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Variable Legend

Timepoint 🕙

Variables

  • Timepoint

Description

  • This variable represents the day the sample was acquired after a positive SARS-CoV-2 PCR test was received

  • Most donors had samples taken at

    • Day 1: When donor tested positive for SARS-CoV-2 (Within acute phase of infection)

    • Day 28: ~ 1 month post infection (near start of convalescent phase)

    • Day 56: ~ 2 months post infection

    • Day 90: ~ 3 months post infection

    • Day 120: ~ 4 months post infection

    • Day 180: ~ 6 months post infection

Disease Severity 😷

Variables

  • Disease severity

Description

  • Categorical variable describing the severity of the SARS-CoV-2 symptoms experienced by the donors

  • The donors would be classified as asymptomatic if no symptoms were present, and symptomatic donors were classified as mild or severe

Clinical Symptoms 🌡️

Variables

  • Fever , Cough, Change or loss of taste, Anosmia, Fatigue, Shortness of breath, Nasal congestion, Sore throat, Myalgia, Arthralgia, Headache, Diarrhoea, Vomiting, Nausea, Chest pain, Anorexia, Asthma

Description

  • Categorical variables describing whether a donor reported having symptoms specific to SARS-CoV-2 infection

  • These variables are assigned binary values, with 0 indicating the donor did not present that symptom and 1 indicating that the donor reported that symptom when sample was taken

Demographics 👤

Variables

  • Sex , Age

Description

  • Sex: Donors were assigned as male (m) or female (f)

  • Age: Age of donor determined in years

Pseudo-Neutralisating Antibodies 🛡️🦠

Variables

  • pseudoNA Abs

Description

  • A measurement of the concentration of neutralizing antibodies from a donor sample required to inhibit 50% of the infection by a SARS-CoV-2 pseudovirus

  • Briefly, this experiment is performed by incubating a plasma sample from a donor with a lentivirus-based SARS-CoV-2 pseudovirus particle expressing the spike protein. The mixture is then incubated with HEK 293 ACE2-transfected cells.

  • Neutralisation titers are reported as the reciprocal of the plasma dilution conferring 50% inhibition (ID50) of pseudovirus infection

Antibody-Dependent Effector Functions 🧪🛡️

Variables

  • ADCD , ADMP , ADNKA, ADNP

Description

  • A measurement of the effector function activity of the antibodies in relation to the neutralisation of the virus

  • Variable names:

    • ADCD: Antibody-dependent complement deposition

    • ADMP: Antibody-dependent monocyte phagocytosis

    • ADNKA: Antibody-dependent NK cell activation

    • ADNP: Antibody-dependent neutrophil phagocytosis

SARS-CoV-2 protein-specific T cell responses 🦠🔬

Variables

  • M T cells elispot , NP T cells elispot, nsp3b T cells elispot , ORF3 T cells elispot, S1 T cells elispot, S2 T cells elispot, Total pos T cells elispot

Description

  • These are variables that were measured using interferon-gamma enzyme-linked immunospot (ELISpot) assays. Specifically, this assay was used to measure T cells that recognize varying proteins in the virus

  • Variable names:

    • M T cells elispot , NP T cells elispot, nsp3b T cells elispot , ORF3 T cells elispot, S1 T cells elispot, S2 T cells elispot : The first term in the variable name (M, NP, nsp3b, ORF3, S1, S2) are SARS-CoV-2 proteins. Hence the T cells variables are measuring the number of T cells that specifically respond to their corresponding protein.

    • Total pos T cells elispot: Total T cells measured using the CEFT positive control peptides

Days post symptoms onset ⌛

Variables

  • Days pso

Description

  • This variable refers to the number of days after the onset of symptoms for a donor

Immunoglobin Assays - Antibody responses 🛡️🔬

Variables

  • S-IgA , S-IgG1 ,S-IgG2 ,S-IgG3 , S-IgG4 , S-IgM , S-IgA memB SARS-CoV2 , S-IgG memB SARS-CoV2 , N-IgG, S-IgG

Description

  • These variables refer to the concentrations of various immunoglobin antibodies with different targets

  • Variable names:

    • S-IgA: Concentration of immunoglobin A antibodies targeting the spike protein

    • S-IgG: Concentration of immunoglobin G antibodies targeting the spike protein

    • S-IgG1 ,S-IgG2 ,S-IgG3 , S-IgG4: Concentration of immunoglobin G subclasses targeting the spike protein

    • S-IgM: Concentration of immunoglobin M antibodies targeting the spike protein

    • S-IgA memB SARS-CoV2: Concentration of immunoglobin A antibodies produced by memory B cells specific to the spike protein

    • S-IgG memB SARS-CoV2: Concentration of immunoglobin G antibodies produced by memory B cells specific to the spike protein

    • N-IgG: Concentration of immunoglobin G antibodies targeting the nucleoprotein

Spike-specific IgG+ Memory B cells 💭🦠

Variables

  • memB 229E , memB HKU1 ,memB NL63 ,MemB OC43 , B cells elispot

Description

  • These variables refer to the concentration of memory B cells that react to various spike proteins in different types of coronavirus

  • Variable names:

    • B cells elispotrefers to the number of memory B cells specific to the general SARS-CoV-2 spike glycoprotein

    • memB 229E , memB HKU1 ,memB NL63 ,MemB OC43refer to the number of memory B cells specific to the coronavirus strain in the variable name. These are seasonal coronaviruses

Meso Scale Discovery (MSD) Assays🔬🧪

Variables

  • 229e MSD , SARS-CoV1 S MSD, SARS-CoV2 N MSD, SARS-CoV2 RBD MSD, SARS-CoV2 S MSD, HcoV-HKU1 S MSD, MERS S MSD, NL63 S MSD, OC43 S MSD

Description

  • These variables are the measurements of antibody levels to various virus spike proteins and other relevant antigens via a MSD multiplexed immunoassay

  • Variable names:

    • 229e MSD, HcoV-HKU1 S MSD, NL63 S MSD, OC43 S MSD: Antibody levels in response to seasonal coronavirus spike proteins

    • SARS-CoV1 S MSD: Antibody levels in response to SARS-CoV-1 coronavirus spike protein

    • SARS-CoV2 S MSD: Antibody levels in response to SARS-CoV-2 coronavirus spike protein

    • SARS-CoV2 N MSD: Antibody levels in response to SARS-CoV-2 coronavirus nucleoprotein

    • SARS-CoV2 RBD MSD: Antibody levels in response to SARS-CoV-2 coronavirus receptor-binding domain

    • MERS S MSD: Antibody levels in response to Middle East Respiratory Syndrome (MERS) spike protein

T cell proliferative responses 🦠🔬

Variables

  • Proliferation M CD4, Proliferation M CD8, Proliferation NP CD4, Proliferation NP CD8, Proliferation ORF3 CD4, Proliferation ORF3 CD8, Proliferation ORF8 CD4, Proliferation ORF8 CD8, Proliferation S1 CD4, Proliferation S1 CD8, Proliferation S2 CD4, Proliferation S2 CD8

Description

  • These variables are the measurement of T cell (specifically CD4 and CD8 T cells) proliferative responses against various SARS-CoV-2 proteins

Responder 🛡️💪

Variables

  • Responder

Description

  • This variable refers to the outcome of immune response durability. A donor is assigned a status of low or high responder

  • Responder status was calculated based on the titer of the anti-nucleocapsid-specific antibodies measured 6 months post symptoms onset.

  • anti-N Ab titer ≥ 1.4 = High responder (seropositive). Low responders were donors who were seronegative

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