Alpha diversity indices for TcGP63I amplicon diversity derived from pairs of congenital Chagas disease cases.

<p>Diversity indices were derived from STs defined at 99% sequence similarity. Bar plot and associated <i>x</i>-axis on the right hand side shows the Shannon diversity index calculated in Mothur [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003458#pntd.0003458.ref034" target="_blank">34</a>], with error bars defining upper and lower 95% confidence intervals.</p

Samples provenance and symptoms.

<p>^a Samples from Goias congenital case</p><p>^x Samples from the same patient taken >12 months apart</p><p>^y Samples from the same patient taken < 6 months apart</p><p>^z Samples taken from the same patient >12 months apart</p><p>Samples provenance and symptoms.</p

Principal coordinates analysis of sequence diversity between chronic Chagas Disease patient TcGP63I antigenic repertoires.

<p>Genetic distances are based on a weighted unifrac metric. Plot A shows diversity comparisons among Go-as asymptomatic (asympt) and symptomatic (sympt) clinical cases, as well as one acute case. Plot B shows Goias cases with symptoms categorised as acute, card (cardiopathy), card + mega (cardiopathy as well as megacolon and / or megaesophagous), mega (megacolon and / or megaesophagous) or asympt (asymptomatic). Plot C shows comparisons among Cochabamba clinical cases (not including congenital cases) classified as either asymptomatic (asympt) and symptomatic (sympt). The dashed circle on plot C indicates samples unambiguously defined as TcI at the ND5 locus. Pairs of sequential isolates from the same patient are labelled x and y respectively.</p

Yang and Neilson estimates for positive selection within and among abundant 97% STs identified in this study.

<p>^a Numbers in brackets represent the number of 99% STs define within each cluster from which estimates were generated.</p><p>^b P values are give for Fisher’s exact tests for deviation from the neutral expectation of Ka/Ks = 0.</p><p>Yang and Neilson estimates for positive selection within and among abundant 97% STs identified in this study.</p

Bar plot showing sequence type identity and abundance defined at 97% similarity for the ND5 locus across all samples.

<p>A—Goias cohort chronic/intermediate cases; B—Cochabamba chronic/intermediate cases; C—Cochabamba congenital cases. Y axes show log transformed abundance (read counts). X axes show clustered bars for individual samples. Sequence type identities are given in the legend. Stars denote congenital pair from Goias. Labels x (6416 / 6452), y (6401 / 6536) and z (6379 / 6445) sample pairs from the same patient at different time points (see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003458#pntd.0003458.t001" target="_blank">Table 1</a>).</p

Analytical sensitivity and analytical specificity of the <i>T. cruzi</i> satDNA OligoC-TesT and kDNA OligoC-TesT on DNA from 6 <i>T. cruzi</i> and 3 <i>T. rangeli</i> reference strains.

<p>DTU = discrete typing unit, NA = not applicable.</p

Demographic characteristics of the participants recruited in the study and specifications of blood collections and reference tests.

<p>Notes: ND: not done; a: ELISA Chagas III, GrupoBios S.A., Chile; b: In house protocol with <i>T. cruzi</i> Tulahuen strain; c: Chagatest ELISA recombinant v. 4.0, Wiener Lab, Argentina; d: Chagatest HAI, Wiener Lab, Argentina; e: In house protocol with <i>T. cruzi</i> Dm28, MC & T strain; f: In house protocol with <i>T. cruzi</i> Dm28,MC & T strain.</p

Sensitivities and specificities of the <i>T. cruzi</i> satDNA and kDNA OligoC-TesTs on 187 Chagas patients and 114 endemic and non-endemic controls from Chile, Argentina, Spain, Sudan and D.R. Congo.

<p>Notes: 95% CI = 95% confidence interval; Non-end. = Non-endemic; I = first repetition; II = second repetition; N.D. = not done due to limited number of test kits available;</p><p>^a All Chagas patients recruited at the Hospital Ramón y Cajal in Madrid were from Bolivian origin.</p