Virological and clinical data for Lassa fever patients.

<p>Due to a variable number of missing values, the number (n) of data points that were included in the analysis is indicated with each category.</p><p>Abbreviations:</p>a<p>Patients who were discharged after recovery.</p>b<p>Patients who died during hospitalization.</p>c<p>1+, Lassa virus RT-PCR was only positive with undiluted plasma; 2+, Lassa virus RT-PCR was positive with 1/10-volume plasma, irrespective of whether the undiluted sample was positive or not.</p>#<p>p<0.01 (PCR-positive survived vs. PCR-positive died).</p

Molecular testing for Lassa virus at ISTH.

<p>(A) Outline of the diagnostic laboratory with pre- and post-PCR areas (“Clean” and “Dirty”, respectively). (B) Inactivation of plasma samples in a chaotropic buffer in a plexiglas box in the inactivation room. All sample manipulations were done behind a plexiglas shield. The box features a UV light source on top for decontamination. (C) Example of an RT-PCR result. From each patient sample, 140 µl and 14 µl were processed (lanes UD [undiluted] and 1∶10, respectively).</p

Geographic origin of Lassa fever cases.

<p>Top: Map of the southern part of Nigeria showing location of Edo State. Most of the samples came from Edo State and the neighboring Ondo State. FCT, Federal Capital Territory. Bottom: Map of Edo State with borders of the Local Governmental Areas (LGA). LGAs with confirmed Lassa fever cases are shaded from light to dark grey depending on the number of cases. The names of the LGAs with case number in parentheses are given below the map.</p

Phylogenetic analysis of Lassa virus sequences.

<p>The sequences of the PCR fragments obtained from positive cases were aligned with published sequences. The latter are identified by GenBank accession numbers. For clarity of presentation, only Nigerian strains are shown. The clusters A, B, and C comprising strains from Edo State and Ondo State were collapsed; these strains are shown separately in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001839#pntd-0001839-g006" target="_blank">Figure 6</a>. Posterior probability values are indicated on the branches. The country of origin of Lassa virus strains is indicated by a prefix: IC, Ivory Coast; NIG, Nigeria. If known, State and city is also shown with the strains (FCT, Federal Capital Territory). Sequences highlighted in boldface have been submitted to GenBank (accession nos. JN651366-JN651400). Lassa virus lineages are indicated left. The novel putative lineage/sub-lineage represented by strain Nig05-A08 <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001839#pntd.0001839-Ehichioya2" target="_blank">[49]</a> is indicated with a question mark.</p

Seasonality of Lassa fever.

<p>(A) Number of cases tested, number of positive cases, and percentage of positive cases per month. (B) Average of incidence figures. The curves in A were smoothened by a sliding window covering a 3-month interval and subsequent averaging of the two years. Error bars indicate the range. The rainfall in Benin City is shown as a bar chart in the background in relative units (July = 360 mm). Climate data were taken from <a href="http://www.climatedata.eu/climate.php?loc=nizz0004&lang=en" target="_blank">http://www.climatedata.eu/climate.php?loc=nizz0004&lang=en</a> (accessed 1 June 2012).</p

Box-plot representation of statistically significant differences between survivors and fatal cases of Lassa fever.

<p>Urea and creatinine blood levels were drawn at admission. Comparison of unpaired groups was performed with the Mann-Whitney test. The number of cases per group is given below the plots in parentheses.</p

Phylogenetic analysis of Lassa virus sequences from Edo State and Ondo State.

<p>Clusters A, B, and C collapsed in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001839#pntd-0001839-g005" target="_blank">Figure 5</a> are shown in detail here. The upper part of cluster C has been moved to the right (dashed line) to facilitate representation of all sequences. Published sequences are identified by GenBank accession numbers. The posterior probability of monophyly of the corresponding clade is indicated on the branches if the probability is ≥0.5. If known, State, Local Governmental Area (C, Central; W, West; E, East; NE, North-East; SE, South-East), and city is shown with the strains. Sequences from fatal cases are marked with (F). Sequences highlighted in boldface have been submitted to GenBank (accession nos. JN651366-JN651400). Note, the tree contains some negative branch length at nodes with low posterior probability. This is a correct computational result which arises from calculation of the branch lengths in the consensus tree.</p