Additional file 1 of Fast and accurate dynamic estimation of field effectiveness of meningococcal vaccines

Supplementary information. Supplementary information on the screening method, the model’s formulation and sensitivity analysis. (2360 KB PDF

VirB3 PHN-Families Phylogeny

<div><p>The PHN-Families of nonconserved genes correlate with their molecular phylogeny. Shown here is the Maximum Likelihood tree of the 33 VIRB3 proteins classified in three PHN-Families (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020173#pcbi-0020173-st001" target="_blank">Table S1</a>). PHN-Families are enclosed in circles, color-coded as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020173#pcbi-0020173-g008" target="_blank">Figure 8</a>, and coincide with monophyletic branches of the phylogenetic tree. Numbers are bootstrap values, and the ruler shows the number of point-accepted mutations.</p><p>doi:10.1371/journal.pcbi. 0020173.g007</p></div

SctJ PHN-Family: Network and Phylogeny

<div><p>In this example we show a representation of a single PHN-family, compared with a reconstruction of the evolutionary history of its components based on molecular phylogenetic data. The two subgroups clearly visible in the PHN representation coincide with monophyletic clades of the phylogenetic tree.</p><p>(A) Network representation of the SctJ PHN-family (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020173#pcbi-0020173-sd001" target="_blank">Protocol S1</a>). Spheres represent proteins; edges are homology relations, color-coded according to the homology level <i>ɛ_ij</i>. The two subgroups are YscJ (T3SS) and FliF (flagellar) proteins. For <i>ɛ</i> = 10⁻⁵, this portion of the PHN falls in the giant component, for the presence of false homology relations with seven outlier proteins (blue spheres, external links to the giant component not shown). After the overlap procedure with θ<i> </i> = 0.5, false links are removed, and all the members of the SctJ family fall in a single PHN-family, shown by the circle.</p><p>(B) Maximum likelihood phylogenetic tree of the SctJ family. Numbers are bootstrap values. The YscJ and FliF subgroups correspond to two distinct evolutionary clades. Organism and group names in the T3SS clade refer to the T3SS classification shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020173#pcbi-0020173-g008" target="_blank">Figure 8</a>.</p><p>doi:10.1371/journal.pcbi. 0020173.g006</p></div

Overlap and PHN-Families

<div><p>By partitioning the network with the overlap procedure for increasing value of θ<i>,</i> we separated the PHN into regions of increasing compactness. The maximum value of the modularity measure <i>Q</i> (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020173#s4" target="_blank">Materials and Methods</a>) allowed us to identify the optimal cutoff value to partition the PHN into families of homologous proteins.</p><p>(Main Graph) <i>Q</i> is shown as a function of θ<i> </i>. The maximum value of <i>Q</i> = 0.723 is found for θ<i> </i> = 0.5.</p><p>(Inset Graph) The dark circles represent the compactness index <i>η</i> after the partitioning (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020173#s4" target="_blank">Materials and Methods</a>) as a function of θ<i> </i>. The white triangle is the value of <i>η</i> of the original PHN for <i>ɛ</i> = 10⁻⁵, which corresponds to the limiting value θ<i> </i> = 0.</p><p>doi:10.1371/journal.pcbi. 0020173.g005</p></div

PHN Topology

<div><p>The compactness index, <i>η,</i> and the clustering index, <i>C,</i> shown here as a function of the E-value cutoff <i>ɛ,</i> describe the global and local topology of the network, respectively. For growing values of <i>ɛ, η</i> rapidly decreases towards 0, while <i>C</i> always has values well above 0.8. These results indicate that the PHN is formed by compact regions that are loosely connected to form globally sparse connected components.</p><p>doi:10.1371/journal.pcbi. 0020173.g004</p></div

PHN Giant Component

<div><p>The fraction <i>n_G</i> of nodes included in the largest connected component of the PHN is shown as a function of the homology cutoff <i>ɛ</i>.</p><p>doi:10.1371/journal.pcbi. 0020173.g003</p></div

T_FH1 ICOS⁺ cells predict functional antibody responses.

<p>Correlations between the number of total circulating CD4⁺ T_FH1 ICOS⁺ cells and the maximum DHI responses observed across the three influenza strains represented in the vaccine, measured at (A) day 28 and (B) day 168 after immunizzation. Dashed lines represent the least squares regressions fit to the data. R: Pearson product-moment correlation coefficient. <i>p</i>: correlation-associated p value.</p

H1N1-specific CD4⁺IL-21⁺ICOS⁺CXCR5⁺ T_FH cells predict functional antibody responses.

<p>Correlations between the number of H1N1-specific CD4⁺IL-21⁺ICOS⁺CXCR5⁺ T_FH cells and H1N1-specific DHI responses measured at (A) day 28 and (B) day 168 after immunizzation. Dashed lines represent the least squares regressions fit to the data. R: Pearson product-moment correlation coefficient. <i>p</i>: correlation-associated p value.</p

Expansion of ICOS⁺ and PD-1⁺ T_FH1 cells after TIIV and ATIIV vaccination.

<p>(<b>A</b>) Number of CD4⁺ T cells expressing CXCR5 and ICOS in human PBMCs after seasonal influenza vaccination. (<b>B</b> and <b>C</b>) Number of T_FH1 cells expressing ICOS and PD-1. Data show three cohorts: saline placebo (n=7), TIIV (n=18) and ATIIV (n=17) at baseline (D0), day 7 (D7) and day 28 (D28) after a single dose of influenza vaccine. Data are shown for each participant and expressed as number of cells in 10⁶ live PBMCs acquired. Non-parametric Wilcoxon’s signed rank test was used for statistical analyses: *<i>p</i> < 0.05, **<i>p</i> < 0.01, and ***<i>p</i> < 0.001 compared to day 0; ^§<i>p</i> < 0.05, ^§§<i>p</i> < 0.01 and ^§§§<i>p</i> < 0.001 compared to saline placebo.</p

H1N1-specific CD4⁺IL-21⁺ICOS⁺ T_H cells subsets expressing or not CXCR5 expand after influenza vaccination.

<p>Number of CD4⁺IL-21⁺ICOS⁺ T_H cells, showing a CXCR5⁺ (black) or CXCR5^- (gray) phenotype, in vaccinated participants after overnight stimulation with A/California/7/2009 (H1N1) antigen or SEB. Data show saline placebo (n=7), and merged TIIV (n=18) and ATIIV (n=17) cohorts at baseline (D0), day 7 (D7) and day 28 (D28) after a single dose of influenza vaccine. Data are expressed as number of cells in 10⁶ live CD4⁺ T cells; mean ± SEM is shown. Non-parametric Wilcoxon’s signed rank test was used for statistical analyses: *<i>p</i> < 0.05, **<i>p</i> < 0.01, and ***<i>p</i> < 0.001 compared to day 0.</p