Comparisons of the prevalence of <i>T</i>. <i>whipplei</i> carriage in children feces between Senegal and Laos.

<p>Comparisons of the prevalence of <i>T</i>. <i>whipplei</i> carriage in children feces between Senegal and Laos.</p

JEV MAC-ELISA results from DCS using CSF-substitutes, 903 filter paper and various protocols for sample spotting.

<p>JEV MAC-ELISA results from DCS using CSF-substitutes, 903 filter paper and various protocols for sample spotting.</p

Anti-JEV IgM ELISA (JEV MAC-ELISA) results of consecutive patient samples comparing Dried Cerebrospinal Fluid Spots (DCS) on filter paper using the pre-cut protocol vs routine neat Cerebrospinal Fluid.

<p>Anti-JEV IgM ELISA (JEV MAC-ELISA) results of consecutive patient samples comparing Dried Cerebrospinal Fluid Spots (DCS) on filter paper using the pre-cut protocol vs routine neat Cerebrospinal Fluid.</p

Study sites: Geographical distribution of four hospitals involved in patient recruitment, in Vientiane (colour map), and with respect to the Lao PDR (grey map).

<p>Study sites: Geographical distribution of four hospitals involved in patient recruitment, in Vientiane (colour map), and with respect to the Lao PDR (grey map).</p

Genetic diversity of 42 genotypes of <i>Tropheryma whipplei</i> obtained from 277 samples.

<p>Phylogenetic trees were constructed using the maximum likelihood method based on the Tamura 3-parameter substitution model. The countries in which the genotype has been detected are presented opposite the genotype, and the number of different individuals in which the genotype has been detected is provided in parentheses. The genotypes of each highly variable genomic sequence (HVGS) have intervened in 22, 13, 17 and 7 different combinations, respectively.</p

Primers and probes evaluated during the study.

<p>Primers and probes evaluated during the study.</p

Development of an improved RT-qPCR Assay for detection of <i>Japanese encephalitis virus</i> (JEV) RNA including a systematic review and comprehensive comparison with published methods - Fig 1

<p>Standard curves of the 1) Pyke, 2) NS2A assays and 3) NS3 assays with G3-RP9-190 on (A) Day 1 and repeated on (B) Day 2. Result of the RT-qPCR run, ‘Cq’, is plotted against the ‘log starting copies number’, at the RNA dilutions detected: Pyke assay 1:10 serial dilutions of G1-769 in triplicate at 10⁻³ to 10⁻⁶; NS2A assay 1:10 serial dilutions of G1-769 in triplicate at 10⁻³ to 10⁻⁷; and NS3 with G3-RP-190 10⁻⁴ to 10⁻⁷. Efficiency = 10^−1/slope-1. R² = Correlation Coefficient. RT-qPCR performed with Fastvirus kit (TaqMan® Fast Virus 1-Step) with a reaction volume of 50μL, sample volume of 30μl, and primer and probe concentrations of 600nM and 300nM respectively. Thermocycling conditions were 50°C for 5 minutes, 95°C for 20 seconds and 45 x (95°C for 15 seconds + x°C for 60 seconds). The optimal annealing temperature ‘x°C’ was different for each assay: 62°C, 60°C and 56°C for the Pyke, NS2A and NS3 assays respectively.</p

Similarity within the EV-A71 genogroups through comparison of the full-length VP1 gene sequences.

<p>Similarity within the EV-A71 genogroups through comparison of the full-length VP1 gene sequences.</p

Molecular differentiation of the EV-A71 genogroups.

<p>The percentages of nucleotide and amino acid divergences were calculated in pairwise comparisons of 59 sequences selected as representative of the EV-A71 genogroups and subgenogroups. A scatter plot was produced with the divergence values to determine a threshold between intra-and inter-genogroup differences.</p

Phylogenetic relationships between EV-A71 full-length VP1 sequences inferred using the Neighbor-Joining method.

<p>The evolutionary distances were computed using the Kimura 2-parameter method. The length of the branches is proportional to the number of nt divergence. The percent of bootstrap replicates is indicated for the main nodes.</p