Additional file 1: of Asymptomatic Plasmodium falciparum infections may not be shortened by acquired immunity

This document contains additional interpretations, analyses and figures based on the results of fitting all four candidate immigration-death models to the long-interval data. The implications of the estimated distributions of infection duration on the time to elimination, on the variation in infection durations and on senescence of infections are briefly discussed

Comparison of haplotypes between adults (cross section) and new infections of the treatment to reinfection study

* indicates significant difference of haplotype frequency between the two compared groups.<p><b>Copyright information:</b></p><p>Taken from "Heterogeneous distribution of drug resistance haplotypes in subsets of the host population"</p><p>http://www.malariajournal.com/content/7/1/78</p><p>Malaria Journal 2008;7():78-78.</p><p>Published online 6 May 2008</p><p>PMCID:PMC2391149.</p><p></p

Comparison of haplotypes between children of the cross sectional surveys and baseline samples and new infections from the treatment to reinfection study (TRS)

There are no significant differences in haplotype frequencies between groups.<p><b>Copyright information:</b></p><p>Taken from "Heterogeneous distribution of drug resistance haplotypes in subsets of the host population"</p><p>http://www.malariajournal.com/content/7/1/78</p><p>Malaria Journal 2008;7():78-78.</p><p>Published online 6 May 2008</p><p>PMCID:PMC2391149.</p><p></p

Correlation of parasite quantification using <i>var</i>ATS, TARE-2, and 18S rRNA qPCRs and parasite densities in Rufiji, Tanzania.

<p>(A) Parasite quantities determined by ultra-sensitive assays and their correlation with 18S rRNA quantification. Quantification was done relative to copy numbers of plasmid standards (18S rRNA, <i>var</i>ATS) or a parasite dilution row (TARE-2). Quantities of samples negative in 18S rRNA qPCR but positive in ultra-sensitive assays are shown in the left (<i>var</i>ATS) and right (TARE-2) panels. (B) <i>P</i>. <i>falciparum</i> densities based on TARE-2, <i>var</i>ATS, and 18S rRNA qPCRs by age (in years). The geometric mean in each age group is marked by a diamond; the median is denoted by a black line.</p

Assay characteristics and limit of detection (LOD) of published <i>P</i>. <i>falciparum</i> detection assays.

<p>^aIsothermal amplification process.</p><p>QT-NASBA, quantitative NASBA.</p><p>Assay characteristics and limit of detection (LOD) of published <i>P</i>. <i>falciparum</i> detection assays.</p

qPCR details and efficiencies of the 18S rRNA, <i>var</i>ATS, and TARE-2 assays.

<p>^aIntercept equals the <i>C</i>_<i>t</i> value of the DNA equivalent of five parasites added to the qPCR reaction.</p><p>^bLength of consensus sequence.</p><p>^cPolymorphism in primer binding sites likely does not permit efficient amplification of all genomic copies. Number of target sequences present in parasite genomes from field samples cannot be determined in absence of the respective genome data.</p><p>qPCR details and efficiencies of the 18S rRNA, <i>var</i>ATS, and TARE-2 assays.</p

<i>P</i>. <i>falciparum</i> prevalence and gametocyte carriage in Rufiji, Tanzania.

<p>(A) Overall <i>P</i>. <i>falciparum</i> prevalence by different diagnostic methods. Error bars represent 95% CIs. (B) <i>P</i>. <i>falciparum</i> prevalence based on TARE-2, <i>var</i>ATS, and 18S rRNA qPCRs by age (in years). Error bars represent 95% CIs. (C) Venn diagram of positivity by <i>var</i>ATS, TARE-2, and 18S rRNA qPCRs. (D) Proportion of gametocyte carriers by <i>pfs25</i> qRT-PCR. Samples were categorized according to the least sensitive method that identified them as <i>P</i>. <i>falciparum</i>–positive. In total, 13 of 126 LM-positive samples were not confirmed by any qPCR, and 11 of these also were negative by RDT (SD Bioline Pan pLDH/PfHRP2), thus these samples should be considered false positive by LM. Three samples had to be excluded from the gametocyte analyses because of missing RNA data.</p

Linkage disequilibrium between 8 markers (MS2, MS7, MS9, MS10, MS12, MS15, MS16, MS20) determined by LIAN software.

a<p>Linkage in Sigimaru was not significant if only unique haplotypes were analyzed (11 samples, <i>I_A^S</i> = 0.0037, <i>P</i> = 0.400.</p

<i>P. vivax</i> samples included in this study.

a<p>based on our initial typing results obtained with 2 loci, <i>msp1</i>F3 and MS16.</p>b<p>number of samples included in the final data set after successful amplification of 12 microsatellite markers (in addition to MS16 and <i>msp1</i>F3).</p>c<p>includes adults and children above 6 months of age.</p

Output of clustering analysis by STRUCTURE Software for 2 clusters (K = 2).

<p>Each column represents one haplotype, the green and red colours show whether an isolate was assigned to cluster 1 or cluster 2. If both colours are present, the haplotype consists of a mixture of markers assigned to cluster 1 and to cluster 2. The samples from Solomon Islands were assigned mostly to one cluster (red), while samples from PNG contain alleles of both clusters.</p