COVID-19 Resources- SystmOne

The CDRC Covid19 System identifies patients who might be eligible for a covid19 vaccination based on the Enhanced Service specification, Green Book and JCVI guidance.   

CDRC will identify patients who may be eligible for Covid19 vaccination but it is up to the individual clinician to confirm that they should receive it. 

Identifying Patients Who Are Likely To Be Eligible 

1. Patient Flag 

Patients who might be eligible for their first vaccination will have this patient status alert (green virus particle) if your unit has opted in to them: 

Eligible patients will be flagged unless: 

• They have declined the vaccine in the last 12 months 
• They are on the palliative care register with GSF C/D status 
• They have an ‘expiring exception’ in the last 12 months e.g. vaccination not indicated 
• They have had covid19 infection in the last 4 weeks (or 12w for healthy 12-15y) 
• Shingles vaccine in the last 7 days 

2. Pop-up Alert 

Eligible patients will display the following pop-up if your practice has opted in to this system 

3. Patient Searches 

Identifying Why A Patient Is Eligible 

Click on the covid19 icon to open the Covid19 vaccination template. The central panel will display the vaccination cohort the patient is in, which dose appears to be due, which brands of vaccine are likely to be suitable, any relevant long term conditions and other appropriate warnings such as recent shingles vaccination or covid infection. 

To identify the specific Read code(s) that have triggered eligibility for influenza vaccination, right click on the syringe icon and select Why is this Alert on this Patient?  You can then expand the report 

Patients can be invited for their covid vaccination in a number of ways. 

Covid19 Vaccination 

1. Opportunistic invitation – eligible patients will be identified by a C19 icon (if practice opted-in) below the demographics box, on the home page or on the LTC Master Template.  Clicking on the icon will launch the covid vaccination template.  This alert will disappear after vaccination, refusal or addition of other exception code.   

2. Using the invitation searches in the CDRC Vaccination>Covid19 3 Invitation report folder 

The reports are separated into housebound and non-housebound patients 

Patients are excluded from these reports if: 

• Vaccination has been declined in the last 12 months 
• Vaccination not indicated or contraindicated codes are recorded in the last 12 months 
• Patient has had an invitation in the last 2 weeks 
• GSF C/D Palliative care stages 
• Covid19 infection in the last 4 weeks (or last 12 weeks for healthy 5-15 year olds) 
• Shingles vaccine in the last 7 days 

NB – patients who should not have a second dose of Astra-Zeneca vaccine (PHx of venous sinus thrombosis, thrombophilia, heparin-induced thrombocytopenia) will be excluded from the AZ report 

Search	Patients
1.1	Non-housebound patients aged 12 or over OR 5-11 with an at risk condition who have yet to have any vaccine
1.11	Non-housebound patients in 1.1 who are higher risk (over 50 or high risk condition)
1.2	Non-housebound healthy 5-11 year olds who have yet to have any vaccine
1.3	Eligible housebound patients who are yet to have any vaccine
2.1	Non-housebound patients who are due a 2nd dose
2.11-2.13	Non-housebound patients who are due a 2nd dose, divided by initial vaccine type
2.2	Housebound patients who are due a 2nd dose
2.4	Searches to identify all patient you are due or will be due second dose – see information about planning searches later in this section
3.1	Non-housebound patients who are due a third primary dose as they were immmunosuppressed when they had their first or second dose (only functions if the CDRC method of flagging these patients was used)
3.2	Housebound patients who are due a third primary dose as they were immmunosuppressed when they had their first or second dose (only functions if the CDRC method of flagging these patients was used)
4.1	All Non-housebound patients due for a booster – this will include many patients who have not responded to multiple invitations for boosters in the past
4.11	Non-housebound patients due for their 1st booster – most of these patients will have not responded to multiple invitations for boosters in the past
4.111	Patients in 4.11 who are higher risk (more important to target)
4.12	Non-housebound patient due for their 1st booster after three course primary vaccination for immunosuppressed patients (only functions if the CDRC method of flagging these patients was used)
4.13	Non-housebound patients who are due for an Autumn 2022 booster – this does not include patients who have never had a booster – use 4.1 to identify patients who need their first booster OR and Autumn booster
4.21	Housebound patients who need a booster (1st booster or Autumn booster)
4.22	Housebound patients who were immunosuppressed at time of 1st or 2nd vaccine who need a booster following their third primary dose (only functions if the CDRC method of flagging these patients was used)
5.1	All non-housebound patients who are eligible for a vaccine (from 1.9.22)
6.1	All housebound patients who are eligible for a vaccine (from 1.9.22)
6.2	All housebound patients who are eligible for or will become eligible for a vaccine (from 1.9.22) – see later information

More information about eligibility, vaccine dose due, vaccine brand recommended and relevant warnings can be seen on the Covid19 Vaccination template 

Invitations can be sent via the S1 Communications Annexe, SMS texting, email, telephone or letter.  Add the code Severe acute respiratory syndrome coronavirus 2 vaccination invitation short message service text message sent Y211f to indicate invitation. This will remove the patient from the invite list for 2 weeks. 

The SMS invitation code is the only one available – add an alternative method of invitation as free text if applicable.  This is not ideal but repeated requests for more codes to NHSD have been ignored. 

Running these searches at fortnightly intervals will ensure that you invite all the eligible patients until they have been vaccinated or a reason for not vaccinating has been recorded.  

Special Groups 

There are searches to identify patients in specific groups, to help more specific targeting: 

Capacity Planning 

The following searches will allow for more detailed second dose planning e.g. to estimate the number of eligible patients in the future 

These searches show all patients who are or will be due a second dose or a booster.  

4.31 and 4.32 identify people who will be due the first booster 

4.41 and 4.42 identify people who will be due any booster from Autumn 2022 – including a 1st booster or a spring booster. 

NB these searches do not exclude the following, so are not suitable for creating lists of people to invite. 

• Patient has had an invitation in the last 2 weeks 
• GSF C/D Palliative care stages 
• Covid19 infection in the last 4 weeks (or last 12 weeks for healthy 12-15 year olds) 
• Shingles vaccine in the last 7 days 

Information for capacity planning can be obtained in two ways: 

1. Use a Report Output 

Show the patients from the relevant search 

Choose Select Output then Pre-defined Output then choose Covid Vaccines 

A table of patients will be shown with data for: last vaccine date; if patient has been flagged as needing 3rd primary dose; 1st vaccine date; 2nd vaccine date; any booster vaccine dates.  This table can be saved as a csv if needed. 

NHS number

Name

Name

Postcode

(Blank)

(Blank)

(Blank)

(Blank)

(Blank)

(Blank)

(Blank)

Last covid vacc

3rd primary dose patient

1st Vacc

2nd Vacc

3rd / Booster Vaccs (1)

3rd / Booster Vaccs (2)

3rd / Booster Vaccs (3)

3rd / Booster Vaccs (4)

xxxxx

xxxxx

xxxxx

xxxxx

01-Dec-21

17-Feb-21

22-Apr-21

01-Dec-21

xxxxx

xxxxx

xxxxx

xxxxx

02-Apr-22

Covid Vaccine Third Dose

21-Jan-21

09-Apr-21

12-Oct-21

24-Jan-22

02-Apr-22

xxxxx

xxxxx

xxxxx

xxxxx

02-Nov-21

05-Feb-21

23-Apr-21

02-Nov-21

xxxxx

xxxxx

xxxxx

xxxxx

02-Nov-21

Covid Vaccine Third Dose

17-Feb-21

28-Apr-21

02-Nov-21

xxxxx

xxxxx

xxxxx

xxxxx

02-Nov-21

23-Jan-21

12-Apr-21

02-Nov-21

xxxxx

xxxxx

xxxxx

xxxxx

03-Feb-22

Covid Vaccine Third Dose

19-Jan-21

25-Mar-21

28-Oct-21

03-Feb-22

xxxxx

xxxxx

xxxxx

xxxxx

04-Nov-21

10-Feb-21

30-Apr-21

04-Nov-21

xxxxx

xxxxx

xxxxx

xxxxx

04-Nov-21

25-Jan-21

13-Apr-21

04-Nov-21

xxxxx

xxxxx

xxxxx

xxxxx

05-May-22

12-Jan-21

30-Mar-21

05-Oct-21

05-May-22

2. Use a Search Breakdown 

Breaking Down 2nd Dose Planning Searches 

For each of the searches you can set the following breakdown options to see all the info you need to plan second doses.   

Demographics – name, telephone number etc (if needed) 

Covid19 Vaccine – All (code 1/2) # (CDRC Vaccinations / Covid19) 

                >Event details 

                                >Event week commencing – gives date of first vaccine 

                                >Event done at – gives location of first vaccine(if needed) 

Then order by Event date and Event done at.   

NB – Patients who are due second AZ but where second AZ is contraindicated are excluded from the AZ report (e.g. history of heparin induce thrombocytopenia) 

If you need a breakdown of all patients who will be due a second dose – use the ‘All vaccine types’ report and use the additional breakdown options. 

Covid19 Vaccine – Moderna Sept 20 – Aug 21 (code or S1 or med) ONLY #/ (CDRC Vaccinations / Covid19) > Reporting ID – patients who had Moderna as first dose 

Covid19 Vaccine – Oxford AZ Sept 20 – Aug 21 (code or S1 or med) ONLY #/ (CDRC Vaccinations / Covid19) > Reporting ID – patients who had Oxford AZ as first dose 

Covid19 Vaccine – Pfizer Sept 20 – Aug 21 (code or S1 or med) ONLY #/ (CDRC Vaccinations / Covid19) > Reporting ID – patients who had Pfizer as first dose 

Covid19 Vaccine – Type – More than 1 #/ (CDRC Vaccinations / Covid19) > Reporting ID – patients where brand of first dose is unclear (e.g. not recorded or more than one brand recorded) 

Covid19 Vaccination – AstraZeneca – patients with clotting contraindications / (CDRCVaccinations / Covid19) > Reporting ID – patients who should not have AZ as second dose 

Breaking Down Booster Dose Planning Searches 4.31 and 4.32 

For each of the searches you can set the following breakdown options to see all the information you need to plan booster doses.   

Demographics – name, telephone number etc (if needed) 

Covid19 Vaccine – 2nd dose (code, latest) # (CDRC Vaccinations / Covid19) 

                >Event details 

                                >Event week commencing – gives date of first vaccine 

                                >Event done at – gives location of first vaccine(if needed) 

Then order by Event date and Event done at.   

If you wish to highlight the patients with current infection, also tick: 

Eligibility – Covid19 Infection confirmed in last 4w # > Strategic Reporting ID > Patient ID 

AND 

Eligibility – Covid19 Infection confirmed in last 12w – aged 12-17 without risk condition #> Strategic Reporting ID > Patient ID 

Breaking Down Spring Booster Dose Planning Searches 4.41 and 4.42 

For each of the searches you can set the following breakdown options to see all the information you need to plan the next doses.   

The breakdown below shows all people who will become eligible for a covid vaccine follow up dose in Spring to Summer 2022 – 2nd dose, booster, spring booster etc and the date of their last vaccine. 

Covid19 Vaccine – (code 1/2/booster) latest # (CDRC Vaccinations / Covid19) 

>Coded entries 

                                >Read code description 

>Event details 

                                >Event week commencing 

Then order by Event date 

Patients with Administration of first dose of SARS-CoV-2 vaccine – will need 2nd dose 

Patients with Administration of second dose of SARS-CoV-2 vaccine – will need booster dose 

Patients with Immunisation course to maintain protection against SARS-CoV-2 – will need 2nd / 3rd (Autumn) booster 

To administer the vaccine click on the C19 icon at the top of the screen. The influenza vaccine
template will open and lead you through the process, adding the correct Read codes. 

For patients without the icon, you can launch template from the CDRC Master Template or add it to one
of your own templates, toolbars or clinical tree. 

The template features 

Section to code exceptions/adverse reactions/refusal.  Relevant codes already in the record are shown in the adjacent panel.  The far right panel here shows all vaccines administered in recent years 

The next sections covers cohorts, reasons for eligibility and warning such as pregnancy. 

The final section allows you to record the vaccine.  Vaccines that do not appear appropriate will be greyed-out.  You can override this by clicking through to the non-standard vaccine tab. This template has been prepared in anticipation that SystmOne will be able to meet MHRA and NHSD standards, possibly in the new year. Until then practices are reminded that Pinnacle is currently the only approved system for the onsite recording of Covid-19 vaccine administration.

The following checks are run when the vaccine protocol is launched 

All protocols 

• Patient is over 16 
• Patient is not pregnant 
• Patient does not have history of adverse reaction to covid 19 vaccine 
• Patient does not have a record of ‘contraindicated’ or ‘not indicated’ in the past 12 months 
• Patient has had any vaccine in the last 7 days 
• Patient has had covid19 infection in the last 28 days 
• Patient has already completed a course of covid19 vaccination 

First vaccination protocols 

Patient hasn’t already had a first dose 

Second vaccination protocols 

The patient has had the first dose of the same vaccine at the appropriate time period e.g. at least 19 days ago for Pfizer. 

The PSD questionnaire will then be displayed with automatic warnings. 

Once the first vaccination is complete, the user will be prompted to book a second appointment for the second dose.  

Guidance 

The guidelines (issued in early September 2021) to identify patients who need a 3rd dose as part of their primary regime are complex (guidance).  Some of the information required might not be coded in the primary care record e.g. biologics being issued in secondary care. 

The guidance is based on looking for patients with significant immunosuppression at the time of 1st and 2nd doses of vaccine 

The following resources can help: 

Searches 

The following searches will help to identify potentially eligible patients 

1.1	Patients who are likely to be eligible for 3rd dose
1.11	Patients in 1.1 who haven’t been flagged as needing a third dose
1.2	Patients who might be due for 3rd dose depending on drug doses/timing
1.21	Patients in 1.2 who haven’t been flagged as needing a third dose
1.3	Patients who have been flagged by the practice as needing a 3rd dose (see below)

Patients will only appear in the first four searches once they have had their second dose of vaccine 

Screening Potential Eligible Patients 

The vast majority of patients in the ‘probables’ 1.1 search will be eligible for a third dose. 

Around 1/4 to 1/3rd of patients in the ‘possibles’ 1.2 search are likely to be eligible for a third dose, with another ~10% probably needing some input from supervising consultants regarding hospital treatment such as biologics. 

For some patients it will be clear why 3rd dose is needed e.g. transplant or chemotherapy before 1st/2nd doses.  For others more information will be needed.  There are two tools which may help with this 

1. Report Output – which shows the list of patients with relevant information. From the search, show the patients, then click on the Select Output button, then tick Pre-defined report output and then choose the ‘probables’ or ‘possibles’ report outputs shown below.  It will usually be easier to use the export to spreadsheet option to view and manipulate the list. 

2. The Covid19 Vaccination template will help with this screening.  The panel will show relevant drug and lymphocyte count information with the covid vaccine administration dates shown. In the example below, the patient was lymphopenic before the first and second doses of vaccine. This template is also useful to view timing and quantity of steroid prescribing in relation to the vaccine doses. 

The process can be streamlined by selecting all patients in the screening list, right clicking on the list, then choose Actions > Use Data Entry Template, then choose the Covid19 Vaccination template, and at the next dialogue box add your details in the staff member box.  S1 will then open each patient’s record with the template.  

Flagging Patients For Third Dose 

As there is no Snomed code to indicate need for booster an alternative is to use a recall.  Ask an administrator to add a recall type with the name Covid Vaccine Third Dose (spelling and spaces important).  Then add a pending recall to any patient who should be offered the booster.  This can be done from the screening template or from a patient list in reporting.  The date of the recall does not matter.  Patients with such a recall will show on the 1.3 search above 

NB – a previous version of this guide suggested using the recall name Covid Vaccine Booster. If you have added this recall, it will still be detected by the system.  Covid Vaccine Third Dose is a more accurate title for the recall.  If you wish to change the recall name you can do so easily Renaming A Recall Type 

Inviting Patients 

See Patient Invitation above

After Vaccination 

Patients who have had a third dose, will need a booster dose sthree months later.  To ensure the system is able to recognise these patients, ensure that the Covid Vaccine Third Dose recall is not deleted.  You may wish to mark the recall as Seen once the patient has had the third dose so the recall doesn’t flag in the pending recalls screen, but this isn’t essential.  In this way you will always be able to show the list of patients who need/needed a third primary dose. 

The following process can help clinicians add a PSD for the covid19 vaccine.  

Step 1. – Create a local copy of the PSD report. 

As you progress through the vaccination programme you will need to update this report with the current cohort. The initial report is set for cohort 2 stage. 

To move this on remove the report highlighted above and replace it with one of these reports 

Run this report which will identify eligible patients in the relevant cohorts with an upcoming appointment who do not already have a PSD recorded within 7 days of that appointment. To see which appointments are due, use the Breakdown options to select the appointment details. 

Select and highlight the relevant patients.  Deselect any patients who are not suitable for vaccination. Click on the magnifying glass icon to display the selected patients.   

At the next screen, click on the scroll to add the PSD 

…..using this text 

‘This patient is eligible to receive  Covid-19 mRNA Vaccine BNT 162b2 0.3mls Intra-Muscular (IM) Injection   in accordance with Public Health England Immunisation against infectious disease (Green Guide) and JCVI recommendations for the purpose of protection against COVID-19. Dr Xxxxx Xxxxx ‘

This PSD will then be displayed on the covid19 vaccination template for 7 days 

Alternatively, use the PSD tab of the covid 19 vaccination template the add the same information to individual patient records.  There is a preset text option for quick entry. 

TPP/Primis Search Issues 

There are significant differences between the searches to identify patient in cohort 6 between CDRC and TPP/Primis 

These differences are summarised in the table below. 

	CDRC	TPP
Hyposplenism
Respiratory	Includes any life-threatening asthma episodes Counts any 3 oral steroids prescriptions in the last 3 months	Only counts 3 oral steroid prescriptions if in consecutive months
CNS	Must have epilepsy QoF code and be taking epilepsy medication	Includes any codes for epilepsy including some seizure codes which may have been one-off events.  Does not look at epilepsy medication. Many patients picked up by this strategy had childhood epilepsy or seizures only. Includes some codes that may have been one-off events e.g. post-concusional syndrome
Chronic liver disease	Includes non-alcoholic fatty liver	Does not include NAFLD Does include ‘fatty liver’ which may have been a transient phenomenon Includes resolved hepatitis B and C
Chronic Kidney Disease		Includes many glomerulonephritis codes which may have been transient – e.g. minimal change nephropathy Does not take into consideration CKD ‘resolved’ codes
Chronic Heart Disease		Includes many codes for valve disease (often mild or benign) – this does not seem to be indicated according to the JCVI criteria unless 1. congenital, 2. causing significant problems such as heart failure Codes for superficial thrombophlebitis included (likely to be a coding error as these codes are children of venous thrombosis) Retinal vein occlusion is included
BMI >40
Serious mental illness		Does not take ‘in remission’ codes into account.
Learning disability
Diabetes		Does not take ‘in remission’ codes into account
Immunosuppression	Will detect any patients whose hospital provided immunosuppressants/biologics are recorded on their S1 repeat templates	Does not take ‘immunosuppression resolved’ codes into account.
Carers**	Only counts ‘non-professional’ carers	Counts professional carer codes as well as non-professional

The following searches will help practices check any differences between CDRC and TPP searches 

The first search identifies people coded as professional carers (‘Carer’) who are not also recorded as informal carers.  The recommended code for informal carers is ‘Patient themselves providing care’. 

The second search shows all patients identified by the TPP searches but not by CDRC. 

Both searches exclude people in cohorts 1-5; those who have been vaccinated already; or where the vaccine has been declined or is not indicated/is contraindicated. 

Cohort 6 CDRC Change Log 

15/2/21	VTE and AF added Asthma limited to those with history of hospital admission or >=3 courses of steroids in the last year Patients <65 in residential care added
19/2/21	Lifethreatening asthma attack added Asthma limited to >=3 courses of steroids in the last 3 months
22/2/21	Epilepsy expanded to included 16 and 17 year olds Neurofibromatosis type 1 and hydrocephalus added to neurological conditions Cardiomyopathy, coarctation of the aorta, LVH and LVSD added to cardiac conditions
24/2/21	Personality disorder included Eating disorder in the last 5 years included
27/2/21	Tuberous sclerosis included
4/3/21	More myeloproliferative conditions added

The following searches (CDRC Vaccination > Covid19 1 Cohorts) identify patients who should definitely not have a first or second dose of the Astra-Zeneca vaccine.  This is a very small group of patients with a history of venous sinus thrombosis, thrombophilia or heparin induced thrombocytopenia. 

The first search identifies all patients in this group. 

The second identifies these patients who have yet to have a coronavirus vaccine – so they can be informed not to have AZ and invited for an alternative vaccine. 

The third identifies these patients who are due to have a second AZ vaccine.  They should be informed not to have a second AZ vaccine and an alternative brand should be administered.  

The ‘Consider Invitation for 2nd Oxford AZ vaccine’ searches now automatically exclude patients in the ‘contraindicated’ group described at the top of this page. 

There are searches to identify some of the commoner quality control issues. 

QC – 2nd dose without first dose	May be due to incorrect coding of the first dose or missing coding of the first dose
QC – AZ and Pfizer on the same day	Both vaccines recorded on the same day – highly likely to be an error
QC – Discordant 1st and 2nd vaccines	May have been a deliberate decision but may have been due to coding error
QC – Unbranded Vaccine	First dose given but brand not specified which makes planning for the second dose more difficult