COVID-19 Second Generation Surveillance System (COVIDSGSS) Dataset

COVID-19 Second Generation Surveillance System (COVIDSGSS) Dataset#

# define target dataset to document
schema = 'nhsd'
table = 'COVIDSGSS'
version = 'v0003'
# import functions from script helper
import sys
script_fp = "../../../../scripts/"
sys.path.insert(0, script_fp)
from data_doc_helper import DocHelper
# create instance
document = DocHelper(schema, table, version, script_fp)
# markdown/code hybrid cell module requirement
from IPython.display import display, Markdown

1. Summary#

display(document.style_table(document.get_dataset_info()))
Dataset descriptor Dataset-specific information
Name of dataset in TRE COVIDSGSS
Other name None
Keywords COVID-19, Testing
Short description UK Health Security Agency’s (UKHSA) Second Generation Surveillance System (SGSS) is used to capture routine laboratory surveillance data on infectious diseases from diagnostic laboratories across England. This dataset comprises results from Pillar 1 swab (antigen) testing for SARS-CoV-2 (i.e. patients in hospital and NHS key workers) and Pillar 2 swab testing (i.e. the wider community at drive through test centres, walk in centres, home kits returned by post, care homes, etc.). A record represents one swab test.
Owner NHS England
Geographical coverage England
Temporal coverage 06/04/2020 onwards
TRE temporal coverage 06/04/2020 onwards
Frequency of update Annually
Date of last extract None
DOI None
Data resolution Swab test
Number of variables None
Number of participants None
Number of observations None
Version None
Key link https://digital.nhs.uk/about-nhs-digital/corporate-information-and-documents/directions-and-data-provision-notices/data-provision-notices-dpns/sgss-and-sari-watch-data
Specific restrictions to data use Research must be related to COVID-19. For examples of research purposes acceptable to NHS England see the COVID-19 Public Health Directions 2020: https://digital.nhs.uk/about-nhs-digital/corporate-information-and-documents/directions-and-data-provision-notices/secretary-of-state-directions/covid-19-public-health-directions-2020

2. Metrics#

The tables below summarise the COVIDSGSS dataset in the UK LLC TRE.

Table 1 The number of participants from each LPS that are represented in the COVIDSGSS dataset in the UK LLC TRE
(Note: numbers relate to the most recent extract of NHS England data)

display(document.style_table(document.get_cohort_count()))
LPS Participant count
ALSPAC 2524
BCS70 2205
BIB 9398
ELSA 1761
EPICN 2405
EXCEED 2945
FENLAND 3135
GLAD 31462
MCS 6770
NCDS58 1691
NEXTSTEP 2077
NIHRBIO_COPING 7170
NSHD46 404
TEDS 3479
TRACKC19 6363
TWINSUK 4074
UKHLS 2660
TOTAL 90523

3. Helpful syntax#

Below we will include syntax that may be helpful to other researchers in the UK LLC TRE. For longer scripts, we will include a snippet of the code plus a link to Git where you can find the full script.

Contents