Phylogenetic tree showing the relatedness of the <i>Leptospira sec</i>Y gene (434-bp fragment) derived from qPCR-positive livestock samples.

<p>The phylogenetic tree was constructed using the maximum likelihood method based on the Tamura-Nei nucleotide substitution model [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006444#pntd.0006444.ref073" target="_blank">73</a>]. The tree with the highest log likelihood is shown and drawn to scale with branch lengths measured in the number of substitutions per site. Sequences from this study are labelled with unique identifiers (C0025-C0658); host species; and GenBank accession numbers (MF955862 to MF955882). Sequence from reference <i>Leptospira</i> serovars are also shown [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006444#pntd.0006444.ref034" target="_blank">34</a>]. Expanded clades show reference serovars closely related to study genotypes. More distantly related species clades are collapsed and shown with species labels only. Host and country locations shown for Africa isolates are show in parentheses. Sequences from this study that show 100% identity with <i>L</i>. <i>borgpetersenii</i> serovar Hardjo are highlighted in blue; non-Hardjo <i>L</i>. <i>borgpetersenii</i> sequences are highlighted in pink; <i>L</i>. <i>kirschneri</i> sequences are highlighted in green and sequences without an attributed species are highlighted in orange. Abbreviations: (sv) serovar; DRC (Democratic Republic of Congo).