Comprehensive Multimodal Immune Response Dataset for LAIV Vaccination in Pediatric Cohorts

Description

Technical info

Description of Variables in the Dataset

This dataset includes a comprehensive set of variables to evaluate immune responses to the live attenuated influenza vaccine (LAIV). Below is a detailed description of each variable, grouped into relevant categories for clarity:

1. Participant Information

• subject_ID: Unique identifier for each participant.
• year: Year of study enrollment.
• sex: Participant’s sex (M for male, F for female).
• z_score_continuous: Weight-for-height Z-score, a continuous variable assessing nutritional status. Higher values indicate better nutrition, while lower or negative values may indicate undernutrition. This metric provides critical insights into the participant's baseline health, which can influence immune responses to vaccination.

2. Responder Status

• max_HAI_responder: Indicates whether the participant had a fourfold or greater increase in haemagglutination inhibition (HAI) titers.
• max_iga_responder: Indicates a twofold or greater increase in mucosal IgA response.
• max_mnp_cd4_responder: A twofold or greater increase in CD4+ T-cell response to vaccine strains.
• max_mnp_cd8_responder: A twofold or greater increase in CD8+ T-cell response to vaccine strains.

3. Haemagglutination Inhibition (HAI) Assays

• h1_hai_v0_gmt, h1_hai_v21_gmt: Baseline (v0) and post-vaccination (v21) HAI titers for H1N1 virus strain.
• H1_HAI_FC: Fold change in HAI titers for H1N1 virus.
• Similar variables exist for H3N2 (h3_hai_*) and influenza B virus strains (b_hai_*).

4. IgA Responses

• ph1n1_na_IgA_V0, ph1n1_na_IgA_V21: Baseline and post-vaccination IgA levels for H1N1 neuraminidase (NA).
• H1N1_NA_FC: Fold change in IgA levels for H1N1 neuraminidase.
• Similar variables exist for H3N2 hemagglutinin (h3n2_ha_IgA_*) and NA (h3n2_na_IgA_*), and influenza B virus hemagglutinin (HA) (bvic_ha_IgA_*) and NA (bvic_na_IgA_*).

5. Cellular Immune Responses

• h1_v0_cd8_ifng, h1_v21_cd8_ifng: Baseline and post-vaccination interferon-gamma (IFNg) levels in CD8+ T cells specific to H1N1 virus.
• H1_CD8_IFNg_FC: Fold change in CD8+ IFNg levels for H1N1 virus.
• Similar variables for CD8+ IL-2 (*_cd8_il2) and other strains (H3N2, B).

6. Influenza Virus Protein Microarray (IVPM)

• NC99_IVPM_H1_V0, NC99_IVPM_H1_V21: Baseline and post-vaccination IVPM titers for NC99 H1N1 strain.
• NC99_H1_FC: Fold change in IVPM titers for NC99 H1N1.
• Additional variables include other H1N1 (e.g., MICH15, Cal09, GD) and H3N2 strains (e.g., SWISS, HK14, KAN), and B/Yamagata lineage (B_PHU_YAM_*).

This HA-based microarray includes HA proteins from a diverse panel of influenza A and B viruses, enabling the simultaneous assessment of antibody reactivity to various subtypes and lineages. In our analysis, we incorporated HA antigens from influenza A H1N1 virus strains such as A/California/07/2009 (CAL09 H1 IVPM) and A/Michigan/45/2015 (MICH15 H1 IVPM), as well as H1 isolates A/New Caledonia/20/1999 (NC99 H1 IVPM) and A/Guangdong Maonan/SWL1536/2019 (GD H1 IVPM). For influenza A virus H3N2, we included HA proteins from A/Switzerland/9715293/2013 (SWISS H3 IVPM), A/Hong Kong/4801/2014 (HK14 H3 IVPM), and A/Kansas/14/2017 (KAN H3 IVPM). Additionally, the microarray featured HA antigens from influenza B viruses, specifically B/Phuket/3073/2013 (B/Yamagata/16/88-like lineage) and B/Washington/02/2019 (B/Victoria/2/87-like lineage).

7. Stalk-Specific Antibody Responses

• cH6_ADCC_AUC_V0, cH6_ADCC_AUC_V21: Antibody-dependent cellular cytotoxicity (ADCC) activity for stalk-specific chimeric HA (cH6/1) at baseline and post-vaccination.
• cH6_ADCC_FC: Fold change in ADCC activity for cH6/1.
• Similar stalk-specific IgA responses (cH6_sIgA, cH7_sIgA) and titers (cH6_Titer). cH7/3

8. Viral Shedding

• h1_v2_shed, h3_v2_shed, b_v2_shed: Viral shedding status on day 2 post-vaccination for H1N1, H3N2, and B.
• h1_v7_shed, h3_v7_shed, b_v7_shed: Viral shedding status on day 7 post-vaccination.

9. Seropositive Status

• h1_v0_seropositive, h3_v0_seropositive, b_v0_seropositive: Indicates whether participants were seropositive for H1N1, H3N2, and B virus strains at baseline. 

10. Nasopharyngeal Microbial Load

• v0_pneumo_ng_log10copies_ul: Baseline nasopharyngeal load of Streptococcus pneumoniae (log10 copies per μL).

11. T Follicular Helper (TFH) Cells

• TFH_CXCR3_ICOS_PD1_V0, TFH_CXCR3_ICOS_PD1_V7: Frequency of activated TFH cells at baseline and day 7.

12. Dendritic and Monocyte Subsets

• v0_mDCs, v2_mDCs, v7_mDCs: Myeloid dendritic cell frequencies at baseline and post-vaccination.
• v0_pDCs, v2_pDCs, v7_pDCs: Plasmacytoid dendritic cell frequencies.
• v0_classical_monocytes, v2_classical_monocytes, v7_classical_monocytes: Classical monocyte frequencies.
• v0_intermediate_monocytes, v0_nonclassical_monocytes: Intermediate and non-classical monocyte frequencies.

13. Pathway Scores

• blood_baseline_go.*: Pathway enrichment scores in blood samples.
• nasal_baseline_go.*: Pathway enrichment scores in nasal samples.
  • Examples include blood_baseline_go.0006415 (translation termination) and nasal_baseline_go.0045088 (innate immune defense).

14. Clustering Information

• cluster: Immunophenotyic groupings assignment based on immune response phenotype derived from immunaut.

This dataset is structured to enable comprehensive analysis of LAIV-induced immune responses, capturing systemic, mucosal, and cellular immunity across multiple parameters, facilitating predictions of immunogenicity and responder classification.