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Afghan refugees - key issues

  • This guideline is intended to provide a brief summary of background and health issues for newly arriving Afghan refugees, noting the additional complexity of Covid, and lockdowns and hotel quarantine (HQ) requirements at the time of arrival. 

    Useful Afghan calendar converter 


    In late August 2021, the Taliban returned to power in Afghanistan - see summary of events. More than 120,000 people were evacuated over the 10 days to 31 August 2021, by many different nations (see media). Evacuees included both foreign nationals, and around 65,000 Afghans. Australia evacuated 4100 people (see Prime Minister's press conference and media), with 3500 travelling on to Australia, including 2500 women and children. Australia allocated 3000 places from the existing humanitarian intake for the initial uplift, and many agencies urged an additional intake of Afghan refugees - see Refugee Council of Australia. There have been more arrivals since the initial cohort (Nov 2021). In January 2022, Minister Hawke announced a further allocation of 15,000 places within the existing humanitarian and family visa programs over the next 4 years, and on 29/3/22, the federal budget allocated an additional humanitarian intake (above the existing humanitarian intake) of 16,500 Afghan refugees over 4 years (funding of $666 million).

    • Population - Afghanistan has a population of around 40 million people. After 40 years of conflict, Afghans also make up one of the largest refugee populations globally - with UNHCR reporting 2.6 million registered Afghan refugees (2.2 million in Iran and Pakistan) and 3.5 million internally displaced people. The country is facing an evolving humanitarian emergency, with over half the population living in poverty, and severe food shortages - see World Food Program and reporting
    • Ethnic groups - the main ethnic groups in Afghanistan are Pashtun, Tajik, Uzbek and Hazara, other groups include Nuristani, Aimak, Turkmen and Baloch
    • Languages - official languages are Pashto and Dari, although there are more than 30 languages spoken and multilingualism is common
    • Religion - The majority of the population are Sunni Islam (including Pashtun and Tajik populations), followed by Shi'a Islam (including Hazara populations)
    • Naming conventions - Afghan names typically consist of a first/personal name alone, which may be a compounded name, female names are usually a single name. Surnames/family names are not customary, but are becoming more common in educated/wealthier groups. When used, surnames often represent tribal/ethnic affiliation or area of origin, and children will take the surname of their fathers. Women do not traditionally adopt their husbands surnames when they marry. 

    Australia announced an Advisory Panel on Australia's Resettlement of Afghan Nationals.  

    Entry visas

    • Some new arrivals have Australian citizenship/permanent residency, others have travelled under Australian refugee visas, many have arrived on Temporary Humanitarian Stay (449) visas - related to the speed of the uplift/evacuation 
      • The 449 visa did not automatically carry Medicare, arrangements were facilitating Medicare access for 449 visas (as of 16/9/21, with around 30% having Medicare allocated by 15 Oct 2021, and 75% by 11 Nov 2021) - however in practice there were delays in new arrivals getting their Medicare details. Please contact the local Humanitarian Settlement Program (HSP) Provider if Medicare access is not in place (Victoria =
        • The 449 is a temporary visa - initial duration was 3m, with an assumption of renewal (to 12m) and longer term transition to permanency. 
          • The 449 not eligible for the MBS refugee health assessment item (707)
          • The 449 is not eligible for NDIS (it is a temporary visa)
          • Temporary visas do not carry rights to family sponsorship 
    • Within the cohort, there are a small number of UHM- see media reporting - these children/young people will be eligible for the Unaccompanied Humanitarian Minor Program.
    • Contact and the HSP provider (Victoria - where individuals details are incorrect, and for individuals where expedited access to permanent visas is required (e.g. unaccompanied humanitarian minors (UHM), individuals requiring access to NDIS). 

    Covid, hotel quarantine procedures, and covid vaccination

    Due to covid, new arrivals were subject to HQ after arrival. New arrivals were placed in HQ in WA, SA, Vic, NSW, Qld and NT - although HQ arrangements (and healthcare available in HQ) varied across the jurisdictions. 

    • New arrivals underwent basic covid and health screening at the airport
    • There were minimal instances of covid in these cohorts
    • Covid testing protocols in HQ varied, but typically individuals were tested several times - e.g. D 0, 4, 8, 12, and 14 and then again at D17 (3 days after release) - also recommended at D21 (7 days after release)
    • In Victoria, there are 3 tiers of HQ hotels - health (covid cases), complex care (other complex needs) and quarantine; 3 new quarantine hotels were stood up for these cohorts. During the period in HQ, the focus of health assessment was on covid symptoms and testing. 
    • Individuals arrived with nothing but immediate clothing, there were systems in place to deliver phones and support immediate material needs, but the process of commencing case work support, Centrelink and Medicare access, and finding accomodation has been complicated because of the HQ period and lockdowns. The Humanitarian Settlement Program (HSP) providers (AMES in Victoria) contacted new arrivals while they are in HQ. 
    • Individuals will have a brief health summary on release from HQ if health concerns were identified during the period of HQ - check with: and for individuals in western Melbourne -
    • Preliminary information suggested large numbers (~40%) of interstate arrivals planned to move to Victoria, and large numbers are arrived from mid-September onwards, having completed HQ interstate.

    Covid vaccination

    • Covid vaccination remains limited in Afghanistan, 2.0% are partially and 1.1% are fully vaccinated against covid, although initial reports suggested a number of new arrivals are vaccinated.
    • Overall less than 2 million doses of covid vaccine have been distributed in Afghanistan - including:
      • Covishield (AZ, made in India, ~500K delivered March 2021)
      • AZD1222 (AZ, made in UK, ~270K delivered June 2021)
      • Johnson and Johnson (~3M delivered July 2021) - note single dose regimen 
      • BBIBP (Sinopharm, ~700K delivered June 2021)
    • All of these vaccines are approved by the WHO (and the Australian government) as recognised covid vaccines
    • Available data suggests no major concerns with mixed dose schedules, there are a number of trials of both AZ and Sinopharm followed by mRNA vaccine - see ATAGI and MVEC guidelines
    • Covid vaccination is an urgent priority after release from hotel quarantine for new arrivals, especially as group accomodation is likely in the short-medium term. 
      • For unvaccinated individuals - please follow local guidelines - e.g. Victoria, also see Immigrant Health Covid-19
      • For partially vaccinated individuals 
        • J&J vaccine - if vaccinated x 1 dose consider complete, need for boosters being assessed, but not currently recommended
        • AZ vaccineAZ second dose, unless contraindicated (anaphylaxis/serious adverse event, or condition listed as precaution for AZ (precautions = cerebral-venous-sinus thrombosis, heparin induced thrombocytopenia, idiopathic splanchnic thrombosis, antiphospholipid syndrome with thrombosis) - give mRNA vaccine instead) - see Cth advice 
        • Sinopharm - either AZ or mRNA vaccine (mRNA preferred <60 years)
        • Intervals - for people who received a 1st dose overseas of a vaccine that is not available in Australia, the recommended interval for a 2nd dose (with one of the vaccines available in Australia) is 4-12 weeks after the 1st dose.
      • The Australian Immunisation Register currently only accepts record for vaccines that are approved in Australia - the AIR was updated to include Sinovac and Covishield (mid-Oct 2021)
    • The Victorian government C-19 taskforce coordinated in-reach covid testing and vaccination for these new arrivals. Vaccinations were provided through IPC Health (west), EACH (south) and coHealth (city) teams, commencing 13/9/21. Around 500 people were vaccinated, if clinicians are seeing this cohort, please ask clients if they have had covid vaccination and also check AIR, and now (Feb 2022) - ensure younger age groups are vaccinated and age 16y+ have boosters.

    Health screening

    Unlike other humanitarian arrivals, newly arrived Afghan refugees will not have had an offshore Immigration Medical Examination (IME) and they may not have a record on the offshore Health Assessment Portal (HAP) system, however it is definitely worth checking HAP, especially for those arriving on refugee visas (who may have commenced the health assessment process prior to the emergency evacuation). The HSP provider can access the HAP number (but not the HAP system) - (Victoria -contact Unfortunately, now (Feb 2022) several months after arrivals, most individuals have still not yet had a post-arrival health assessment, and may not have had catch-up vaccination (which may result in reduced Centrelink due to No Jab No Pay). 

    BUPA IME assessment

    • BUPA is completing IME for new Afghan arrivals -  we suggest individuals take a copy of any results to their BUPA IME, and send on any results to local BUPA services, which will hopefully avoid the need for repeat/duplicate tests.
    • BUPA contact email is 
    • BUPA test protocols are as follows (as of 30/9/21 and confirmed 24/11/21):
      • age <2 years - medical exam (no blood tests)
      • age 2-10 years - medical exam, IGRA or TST
      • age 11-15 years - medical exam (no blood tests), CXR
      • age 15 years and older - medical exam, HIV, HBsAg, HCV, HIV, syphilis screening, CXR
      • Unaccompanied minors - HIV, HBsAg (all ages), + age based as above.
    • Key points
      • Positive TB screening or blood-borne virus tests are disclosed to the client (who is called back for an appointment) and will be referred to local TB services/health service
      • Clients get a 'duty of care' letter with limited clinical information and the HSP is notified
      • There is no medical referral process or handover for any other findings on the IME - we have raised this with DHA
      • Clients do not get a copy of their test results unless they request them (BUPA request form (in English) & emailing the local pathology provider (Victoria = Dorevitch -
      • Screening results are uploaded onto the HAP system - health providers are reporting these results have not been available in HAP, and HAP numbers have been difficult to identify. 

    Recommended health assessment

    All new arrivals should have an initial health assessment after release from HQ. Timing, especially in NSW and Victoria was affected by health service access with the Covid situation and delays in Medicare.

    Screening tests

    • Children
      • All: FBE/film, ferritin, B12, vit D/Ca/PO4/ALP, IGRA or TST, HBsAg, cAb, sAb, strongyloides, malaria, faecal COP;
      • Age/risk based: HCV, HIV 15y+/clinical/UHM, STI screening, syphilis (clinical/UHM), varicella 14y+ if no Hx, H pylori (Sx)
    • Adults 
      • All: FBE/film, IGRA, HBsAg, cAb, sAb, HIV, strongyloides, malaria, faecal COP
      • Age/risk based: ferritin (women, men with RF), B12 (esp breastfeeding women), vit D, rubella (women), varicella (if no Hx(, HCV, STI screening, syphilis, H pylori (Sx)
      • Catch-up primary care: HPV screen (women 25-74y), Alb:creat/eGFR (30y+ if high risk), BSL/HbA1C (40y+), lipids (45y+), FOBT (50y+), Mammogram (women 50-74y)
    • Note screening for schistosoma and HCV* is not routinely required for people from Afghanistan (*screen for HCV if risk factors identified). We suggest routine screening for malaria and for B12 deficiency in people from Afghanistan (see below). 

    Special note: B12 screening and preventive treatment in Afghan cohorts

    We have seen widespread B12 deficiency in children from Afghanistan. 

    • We suggest FBE, ferritin, B12 and folate screening for all new arrivals from Afghanistan. 
    • In infants, and anyone with poor nutrition, disability or neurological symptoms (all ages) - prioritise early screening, and also check serum homocysteine, and urine methylmalonic acid (Note - these tests may not be possible, and also may be billed outside the hospital setting).
    • Where screening will be delayed, commence 3m oral B12 supplements (100 mcg oral daily, all ages), or give 1000 mcg IMI if possible.
      • When screening is later completed: if B12 levels are replete - stop supplements and repeat levels in 3-6 months, if levels remain low, complete serum homocysteine & urine methylmalonic acid, and seek specialist advice.
    • Provide appropriate dietary advice.
    • In breastfeeding infants with low B12 - seek specialist advice, and ensure their mothers also have screening for B12 and treatment if deficiency identified. 

    Catch-up immunisation

    Catch-up immunisation will be required for everyone, including full catch-up for anyone without a written record of vaccination, Covid vaccination is also a priority.

    • Covid vaccination can now be given at the same time as other vaccines- see Department of Health advice 
    • The immunisation schedule in Afghanistan includes: BCG, rotavirus, DTwP-Hib-HBV, Td, IPV/OPV, measles, conjugate pneumococcal (i.e. no mumps, rubella, meningococcal ACWY, varicella/zoster, HPV or influenza)
    • Note - RCH/MVEC protocols for catch-up vaccination after chemotherapy use infanrix-hexa and MMR-V up to age 18y, this reduces needles required - we are exploring this as an option for these cohorts. AIR will accept these vaccines for adolescents, **AIR data entry - use other, and enter by antigen, and then accept queries. 
    • We have seen many families with excellent quality overseas vaccination records - these can be entered on AIR - you will need an Afghan calendar converter (!)

    Acute physical and mental health considerations

    • Covid remains a primary acute health consideration - during and after HQ, especially where group accomodation is used
    • Initial reports suggested a number of children have diarrhoeal illnesses - also consider hepatitis A in the differential diagnosis
    • Measles was reported in Afghan arrivals to the US as of 11 Sep 2021 - see media, there have been no cases in Australia in this cohort to date
    • Emergency department presentations - a number of individuals have required ED presentations. In this situation it is important to remember:
      • Individuals may not yet have Medicare, ensure local billing processes record them as refugees/asylum seekers rather than international arrivals
      • Individuals may not yet have any phone or address details or may be in the process of moving
      • Liaise early with the HSP provider (Victoria = AMES, and at RCH, contact Immigrant health if needed)
    • Disability and equipment needs -  some individuals within the cohort have disability/equipment needs, while this may be complex during the HQ period, it is not a reason for hospital admission. Equipment access has also been difficult with the 449 visa status and lack of NDIS access.
    • Medications - individuals who have had an offshore assessment should arrive with 1 month supply of medications, HQ staff can organise medications if needed in Victoria (and most other jurisdictions)
    • Mental health - individuals may have been separated from immediate family, and there has been wide ranging impact on other Afghan-background populations in Australia. Distress may be amplified by separation and the HQ period, local HQ processes include mental health and social work support, and in-reach trauma counselling services may be available. In Victoria - Foundation House - (and note that the person is an Afghan arrival)

    In Victoria, each of the short term accomodation sites had a designated refugee health team providing triage and addressing immediate needs.  Refugee Health Program nurses can assist in ensuring individuals are linked with local primary care.

    • Contact:, AMES can also provide HAP numbers if available.
    • For individuals in the west contact -, north; central sites are being supported by and Monash Refugee Health.
    • From 8/10/21-Dec 2021, there was a nurse led clinic supporting clients with immediate health needs in the short term accomodation in the CBD, located at the AMES Multicultural hub (0499257260 or Clients could self-refer, or be referred by service providers/case managers. This service expanded to include GPs, MCH (age <4y) and immunisation catch-up (<10y) as of Nov 2021, then closed over Xmas 2021.


    In mid-September most of the new arrivals were still in HQ - after completion of 14 days quarantine most arrivals moved to shared accomodation. As of late Sep 2021 there were around 1800 new Afghan arrivals in Melbourne, in designated short-term accommodation sites. Immediate priorities for large new arrival cohorts include:

    • Immediate (and subsequent) material needs
    • Identifying any unaccompanied minors
    • Interstate transfers (for those moving across state borders)
    • Covid education and vaccination - as above
    • Short-term and then longer-term accomodation - often involving movement across LGAs and services in the early period of settlement
    • Casework - community and household orientation 
      • Centrelink access - for difficulties with Centrelink access contact 
      • Finalising Medicare access - this process was delayed, but Medicare cards will be backdated to arrival, hence billing can be completed retrospectively.
    • Linking with primary care, and where needed, specialist and/or mental health care
    • Health assessments, and catch-up vaccinations
    • Education enrolment (children and young people)  - NB assess age, prior schooling and grade level placement - hubs for new arrivals initially planned in Dandenong High School; Point Cook Secondary College; Gladstone Park Secondary College; Roxburgh College; Brunswick Secondary College; Tarneit Secondary College; Werribee Secondary College; Lakeview Senior College. 

    We will continue to update this page as more information becomes available. 


    There has been wide ranging impact on Afghan communities in Australia, including those who arrived seeking asylum - this is an active consideration in clinic reviews of any new/existing patients. 

    Immigrant health clinic resources. Author Georgie Paxton, Jen Schaefer, Sep 2021, last update 12 Apr 2022  - Contact: