Additional file 1: of Using the hierarchical ordinal regression model to analyse the intensity of urinary schistosomiasis infection in school children in Lusaka Province, Zambia

Multilingual abstract in the five official working languages of the United Nations. (PDF 656 kb

Flow-chart showing the steps used to assemble the GNTD database.

<p>1. PubMed <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001404#pntd.0001404-PubMed1" target="_blank">[24]</a>, ISI Web of Knowledge <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001404#pntd.0001404-ISI1" target="_blank">[25]</a>, African Journal Online (AJOL) <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001404#pntd.0001404-African1" target="_blank">[26]</a>, Institut de Recherche pour le Développement (IRD)-resources documentaries <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001404#pntd.0001404-IRD1" target="_blank">[28]</a>, WHO library archive <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001404#pntd.0001404-WHO2" target="_blank">[27]</a>, Doumenge et al. <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001404#pntd.0001404-Doumenge1" target="_blank">[17]</a>; 2. Dissertations and theses in local universities or public health departments, ministry of health reports, other reports and personal communication. 3. Proforma and MySQL database include: (i) data source (authors); (ii) document type; (iii) location of the survey; (iv) area information (rural or urban); (v) coordinates (lat long in decimal degrees); (vi) method of the sample recruitment and diagnostic technique; (vii) description of survey (community-, school- or hospital-based); (viii) date of survey (month/year); and (ix) prevalence information (number of subjects examined and positive by age group and parasite species).</p

Observed prevalence of <i>S. mansoni</i> based on current progress of the GNTD database in Africa.

<p>The data included 4604 georeferenced survey locations. Prevalence equal to 0% in yellow dots, low infection rates (0.1–9.9%) in orange dots, moderate infection rates (10.0–49.9%) in light brown dots and high infection rates (≥50%) in brown dots. Cut-offs follow WHO recommendations <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001404#pntd.0001404-WHO3" target="_blank">[35]</a>.</p

Observed prevalence of <i>S. haematobium</i> based on current progress of the GNTD database in Africa.

<p>The data included 5807 georeferenced survey locations. Prevalence equal to 0%, low infection rates (0.1–9.9%), moderate infection rates (10.0–49.9%) and high infection rates (≥50%) indicated by a red scale from light red to dark red. Cut-offs follow WHO recommendations <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001404#pntd.0001404-WHO3" target="_blank">[35]</a>.</p

Number of <i>Schistosoma</i> spp. survey locations in the GNTD database in Africa stratified by country.

<p>Number of survey locations of <i>S. mansoni</i>, <i>S. haematobium</i>, <i>S. intercalatum</i>, <i>S. bovis</i>, <i>S. matthei</i> and <i>S. margrebowiei</i> as of 10 January 2011.</p

African map of schistosomiasis survey locations based on current progress of the GNTD database.

<p>Survey locations are represented by pink squares for <i>S. matthei</i>, blue diamonds for <i>S. margrebowiei</i>, yellow stars for <i>S. intercalatum</i>, green crosses for <i>S. bovis</i>, brown dots for <i>S. mansoni</i> and red triangles for <i>S. haematobium</i>. Surveys where subjects were screened for co-occurrence of multiple species are indicated with overlapping symbols.</p

Neighbour-joining <i>nad</i>1 tree topology supporting the topology of the <i>cox</i>1 tree.

<p>Nodal supports for the 2 groups are marked and details of the samples representing H1, “red dot”, are shown in the sub tree. Each terminal branch is labelled with the individual haplotype codes as detailed in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001882#pntd.0001882.s001" target="_blank">Table S1</a>.</p

Overall and regional <i>cox</i>1 diversity.

<p><i>n</i> = number of samples sequenced; <i>u</i> = number of unique haplotypes found within the region; <i>h</i> = haplotype diversity ± standard deviation; <b>∏</b> = nucleotide diversity.</p>*<p>samples form laboratory passaged or pooled larval stages. For these samples individual worms were not treated as individual samples but instead each different haplotype found was treated as an individual sample.</p>**<p>For Zanzibar the whole data set of Webster et al. <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001882#pntd.0001882-Webster2" target="_blank">[25]</a>, was used and due to the high number of worms sampled and high diversity found, individual worms were treated as individual samples. This was also used in the analysis of the diversity overall and in the Indian Island region.</p>***<p>This included samples from Zanzibar, Madagascar, Mauritius and Mafia.</p

Neighbour-joining <i>cox</i>1 tree topology.

<p>Nodal supports for the 2 groups are marked and details of the samples representing H1, “red dot”, are shown in the sub tree. Each terminal branch is labelled with the individual haplotype codes as detailed in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001882#pntd.0001882.s001" target="_blank">Table S1</a>.</p

Within locality <i>cox</i>1 diversity.

<p><i>n</i> = number of samples sequenced; <i>u</i> = number of unique haplotypes found within the region; <i>h</i> = haplotype diversity ± standard deviation; <b>∏</b> = nucleotide diversity.</p>*<p>Only localities where miracidial populations were collected and the data from Zanzibar <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001882#pntd.0001882-Webster2" target="_blank">[25]</a> were included.</p><p>The Genbank Accession numbers for the <i>cox</i>1 data are JQ397330–JQ397399 and for the <i>nad</i>1 data are JQ595387–595404 (see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001882#pntd.0001882.s001" target="_blank">Table S1</a>).</p