COVID-19 vaccination programme

This guidance provides detail about the third phase of the COVID-19 vaccination programme in England. It includes information about the medical exemption process and emerging information in relation to the Omicron variant.

Location: England
Audience: GPs Practice managers
Last reviewed: 23 December 2021
COVID virus illustration

Third phase launch

NHSE/I released the ES (enhanced service) specification for the third phase of the CVP (COVID-19 vaccination programme) in September 2021. As with the previous phases, it is delivered by groups of practices, generally covering PCN (primary care networks) footprints.

This third phase was initially focussed on booster vaccinations for those groups prioritised in the first phase of the programme (1-9), including:

  • those living in residential care homes for older adults
  • all adults aged 50 years or over
  • frontline health and social care workers
  • those aged 16 to 49 years with underlying health conditions that put them at higher risk of severe COVID-19, and adult carers
  • adult household contacts of immunosuppressed individuals.

It also included the continuation of the offer of vaccination to those patients who did not take up or were previously not eligible to receive vaccination in phases 1 and 2.

The service specification arrangements for this phase of the programme initially mirrored the arrangements for the previous phases. Groupings would still get the £12.58 item of service fee for each vaccine administered. An additional £10.00 payment would again be paid for vaccinating those who are housebound or resident in a care home.

In November 2021, those aged 40-49 with underlying health conditions were added to those eligible for booster vaccinations.

The prioritised groups also include those who are housebound and those severely immunosuppressed. The NHS will offer vaccination in descending age groups, with priority given to older adults and those in a COVID-19 at-risk group.


Changes following the emergence of the Omicron variant

Following the identification of the COVID-19 Omicron variant, the Government has accepted JCVI advice to widen the age range for vaccine eligibility to include all aged 16 to 39 years and to shorten the time from last vaccination to booster from six to three months. This shortening of time will be reflected in the national booking service by 13 December.

As of 20 December, 12 to 15 year-olds are able to receive a second dose of the Pfizer vaccine, no sooner than 12 weeks after their first dose. 

Fourth doses for severely immunosuppressed patients

Severely immunosuppressed individuals who have completed their primary course (three doses) should be offered a booster dose with a minimum of three months between the third primary and booster dose.

Those who have not yet received their third dose may be given the third dose now to be able to receive their further booster dose in three months. This is in line with the clinical advice on optimal timing.

Changes to payments

To support the quicker roll-out of boosters, NHSE/I has announced that there will be some additional funding to support PCN groupings to step up capacity by increasing:

  • the IoS (item of service) fee for COVID-19 vaccinations to £15 from 1 December 2021 to 31 January 2022 (Mondays to Saturdays)
  • the IoS fee to £20 for vaccinations administered on Bank Holidays and Sundays from 1 December 2021 to 31 January 2022
  • the IoS fee to £20 for the full period running 25th December to the 3rd January inclusive
  • the supplement for vaccination of housebound patients from £20 to £30 between 1 December 2021 and 31 December 2022, backdated for those already carried out.
Groupings wishing to join the vaccination programme in the third phase


Practices wishing to opt-in to the phase 3 enhanced service to deliver in early January as part of a PCN (primary care network) need to notify their local commissioner by 3pm on 10 December.

Moving vaccines within a PCN grouping

Considering the need to rapidly expand capacity, the MHRA (Medicines and Healthcare products Regulatory Agency) has expanded the circumstances in which the COVID-19 vaccine may be moved within PCN grouping’s sites.

GP practices within a PCN grouping may move COVID-19 vaccine from their designated site to collaborating individual GP practices within the PCN grouping to increase take-up of the vaccine.

Movement continues to be subject to:

  • all requirements and guidance on the movement, storage and handling of COVID-19 vaccines being adhered to
  • there being no onward movement of the vaccine. For example, it is not permitted for a PCN to transport the COVID-19 vaccine from the PCN Grouping’s designated site(s) to a collaborating individual GP practice and then onto a pop-up site or care home etc
  • the arrangements being reflected in the PCN grouping’s collaboration agreement.

The NHSE template collaboration agreement has now been updated to reflect these changes.

Suspension of the post-vaccination observation period

The post-vaccination 15 minute observation period for the Pfizer vaccine has been temporarily suspended to allow for an increase in vaccinations being carried out.


Vaccination medical exemptions process

A systematic medical exemptions process has been introduced to ensure that those who, for medical reasons, should not be vaccinated (and/or be tested) for COVID-19 are not disadvantaged.

Given the need for clinical judgement and access to patient records, GPs, secondary care clinicians and midwives have all been requested to assess applications.

Steps have been taken to ensure this does not impact workload (eg. no appointment will be required and there will be a pre-screening process).

Read the BMA guidance detailing the process, clinical criteria, and payment mechanism.


The vaccines

There are three vaccines currently being supplied for the vaccination programme., Pfizer, AstraZeneca and Moderna. As these and other vaccines are developed and tested, their characteristics might change.

The PGDs (Patient group directions) and national protocols for Moderna and Pfizer will be updated by 13 December. Both vaccines should be used with equal preference in the COVID-19 booster programme.


Details of available workforce support are available on the Future NHS website.

AstraZeneca vaccine and under 30s

MHRA, JCVI and EMA have all made announcements on serious thromboembolic events with concurrent thrombocytopenia associated with the use of the AstraZeneca vaccine.

This small number of serious adverse events needs to be seen in the context of over 4m COVID-19 infections since the start of the pandemic causing more than 120,000 deaths.

JCVI guidance states that AstraZeneca should only be used for first and second doses for those aged over 30. They are now recommending that 18–29-year-olds who do not have underlying health conditions putting them at increased risk of COVID-19 should be offered an alternative to the AstraZeneca vaccine where available.

MHRA and JCVI confirmed that the risk/benefit of getting the vaccine is favourable for the vast majority of people, but more 'finely balanced' in younger people.


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