Table 2 Description of data sources used to estimate vaccine effectiveness

Pillar 1 and 2 testing data

SARS-CoV-2 PCR testing in England is undertaken by hospital and public health laboratories (Pillar 1), as well as by community testing (Pillar 2). Pillar 1 testing data is available from UKHSA labs and NHS hospitals for those with a clinical need, and health and care workers. Pillar 2 community testing is available to anyone with symptoms consistent with COVID-19 (high temperature, new continuous cough, or loss or change in sense of smell or taste), anyone who is a contact with a confirmed case, care home staff and residents, and to those who have self-tested as positive using a lateral flow test (LFT). SGTF information to classify variants is available from some Pillar 2 tests.

Date of birth (age), period (week of the test), variant status (where it was determined by SGTF or period), previous positivity

NIMS vaccination record

The National Immunisation Management System (NIMS) contains demographic information on the whole population of England who is registered with a general practice physician in England and is used to record all COVID-19 vaccinations.

Vaccination status, index of multiple deprivations, ethnicity, geographic region, date of birth, health and social care worker status, clinical risk group status, clinically extremely vulnerable, severely immunosuppressed, care home status

Genomics data

Sequencing and genotyping are undertaken through a network of laboratories, including the Wellcome Sanger Institute. Whole-genome sequences are assigned to UKHSA definitions of variants based on mutations. Data were provided by the Genomics Cell at UKHSA.

Variant status (sequencing and genomics)

Secondary Care Hospital Admission Data (SUS)

SUS is the national electronic database of hospital admissions that provides timely updates of ICD-10 codes for completed hospital stays for all NHS hospitals in England. Up to 24 ICD-10 diagnosis fields can be completed in SUS for each admission with the first diagnosis field indicating the primary reason for admission. Length of stay was calculated as the date of discharge−date of admission. Where multiple admissions were linked to the same sample date the first admission after the sample date was retained and episode length was calculated by summing the stay length for each admission. Data were restricted to those with ARI in the first diagnosis field and where the length of stay was at least two days.

Emergency Care Hospital Admission Data (ECDS)

Emergency Care hospital admissions include hospital admissions through emergency departments but not elective admissions. Admissions due to an injury were excluded. Admissions were identified where the Emergency Care Destination code was either discharged to a ward, intensive care unit, coronary care unit, high dependency unit, or where there was a date on which the decision to admit the patient was made. Admissions with an acute respiratory illness (ARI) SNOMED coded as the reason for attending emergency care were flagged.