Repeat sequences of unexpected amplicons.

<p>Central motifs:</p><p>HTQKN = HASPB1-like.</p><p>HAH-N = HASPB2 like.</p

Multiple amplicons corresponding to kinesin tandem repeats are produced by PCR primers LdonK39F and LdonK39R.

<p>Amplifications from strains HU3 (LV9), Hussen, and UGX-MARROW, are depicted. Major amplicon sizes differ by 117 bp, the size of the nucleotide sequence encoding the 39aa repeat in the kinesin gene; mk = Hyperladder I (Bioline).</p

<i>Leishmania</i> rK39 and HASPB antigen repeats and the PCR primer target sequences.

<p>Repetitive coding regions depicted as filled boxes, PCR primers underlined, and 5′ and 3′ binding positions with amplicons are indicated by dashed lines. [A] Kinesin gene comparison for primer design (* = non-conserved nucleotide). [B] HASPB1 GenBank sequence displays 22× perfect 14aa repeats. [C] HASPB2 GenBank sequence displays 3 imperfect repeats.</p

East African <i>L. donovani</i> strains for which sequences were determined, with GenBank accession numbers.

a<p>MON and LON reference numbers refer to multilocus sequence enzyme electrophoresis (MLEE) profiles.</p

GenBank sequences used in comparisons.

a<p>Described in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002057#pntd.0002057-Dey1" target="_blank">[11]</a> as clinical isolate, not laboratory strain, so WHO code not given here.</p>b<p>Described in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002057#pntd.0002057-Takagi1" target="_blank">[12]</a> as isolated from a Bangladeshi patient, but MHOM/IN/80/DD8 is also reported as being from India <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002057#pntd.0002057-WHO2" target="_blank">[6]</a>.</p>c<p><i>L. infantum</i> reference genome.</p>d<p><i>L. donovani</i> reference genome.</p>e<p>GenBank numbers refer to locations on the entire chromosome 23 sequence, to which both the kinesin and HASPB BLAST searches map.</p

rK39 polymorphism among East African <i>L. donovani</i> strains and in comparison with the LcKin diagnostic rK39 sequence.

a<p>LcKin is derived from <i>L. infantum</i> (<i>L. chagasi</i>).</p>b<p>LdK39 is derived from <i>L. donovani</i>.</p>c<p>P = pre-repeat region.</p><p>– = not determined here.</p

Predicted (1064 bp, 260 bp) amplicons and unpredicted (∼400–500 bp) amplicons with HASPB PCR primers LdonHASPBfor and LdonHASPBrev.

<p>Amplifications from strains HU3 (LV9), Hussen, UGX-MARROW, and LRC-L57, are depicted; mk = Hyperladder I.</p

Haplotype analysis per marker for the 96 strains included in the present study.

<p>Percentages are relative to the number of different alleles.</p>*<p>HD - haplotype diversity.</p

Phylogenetic relationship of <i>Leishmania (Viannia)</i> inferred from concatenated sequences of G6PD, 6PGD, MPI, ICD fragments.

<p>The phylogenetic tree was constructed using number of differences and the NJ method. Only DSTs comprised in any clonal complexes (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001888#pntd-0001888-g004" target="_blank">Figure 4</a> and <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001888#pntd.0001888.s001" target="_blank">Table S1</a>) were included. Bootstrap values (percentages of 500 replicates) above 50% are indicated at the nodes.</p

eBURST diagrams of analyzed <i>Leishmania (Viannia)</i> strains.

<p>Six clonal complexes were found: CC1: <i>L. lainsoni</i>; CC2 <i>L. naiffi</i>; CC3 <i>L. shawi</i>; CC4 <i>L. braziliensis</i>; CC5 <i>L. braziliensis</i>; CC6 <i>L. guyanensis</i>. Predicted founders were identified for CC4 (DST12) and CC6 (DST37; IOC/L565). Only homozygous DSTs were used (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001888#pntd.0001888.s001" target="_blank">Table S1</a>).</p