Odd ratios obtained for each method by using real-time PCR as the reference.

<p>OR: odd ratio; CI: confidence interval.</p

Results of the EQA for molecular detection of CCHFV – Part 1.

<p>+: positive (17): Midilli et al., 2007.</p><p>−: negative (30): Wölfel et al., 2007.</p><p><b>bold</b>: quantified result (32): Drosten et al., 2002.</p>*<p>: correct strain (35): Rodriguez et al., 1997.</p><p>FN: false negative result (36): Schwarz et al., 1996.</p><p>qRT: real-time RT-PCR (c): commercial assay.</p><p>nRT: nested RT-PCR (h): in house assay.</p><p>cRT: conventional RT-PCR.</p

MLVA clustering and SNP branch assignment of 68 previously published <i>Y. pestis pestis</i> branches 1 and 2.

<p>Sixty-eight strains from the 1 and 2 branches previously investigated by both MLVA25 and SNP analysis are displayed <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Li1" target="_blank">[5]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Morelli1" target="_blank">[6]</a>. For completion, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone-0030624-t001" target="_blank">Table 1</a> gives further information about assignment of biovar, genotype, and origin. Colors reflect MLVA clustering as suggested by Li et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Li1" target="_blank">[5]</a>. The SNP branch assignment of each strain as defined by Morelli et al. is indicated (column <i>Morelli2010</i>) together with the strain ID and biovar designation <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Morelli1" target="_blank">[6]</a>. Bootstrap support values are indicated for each node. The results of CRISPR analysis according to Cui et al. are given in column <i>group </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Cui1" target="_blank">[18]</a>. * This strain shows a Medievalis phenotype due to a different mutation in the napA gene compared to the mutation causing the Medievalis phenotype in the Medievalis biovar, as demonstrated by Pourcel et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Pourcel1" target="_blank">[13]</a>.</p

Protospacers for newly identified spacers a6′, a85–88, and b48–49.

<p>Protospacers for newly identified spacers a6′, a85–88, and b48–49.</p

Results of the EQA for molecular detection of CCHFV – Part 2.

<p>+: positive (21): Duh et al., 2006.</p><p>−: negative (30): Wölfel et al., 2007.</p><p>n.d.: not determined (32): Drosten et al., 2002.</p><p><b>bold</b>: quantified result (33a): Midilli et al., 2009 (Europe 1).</p>*<p>: correct strain (33b): Midilli et al., 2009 (Europe 2).</p><p>FN: false negative result (34): Papa. et al., 2007.</p><p>PN: false positive result (35): Rodriguez et al., 1997.</p><p>qRT: real-time RT-PCR (36): Schwarz et al., 1996.</p><p>nRT: nested RT-PCR (37): Deyde et al., 2006.</p><p>cRT: conventional RT-PCR (38): Burt et al.,1998.</p><p>(c): commercial assay (39): Burt et al., 2005.</p><p>(h): in house assay.</p

Minimal spanning tree of the strains as shown in <b>Figures 1</b> and <b>2</b> using the same color code.

<p>The figure is based on the same data set as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone-0030624-g001" target="_blank">Fig. 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone-0030624-g002" target="_blank">2</a>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone-0030624-t001" target="_blank">Table 1</a> gives further information about assignment of biovar, genotype, and origin. Basic correlation and grouping of genotypes is similar compared to previously published <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone-0030624-g002" target="_blank">Fig. 2</a> in Morelli et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Morelli1" target="_blank">[6]</a>.</p

MLVA clustering and SNP branch assignment of 66 previously published <i>Y. pestis microtus</i> and <i>pestis</i> 0, 1 and 3 branches.

<p><i>Microtus</i> and strains from the 0 and 1 branches so far investigated by MLVA25 and by SNP analysis are shown <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Li1" target="_blank">[5]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Morelli1" target="_blank">[6]</a>. Three Ulegeica, two Hissarica and nine Altaica strains not investigated by SNP analysis are also included. For completion, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone-0030624-t001" target="_blank">Table 1</a> gives further information about assignment of biovar, genotype, and origin. Colors reflect MLVA clustering as suggested by Li et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Li1" target="_blank">[5]</a>. The SNP branch assignment of each strain as defined by Morelli et al. is indicated (column <i>Morelli2010</i>) together with the strain ID and biovar designation <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Morelli1" target="_blank">[6]</a>. The results of CRISPR analysis according to Cui et al. are shown in column <i>group </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Cui1" target="_blank">[18]</a>. Bootstrap support values are indicated. The figure shows the satisfying terminal branches clustering achieved by MLVA but the sometimes incorrect and usually low bootstrap values of deep branching nodes illustrating the complementarity of the two methods.</p

MLVA25 assignment of four clusters of the investigated Mongolian <i>Y. pestis</i> strains.

<p>MLVA25 tree of 16 investigated Mongolian <i>Y. pestis</i> strains (marked with color and boxes) representing four of the 6 clusters, and various <i>Y. pestis</i> strains originating from <i>microtus</i> and <i>pestis</i> biovars. For each strain, the tentative SNP branch or node according to Morelli et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Morelli1" target="_blank">[6]</a> as deduced by the presence of a linking strain in the same MLVA cluster is indicated by a question mark. Strain name, CRISPR profile as investigated in this study, and the sampling site (Focus) are listed.</p

CRISPR genotypes.

<p>CRISPR genotypes.</p

Overview of <i>Y. pestis</i> subspecies, biovar, genotype, and natural foci as suggested by different authors [4], [5], [6], [7], [18], and as deduced in this study.

<p>*abbreviations as defined by Achtman et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Achtman1" target="_blank">[7]</a> and Morelli et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Morelli1" target="_blank">[6]</a>: PE – pestoides (<i>microtus</i>), ANT – Antiqua, IN – Intermedium, ORI – Orientalis, and MED – Medievalis; Intermedium in Morelli et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Morelli1" target="_blank">[6]</a> has not the same meaning as intermedium defined by Li et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Li1" target="_blank">[5]</a> which refers to Rhamnose positive <i>Y. pestis pestis</i> isolates.</p><p># prefix refers to foci as described by Anisimov et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Anisimov1" target="_blank">[4]</a>. Numbers without # refer to Mongolian foci as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone-0030624-g004" target="_blank">Figure 4</a>.</p