Mismatch distribution analyses of EPD-PCR and clone sequence datasets.

<p>Individuals are ordered such that first four individuals with a single infection (as determined by EPD-PCR) are shown (B2, B3, B4 and T3; above the bar) followed by individuals with super-infections (below the bar). Plots are paired for each individual with the EPD-PCR dataset on the left and the bulk-PCR clone dataset on the right. EPD-PCR distributions are black; bulk-PCR clone distributions identified as unimodal (ΔAICc<2) are green; bulk-PCR clone distributions identified as bimodal are purple (ΔAICc>2).</p

False negativity and positivity as a function of the number of bulk-PCR products analysed.

<p>(a) Probability to detect bimodality (<i>i.e.</i>, super-infection) in the frequency distribution of the number of mismatches per pair of sequences as a function of the number of bulk-PCR products analysed and for subjects for which EPD-PCR revealed a super-infection (n = 6); (b) Probability to detect bimodality in the frequency distribution of the number of mismatches per pair of sequences as a function of the number of bulk-PCR products analysed and for subjects for which EPD-PCR revealed a single infection (n = 4). Shown are median, quartiles, minimum and maximum, of the respective probabilities per subject.</p

Median joining network of bulk PCR product clone sequences.

<p>As in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036570#pone-0036570-g001" target="_blank">Figure 1</a>, the networks are ordered by infection status. Within each network, node size is proportional to the frequency of sequence occurrence (total n = 25 for each individual). Branch lengths are directly related to the number of mutations between sequences, with values noted for differences greater than two base pairs. Clone haplotypes a–f (as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036570#pone-0036570-t001" target="_blank">Table 1</a>) are noted within or adjacent to their corresponding node. Networks generated using TCS were highly similar (data not shown).</p

Chronogram of BKPyV and JCPyV-related polyomaviruses

<p>This tree was generated from the analysis of conserved blocks of a whole genome alignment using BEAST v1.8.2 under the model of nucleotide substitution best supported by jModelTest v2.1.4, assuming a lognormal relaxed clock and using a speciation prior (birth-death) on the tree shape. The same topology was obtained using PhyML v3. PtrotPyV1 is highlighted in blue. Branch support values are reported above branches (bootstrap values/posterior probability). Root posterior probabilities are reported under branches in black half circles; the tree is rooted on the best supported root. A grey half circle pinpoints the position of the root as determined in another PhyML analysis including the closest available outgroup (the sea otter polyomavirus 1, NC_025259). The accession numbers of the sequences appearing in this figure are as follows: AB269859, AB767295, AB767299, AY386378, AY614708, DQ435829, JX159985, KJ577598 and KT184855.</p

Antibiogram of <i>P. multocida</i> isolates (according to the standards given by CLSI [56]).

<p>S: susceptible; R: resistant; I: intermediate.</p

Alignment of all clone sequences generated in the course of this study

FASTA file comprising 915 SFV int sequences

Origins and characteristics of <i>Pasteurella multocida</i> isolated in this study.

a<p>Identified by PCR <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024236#pone.0024236-Chi1" target="_blank">[24]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024236#pone.0024236-Kndgen1" target="_blank">[25]</a>.</p>b<p>Identified by cultivation and subsequent phenotypical characterization.</p><p>HMPV  =  Human Metapneumovirus</p

Dendrogram showing macrorestriction patterns of <i>P. multocida</i> isolates after digestion with <i>SmaI</i>.

<p>Cluster analysis of Dice similarity indices (UPGMA) was exerted to generate a dendrogram depicting the relationships among PFGE profiles using the BioNumerics software (optimisation 0.5%, position tolerance 1.0%). <i>P. multocida</i> reference strain ATCC 43137 served as methodological control.</p

Virulence-associated gene profiles of <i>P. multocida</i> isolates from chimpanzees.

<p>+: positive; −: negative.</p

Biochemical profiles of <i>P. multocida</i> isolates from chimpanzees.

<p>+: positive; −: negative; +/−: ambiguous result.</p