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🩸 Serology

About

  • In EAVE-II we have access to two serology datasets.
  • These contain measurements of IgG (Immunoglobin-G) in individual's blood serum.
  • Measurements:
    • Quantative: IgG (Binding Activation Units [BAU])
    • Qualitative: Postivie/Equivocal/Negative
  • Key Timestamps:
    • Sampledate_iso: the date the measurement was taken from the individual
    • SpecimenDate: the date the measurement was received in the lab
  • Different assays were used for the different datasets (see details below).

Primary Care

serology_primcare_july22_v3.rds

Information

value
size 1164587
mtime 2022-07-14 10:46:55
ctime 2022-07-14 10:46:55
file serology_primcare_july22_v3.rds
nrows 66531

Columns

name type label examples description
EAVE_LINKNO chr EAVE Study Identifier EAVE-II Identifier, pseudoynmised CHI numbers are used to create randomly assigned study index numbers.
LabSpecimenNo chr Number of laboratory specimen Number of laboratory specimen
Sampledate_iso dttm Sample Date 2020-07-27, 2020-11-30, 2020-12-07, 2020-07-20, 2020-09-07 The date the serology measurement was taken from the individual (in ISO format)
year dbl Year 2021, 2020, 2022 Year of the lookup file used to determine the Health Boards
isoweek dbl Week of Pandemic 25, 30, 23, 32, 31 Week since the start of the pandemic
sex chr Sex (number) F, M Sex at birth, extracted by the serology team, it should not be trusted to be accurate
age dbl Age 16, 19, 18, 17, 15 Age of the study given in years, extracted from the serology files - and shouldn't be well trusted
healthboard chr Health Board NHS Greater Glasgow and Clyde, NHS Lothian, NHS Lanarkshire, NHS Fife, NHS Tayside The Scottish Health Board in which the individual was registered with.
SpecimenOrigin chr Origin of specimen Hospital Where was the specimen taken. This is a primary care dataset, all values are 'Hospital'?
DateCollected dttm Date Collected 2020-12-09, 2021-01-14, 2020-10-15, 2020-12-16, 2020-10-08 The date that the specimen was collected from the origin (where it was taken)
EcossDateReceived dttm ECOSS Date 2020-12-09 23:21:50 The date in which the data was transfered into ECOSS
SpecimenDate dttm Specimen Date 2020-12-09, 2021-01-14, 2020-10-15, 2020-12-16, 2020-10-08 The date in whcih the specimen was tested by the assay for IgG levels (note: use Sampledate_iso for the date in which the blood specimen was extracted from the study
SpecimenTypeRaw chr Specimen Type Raw STS Raw code for the specimen type (always STS as this is blood serum data)
SpecimenType chr Specimen Type Serum Always 'Serum' as this is serology dataset
SpecLevel2Group chr Blood other
SpecLevel1Group chr Normally Sterile Site
OrganismRaw chr Organism Raw (stest) covid-19 (sars-cov-2) igg,negative, (stest) covid-19 (sars-cov-2) igg,>positive, (stest) covid-19 (sars-cov-2) igg,equivocal Raw data of the test result from the assay
Type chr Type 2019-nCoV IgG Type of measurement (almost always IgG 2019-nCoV)
OriginalOrganism chr Original organism Coronavirus 2019-nCoV IgG negative, Coronavirus 2019-nCoV IgG, Coronavirus 2019-nCoV IgG equivocal Original organism - Coronavirus 2019 positive or negative
test_result_qual chr Qualitative Test Result Negative, Positive, Equivocal Qualitative test results from the assay for the presence (or lack thereof) of IgG to SARs-CoV-2. The assay defines the threshold that determines +ve or -ve tests.
test_result_quant chr Quantative Test Result <3.8, >2080.00, <4.81, <3.80, >400.0 IgG measurements in Binding Activation Units [BAUs] that are measured by the assay. There are values that are truncated above/below certain values as the result was out-of-bounds of the assay's sensitivity for these.
QNum dbl Quantative Measumrent Value (Number) 4.9, 3.9, 4.3, 4.4 The raw quantative number value, removing truncated values (note: not so safe to use this as values below AND above the assay threshold have been set as NA
Text chr Text covid-19 - antibodies covid-19 (sars-cov-2) igg: positive specimen type: serum -------------------------------------------------------------------- dr sally mavin, clinical scientist final report, covid-19 - antibodies covid-19 (sars-cov-2) igg: negative specimen type: serum -------------------------------------------------------------------- released from instrument: liaisonxl 12/06/20 at 1:37 pm final report, covid-19 - antibodies covid-19 (sars-cov-2) igg: negative specimen type: serum -------------------------------------------------------------------- released from instrument: liaisonxl 05/03/21 at 9:19 am final report, covid-19 - antibodies covid-19 (sars-cov-2) igg: negative specimen type: serum -------------------------------------------------------------------- released from instrument: liaisonxl 14/09/20 at 11:13 am final report Raw text output from the final report

Overview

  • People who have attended primary care during the pandemic and had their blood taken (for unspecified reasons)
  • The selection of samples to test for IgG was performed in such as way so that the cohort is fairly representative of the scottish population (in terms of age and sex)
    • note: with the exception of under 15s, ages 15-20 are oversampled inorder to account for a lack of blood samples of young children
    • Due to attending primary care, the cohort is less healthy than the Scottish Population
  • Approximately 60,000 samples; some individuals with multiple samples
  • Covers the period March 2020 - March 2022

Assay Information

  • Diasorin SARS-CoV-2 IgG assay was used up to the week commencing 12th Apr 2021, with Diasorin SARS-CoV-2 TrimericS IgG used thereafter

Important

Due to a change in assays used in the measurement of antibodies for the primary care cohort, the data must be transformed for the results to be consistent between the two assays that were used 

df_serology_primcare <- df_serology_primcare %>%
                        mutate(IgG = ifelse(Sampledate_iso < "2021-04-12",2.6*IgG,IgG),
                               QualResult = ifelse(IgG<33.8,"Negative", "Positive"))

Blood Donors

serology_snbts_july22_v3.rds

Information

value
size 544427
mtime 2022-07-14 10:46:55
ctime 2022-07-14 10:46:55
file serology_snbts_july22_v3.rds
nrows 46227

Columns

name type label examples description
EAVE_LINKNO chr EAVE Study Identifier EAVE-II Identifier, pseudoynmised CHI numbers are used to create randomly assigned study index numbers.
SampleID chr Sample ID Original Sample ID from the serology team
age dbl Age 57, 55, 56, 54, 52 Age of the study given in years, extracted from the serology files - and shouldn't be well trusted
sex chr Sex (number) F, M Sex at birth - extracted from the serology files/team - it should not be trusted as being reliable
isoweek dbl Week Number 28, 36, 32, 41, 51 Week number since the start of the pandemic
year dbl Year 2021, 2020, 2022 Year of the lookup file used to determine the Health Boards
Sampledate_iso dttm Sample Date 2021-12-20, 2020-07-02, 2021-12-30, 2020-07-06, 2022-01-14 The date the serology measurement was taken from the individual (in ISO format)
hb chr Health Board NHS Lothian, NHS Greater Glasgow and Clyde, NHS Tayside, NHS Grampian, NHS Lanarkshire The Scottish Health Board in which the individual was registered with
assay chr Assay Euroimmune, Abbott Antibody Assay machine was was used when measuring the blood serum sample for the presence of IgG antibodies to SARs-CoV-2
test_result_qual chr Qualitative Test Result Positive, Negative, Equivocal Qualitative test results from the assay for the presence (or lack thereof) of IgG to SARs-CoV-2. The assay defines the threshold that determines +ve or -ve tests.
test_result_quant chr Quantative Test Result 0.1, 0.02, 0.2, 0.01, 0.03 IgG measurements in Binding Activation Units [BAUs] that are measured by the assay. There are values that are truncated above/below certain values as the result was out-of-bounds of the assay's sensitivity for these.

Overview

  • People who have donated blood throughout the pandemic
  • There is a bias towards young females as they donate blood more regularly than other groups (comparitavely)
  • This is a typically healthy/younger cohort than the Scottish Population
  • Approximately 40,000 samples
  • Covers the period March 2020 - March 2022

Assay information

  • Abbott SARS-CoV-2 IgG assay was used up until the week commencing 19th Oct 2020 followed by EuroImmun SARS-CoV-2 IgG ELISA
Last update: August 25, 2022
Created: August 25, 2022

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