Expected (<i>H_e</i>) and observed (<i>H_o</i>) heterozygosity for <i>TLR9</i> gene, in relation to seropositivity for <i>Small Ruminant Lentivirus</i> (<i>SRLV</i>), <i>C. abortus</i> (<i>CA</i>) or <i>M. avium</i> subsp. <i>paratuberculosis</i> (<i>MAP</i>) in three sheep flocks from different breeds.

<p>Expected (<i>H_e</i>) and observed (<i>H_o</i>) heterozygosity for <i>TLR9</i> gene, in relation to seropositivity for <i>Small Ruminant Lentivirus</i> (<i>SRLV</i>), <i>C. abortus</i> (<i>CA</i>) or <i>M. avium</i> subsp. <i>paratuberculosis</i> (<i>MAP</i>) in three sheep flocks from different breeds.</p

SNPs and alleles identified in ovine <i>TLR9</i> and <i>MyD88</i> genes.

a<p>Numbering corresponds to NM_001011555.1 <i>TLR9</i> and to NM_001166183.1 <i>MyD88</i> sequences, counting as position 1 the nucleotide A of the ATG codon.</p>b<p>Alleles 05–11 correspond to <i>TLR9</i> and alleles 01–02 to <i>MyD88</i>.</p

Association of <i>ΤLR9</i> genotypes with seroprevalence for <i>Small Ruminant Lentivirus</i> (<i>SRLV</i>), <i>C. abortus</i> (<i>CA</i>) or <i>M. avium</i> subsp. <i>paratuberculosis</i> (<i>MAP</i>) in three sheep flocks from different breeds.

<p>+: seropositive animals,</p><p>−: seronegative animals.</p

Pair-wise analysis of the MHC class II frequencies in controls, total patients and WNND/WNF* subpopulations.

<p>P values in bold indicate significance.</p

Pair-wise analysis of homozygous/heterozygous state in controls, total WNV cases and WNND/WNF^* subpopulations.

<p><i>P</i> values in bold indicate significance^.</p

The official nomenclature of the identified alleles and their frequency in European populations together with the respective allelic frequencies found in this study (column Greece) [24].

<p>The official nomenclature of the identified alleles and their frequency in European populations together with the respective allelic frequencies found in this study (column Greece) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165952#pone.0165952.ref024" target="_blank">24</a>].</p

Graphs of the kinetics of diagnostic test kinetics used in the paper.

<p>Top: Diagnostic test kinetics for whooping cough, with an antibody test (solid line) and a test measuring bacterial load (dashed line). Bottom: Diagnostic test kinetics for bluetongue, with an antibody test (solid line), and a test measuring viral load (dashed line). The graph is showing idealised test kinetics, based on published data for whooping cough [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004901#pcbi.1004901.ref034" target="_blank">34</a>,<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004901#pcbi.1004901.ref035" target="_blank">35</a>] and bluetongue [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004901#pcbi.1004901.ref036" target="_blank">36</a>] tests(see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004901#sec008" target="_blank">methods</a> for details).</p

Hindcasted epidemic trends compared to the true lognormal trends.

<p>Each row shows 80 hindcasted posterior mean trends (each estimated trend shown in thin red lines), estimated from between 30 and 100 test results, with exposure times generated using one of four different lognormal epidemic trends (see main text; true trend shown in black), and assuming a lognormal measurement error of 1.3 for the diagnostic tests. Vertical dashed line indicate the time of the cross-sectional sampling.</p

Log likelihood of inferred times of exposure as a function of true time since exposure.

<p>The log likelihood values plotted are conditional on test data generated assuming that the individual was exposed to whooping cough (top row) or bluetongue (bottom row) at the true time. Both the X and Y axes are on a log scale. Each pixel represents the value of the likelihood at a time of exposure given by the Y axis, given 10 test results, generated assuming a time since exposure given by the X axis. The colour of the pixel indicates the likelihood for an estimated time, given the sample data, with dark red being most likely, and pale yellow being least likely. A clear, dark red diagonal indicates that the time since exposure is easily recoverable, while a more diffuse diagonal indicates higher levels of uncertainty (see the <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004901#sec002" target="_blank">results</a> section for details). The first column shows results based only on data from the antibody test relevant to the disease in question, the middle column results based on an appropriate nucleic acid test, and the right hand column shows the results based on both tests. (See text for details.)</p

Relationship between prediction accuracy and sample size, as measured with R².

<p>Each boxplot represents the results of applying the hindcasting framework to ten different data sets generated with the same set of parameters.</p