NBR CITIID COVID-19 Cohort
Please cite our work if this resource is useful to you and your research.

Bergamaschi L, et al. (2021) Delayed bystander CD8 T cell activation, early immune pathology and persistent dysregulation characterise severe COVID-19. medRxive. https://doi.org/10.1101/2021.01.11.20248765

In a study of 207 SARS-CoV2-infected individuals with a range of severities followed over 12 weeks from symptom onset, we demonstrate that an early robust bystander CD8 T cell immune response, without systemic inflammation, is characteristic of asymptomatic or mild disease. Those presenting to hospital had delayed bystander responses and systemic inflammation already evident at around symptom onset. Such early evidence of inflammation suggests immunopathology may be inevitable in some individuals, or that preventative intervention might be needed before symptom onset. Viral load does not correlate with the development of this pathological response, but does with its subsequent severity. Immune recovery is complex, with profound persistent cellular abnormalities correlating with a change in the nature of the inflammatory response, where signatures characteristic of increased oxidative phosphorylation and reactive-oxygen species-associated inflammation replace those driven by TNF and IL-6. These late immunometabolic inflammatory changes and unresolved immune defects may have clinical implications.

NBR CITIID Patient Metadata Download

One entry per participant

Patient_IDStudy participant ID
Disease_statusCOVID19 case or swab-negative control
AgeAge at study recruitment
GenderSelf reported gender
COVID19_swab_PCRCOVID19 swab PCR outcome at study recruitment (controls were confirmed COVID19 serology negative, see Methods)
CT_first_pos_swabCOVID19 swab PCR cycle threshold
COVID19_symptomsSymptomatic or asymptomatic infection (with or without previous symptoms) at study recruitment. Note, previous symptoms in asymptomatic participants could not be confirmed COVID19-specific.
Max_resp_supportMaximum respiratory support over course of follow-up
Hospital_outcomeDeceased or alive at end of hospital admission or study follow up period
Severity_groupDisease severity classification based on maximum respiratory support
Severity_group_paperAlphabetised severity classification used in publication
NBR CITIID Timepoint Metadata Download

Multiple entries per participant

Patient_IDStudy participant ID
Sample_IDSample ID, incorporating approximate day of follow-up from study design
Days_from_symptom_or_swabDays between reference date (group A, date of first positive swab; groups B-E, date of self-reported symptom onset) and follow up
Current_resp_supportCurrent respiratory support on day of follow up
hsCRP_mg/LHigh-sensitivity C-reactive protein measure (mg/L)
NBR CITIID Serum Measurements Download
Serum Measure
Sample_ID Sample ID, incorporating approximate day of follow-up from study design (see FILE 1 and 2 for metadata)
IL6_pg.mL Interleukin 6 concentration (pg/mL) measured by standard clinical assay (Addenbrooke's Hosptial)
TNFa_pg.mL Tumour necrosis factor aplpha concentration (pg/mL) measured by standard clinical assay (Addenbrooke's Hosptial)
IL1B_pg.mL Interleukin 1 beta concentration (pg/mL) measured by standard clinical assay (Addenbrooke's Hosptial)
IL10_pg.mL Interleukin 10 concentration (pg/mL) measured by standard clinical assay (Addenbrooke's Hosptial)
IFNg_pg.mL Interferon gamma concentration (pg/mL) measured by standard clinical assay (Addenbrooke's Hosptial)
C3a_pg.mL Concentration of C3 activation product C3a measured by ELISA in EDTA plasma (pg/mL)
C3c_ng.mL Concentration of C3 activation product C3c measured by ELISA in EDTA plasma (ng/mL)
TCC_mAU.mL Concentration of terminal complement complex measured by ELISA in EDTA plasma (mAU/mL)
Spike.IgG Quantified SARS-CoV-2 spike protein IgG antibody titre determined by ELISA
N.IgG Quantified SARS-CoV-2 nucleocapsid protein IgG antibody titre determined by ELISA
Spike.IgA Quantified SARS-CoV-2 spike protein IgA antibody titre determined by ELISA
N.IgA Quantified SARS-CoV-2 nucleocapsid protein IgA antibody titre determined by ELISA
Spike.IgM Quantified SARS-CoV-2 spike protein IgM antibody titre determined by ELISA
N.IgM Quantified SARS-CoV-2 nucleocapsid protein IgM antibody titre determined by ELISA
AUC.Spike.IgGArea under titration curve, spike IgG ELISA at serial serum dilutions
AUC.Spike.IgAArea under titration curve, spike IgA ELISA at serial serum dilutions
AUC.Spike.IgMArea under titration curve, spike IgM ELISA at serial serum dilutions
AUC.N.IgG Area under titration curve, nucleocapsid IgG ELISA at serial serum dilutions
AUC.N.IgA Area under titration curve, nucleocapsid IgA ELISA at serial serum dilutions
AUC.N.IgM Area under titration curve, nucleocapsid IgM ELISA at serial serum dilutions
NBR CITIID Cells Download
Cell type
Sample_IDSample ID, incorporating approximate day of follow-up from study design (see FILE 1 and 2 for metadata)
[Cell populations]Absolute count (cells/uL) of cell populations derived from peripheral blood mononuclear cells. Measured by flow cytometry and enumerated using BD TruCount (see Methods)
NBR CITIID Cytof Download
Sample_IDSample ID, incorporating approximate day of follow-up from study design (see FILE 1 and 2 for metadata)
[Cell populations]Cell proportions as percentage of parent population in whole blood Measured by mass cytometry (see Methods)
NBR CITIID RNASeq Download

Normalised gene expression counts derived from RNA sequencing of whole blood PAXGene tubes, Sample ID as columns, gene IDs as rows.