without another cause identified) following expert review.


  • A history of cerebral venous sinus thrombosis (CVST), Heparin-induced thrombocytopenia (HIT), idiopathic splanchnic (mesenteric, portal, splenic) thrombosis.
  • Has a history or diagnosis of antiphospholipid syndrome with thrombosis.

Special considerations

  • Pregnancy

Requests can be made using the Request for access to Pfizer vaccine as a mixed dose schedule (DOCX 37KB).

Vaccine information

COVID-19 Pfizer (COMIRNATY™) vaccine

COVID-19 AstraZeneca (ChAdOx1-S) vaccine

Cold Chain Management

COVID-19 vaccines have specific storage requirements. Further information is available at:

In the event of a cold chain breach effecting COVID 19 vaccines:

  • Isolate affected vaccines in the recommended temperature range.
  • Label ‘Do not use’.
  • Notify the Commonwealth Vaccine Operations Centre (VOC) immediately on 1800 318 208.

Referring patients with a history of severe allergic reactions

The South Australian COVID-19 Specialist Immunisation Clinic (SACSIC) provides specialist services for those identified as at risk for adverse events following immunisation (AEFI) or those who experience AEFIs in the context of a COVID-19 vaccine.

Referral criteria

Referrals can be made by GPs to the SACSIC if patients have a history of:

  • Immediate (within 2 hours) and generalised symptoms of a possible allergic reaction (eg hives) to a previous dose of a COVID-19 vaccine.
  • Anaphylaxis or generalised allergic reaction (without anaphylaxis) to any component of the COVID-19 vaccine to be administered (eg PEG/macrogol in the Pfizer/BioNTech vaccine, polysorbate 80 in the Astra Zeneca vaccine).
  • Polyethylene Glycol (PEG, aka macrogol) or polysorbate 80 related reactions and/or a history of multiple allergic reactions to other medications containing PEG or polysorbate (please check the ingredients of the patient’s current/previously tolerated medications as they may contain PEG/polysorbate).
  • Mastocytosis with a raised tryptase and recurrent anaphylaxis.
  • Severe unexplained illness after receiving COVID-19 vaccination requiring hospitalisation for greater than 24 hours.

Please note any patient with a history of cerebral venous sinus thrombosis (CVST), heparin-induced thrombocytopaenia (HIT), idiopathic splanchnic vein thrombosis (mesenteric, portal or splenic), antiphospholipid syndrome with thrombosis and/or thrombosis with thrombocytopaenia (TTS) can be directed to a SA Health COVID-19 Vaccination Clinic for the Pfizer vaccine once a Request for access to Pfizer vaccine for people over 60 form (RTF 868KB) has been completed by their GP.

Referral process

All referrals to the South Australian COVID-19 Specialist Immunisation Clinic must be forwarded via fax or email using the SACSIC Referral Form (PDF 47KB).

For further information is available at:

Reporting adverse reactions (mandatory)

As of 13 April 2021, an adverse advent following immunisation (AEFI) is a notifiable condition in South Australia pursuant to section 63(2) of the South Australian Public Health Act 2011. Medical practitioners and diagnostic laboratories are legally required to notify AEFI.

An AEFI refers to any untoward medical occurrence that follows immunisation, whether expected or unexpected, and whether triggered by the vaccine or only coincidentally occurring after receipt of vaccine.

All immunisation providers should notify any serious or unexpected AEFI, or any AEFI which resulted in healthcare attendance to SA Health. Members of the public are also able to report.
The South Australian Vaccine Safety Surveillance System (SAVSS) monitors AEFI for South Australia. Information from AEFI reports received by SA Health will be sent to the Therapeutic Goods Administration (TGA).

Health professionals are required to:

Be alert for any persistent, unexpected or severe AEFI, related to any vaccine.

Notify serious or unexpected AEFI, or any AEFI which resulted in healthcare attendance to SA Health:

  • Online: Use the online Vaccine Reaction Report Form. On completion of the online report form, a lodgement number will be issued. If you have provided an email address, the option to receive confirmation including your lodgement number by email, is available. There is also an option to print a copy of your report.
  • Telephone: Alternatively you can phone the COVID-19 Clinical Advisory Service; Immunisation Section, Communicable Disease Control Branch between 8.30 am – 5.00 pm Monday to Friday on 1300 232 272. Serious AEFI related to COVID vaccines can also be reported on this number outside of business hours.

Reporting program errors

Program errors or vaccine administration incidents (medication incident) and may include, administration of an incorrectly prepared, or compromised (affected by a Cold Chain Breach or incorrectly stored) vaccine, administration of a vaccine where a contraindication exists; incorrect route of administration or failure to observe minimal interval between vaccination doses.

COVID-19 Vaccine Program errors can be reported via:

Program Error reports also need to be reported to the to COVID-19 Vaccine Operations (VOC).

Vaccine safety surveillance

AusVaxSafety is the national system for monitoring vaccine safety in Australia and will actively follow up people who receive a COVID-19 vaccine by sending them an SMS or email with a short survey that asks if they experienced an AEFI.

SA Health vaccination clinics involved with active vaccine surveillance encourage participation via a QR Code system that is integrated with VaxTracker surveillance tool.

Active vaccine safety surveillance clinic information:

Vaccination exemptions

Some people are required to be vaccinated against COVID-19 under a relevant Emergency Management Act 2004 direction as a condition of their employment. A person must meet certain eligibility requirements in order to apply for an exemption.

Exemptions are limited to the below circumstances:

  • the person has a medical certificate or letter from a legally qualified medical practitioner certifying that the person:
    • has a medical exemption from receiving a TGA approved COVID-19 vaccine on either a permanent or temporary basis in accordance with the guidelines published by ATAGI; or
    • has a medical exemption on either a permanent or temporary basis from receiving the preferred vaccine as recommended by ATAGI for the person’s age; or
    • has an appointment to be assessed by a medical specialist or has commenced an assessment with a medical specialist to determine whether they have a medical exemption from receiving a COVID-19 vaccine on either a permanent or temporary basis in accordance with the guidelines published by ATAGI; and
    • the certificate or letter specifies the nature of the exemption and the basis on which it applies; and
    • the Chief Public Health Officer or her delegate has endorsed the exemption; and
    • the person provides the operator of the healthcare setting with a copy of the endorsement

The certificate or letter must clearly outline the reason for the exemption and which direction applies to their employment. The Chief Public Health Officer or her delegate must endorse the exemption.

  1. You will need to get a medical certificate from a qualified medical practitioner that clearly outlines the reason for an exemption in line with the Australian Technical Advisory Group on Immunisation (ATAGI) guideline:
  2. Your medical practitioner must complete an SA Health Chief Public Health Officer Immunisation Exemption Application Form.
  3. Submit your completed form and medical certificate to
  4. Your application for an exemption must be approved by the Chief Public Health Officer (CPHO). If approved, the CPHO will provide a signed exemption letter that can be provided to the RACF.

Workforce training

To ensure the workforce is competent in the safe management and administration of COVID-19 vaccines, health practitioners must undertake specific mandatory training prior to order or administering any COVID-19 vaccinations.

For further information visit the Immunisation provider training and education page.

Resources for COVID-19 vaccine providers

Related SA Health Policies