Study profile: Of the 427 participants screened, 425 were enrolled and started on ART at the three sites.

<p>Three hundred and twenty one participants completed their 12 months visit and had viral load results available at baseline and month 12. Forty nine had viral loads equal or above 1000 copies/ml and were genotyped. Of these 35 participants had HIV drug resistance mutations.</p

Geographic locations of Ebola HF outbreaks and phylogenetic relationships of representative filoviruses.

<p>(A) Map of Africa showing the sites of all known ebolavirus outbreaks denoted by colored circles for <i>Zaire ebolavirus</i> (yellow), <i>Sudan ebolavirus</i> (green), and <i>Côte d'Ivoire ebolavirus</i> (red). The expanded map of Uganda shows the location of the communities of Bundibugyo and Kikyo (black circles) in western Uganda, the site of the recent outbreak of <i>Bundibugyo ebolavirus</i>. Also shown on the Uganda map are the cities of Kampala (capital), Entebbe (international airport) and Gulu (the site of an outbreak of <i>Sudan ebolavirus</i> in 2000, the largest known Ebola HF outbreak on record). (B) Phylogenetic tree comparing full-length genomes of ebolavirus and marburgvirus by Bayesian analysis. Posterior probabilities greater than 0.5 and maximum likelihood bootstrap values greater than 50 are indicated at the nodes.</p

Clinical history of typhoid fever patients, Kasese and Bundibugyo Districts, April 15, 2011–January 6, 2012.

†<p>For some items, n may vary by small numbers due to “don't know” responses.</p><p>*Percentage totals may be >100%; respondents could select ≥1 source of care and antibiotic.</p>‡<p>Kasese patients: 1 school nurse; Bundibugyo patients: 5 friend or relative.</p>‡‡<p>Kasese patients: 1 each cephalexin, erythromycin, gentamycin, 4 unknown; Bundibugyo patients: 1 each ceftriaxone and doxycycline, 2 unknown.</p

Demographic characteristics of patients with suspected or confirmed typhoid fever, Kasese and Bundibugyo districts, Uganda, August 1, 2009–December 31, 2011.

<p>*Includes 12 patients for whom intestinal perforation status was reported by clinician as “don't know”.</p><p>**Includes 7 patients for whom intestinal perforation status was reported by clinician as “don't know” and 33 patients for whom intestinal perforation status could not be determined from district linelist.</p>†<p>For some items, n may vary by small numbers due to “don't know” or missing responses.</p>‡<p>Wilcoxon rank-sum test (median age) or Fisher's exact test (gender) for difference between Kasese patients with and without intestinal perforation.</p>‡‡<p>Wilcoxon rank-sum test (median age) or Fisher's exact test (gender) for difference between Bundibugyo patients with and without intestinal perforation.</p>a<p>Median age different by gender among all Kasese patients (<i>P</i> = 0.002) and among patients with intestinal perforation from Kasese (<i>P</i> = 0.0004) and Bundibugyo (<i>P</i> = 0.03). Median age did not differ significantly by gender among patients without intestinal perforation in either district.</p

Clinical features^*of typhoid fever patients reported on case report forms, Kasese and Bundibugyo Districts, April 15, 2011–December 31, 2011.

<p>*Case definition specified that fever and abdominal pain must be present.</p>†<p>For some items, n may vary by small numbers due to “don't know” responses.</p

Seasonal Pulses of Marburg Virus Circulation in Juvenile <em>Rousettus aegyptiacus</em> Bats Coincide with Periods of Increased Risk of Human Infection

<div><p>Marburg virus (family <em>Filoviridae</em>) causes sporadic outbreaks of severe hemorrhagic disease in sub-Saharan Africa. Bats have been implicated as likely natural reservoir hosts based most recently on an investigation of cases among miners infected in 2007 at the Kitaka mine, Uganda, which contained a large population of Marburg virus-infected <em>Rousettus aegyptiacus</em> fruit bats. Described here is an ecologic investigation of Python Cave, Uganda, where an American and a Dutch tourist acquired Marburg virus infection in December 2007 and July 2008. More than 40,000 <em>R. aegyptiacus</em> were found in the cave and were the sole bat species present. Between August 2008 and November 2009, 1,622 bats were captured and tested for Marburg virus. Q-RT-PCR analysis of bat liver/spleen tissues indicated ∼2.5% of the bats were actively infected, seven of which yielded Marburg virus isolates. Moreover, Q-RT-PCR-positive lung, kidney, colon and reproductive tissues were found, consistent with potential for oral, urine, fecal or sexual transmission. The combined data for <em>R. aegyptiacus</em> tested from Python Cave and Kitaka mine indicate low level horizontal transmission throughout the year. However, Q-RT-PCR data show distinct pulses of virus infection in older juvenile bats (∼six months of age) that temporarily coincide with the peak twice-yearly birthing seasons. Retrospective analysis of historical human infections suspected to have been the result of discrete spillover events directly from nature found 83% (54/65) events occurred during these seasonal pulses in virus circulation, perhaps demonstrating periods of increased risk of human infection. The discovery of two tags at Python Cave from bats marked at Kitaka mine, together with the close genetic linkages evident between viruses detected in geographically distant locations, are consistent with <em>R. aegyptiacus</em> bats existing as a large meta-population with associated virus circulation over broad geographic ranges. These findings provide a basis for developing Marburg hemorrhagic fever risk reduction strategies.</p> </div

Diversity of PFGE patterns among <i>Salmonella</i> Typhi isolated from Kasese and Bundibugyo patients.

<p>Each <i>Xba</i>I/<i>Bln</i>I PFGE pattern combination is represented by a different shading; pattern combinations designated by letter are shared across districts and/or years. <i>Salmonella</i> Typhi isolated from October 18–December 31, 2011 were from 13 Bundibugyo and 5 Kasese patients; among these, we observed 6 and 4 pattern combinations, respectively. Investigations in Kasese from March 4–April 17, 2009 yielded 33 <i>Salmonella</i> Typhi isolates, among these 13 pattern combinations were identified <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002726#pntd.0002726-Neil1" target="_blank">[6]</a>.</p

Cases of typhoid fever in Bundibugyo, by age, gender, and intestinal perforation status.

<p>January 1–December 31, 2011, n = 244 with known age, sex, and intestinal perforation status, *<i>P</i> = 0.03 and **<i>P</i> = 0.0006.</p

Selected characteristics of patients with suspected typhoid fever, by intestinal perforation (IP) status, April 15, 2011–January 6, 2012.

<p>*For some items, n may vary by small numbers due to “don't know” responses.</p><p>**Fisher's Exact test.</p>†<p>Percentage totals may be >100%; respondents could select ≥1 source of care and antibiotic.</p>‡<p>Patients with intestinal perforation: 1 each ceftriaxone, gentamycin, and unspecified; patients without intestinal perforation: 1 each cephalexin, doxycycline, erythromycin, and gentamycin, and 5 unspecified.</p

Summary of <i>Rousettus aegyptiacus</i> found positive for Marburg virus in multiple tissues by Q-RT-PCR.

<p>For reference, approximate TCID50 values for positive tissues were derived from a standard curve of diluted stock virus (371Bat Uga 2007) assayed using the identical Q-RT-PCR assay as that used for the tissues.</p><p>J = juvenile bat (non-pup; forearm length ≤89 mm).</p><p>A = adult bat (forearm length >89 mm).</p><p>++++ = Ct 20–25 = (50,000–1,500,000 TCID₅₀/ml).</p><p>+++ = Ct 25–30 = (2000–50,000 TCID₅₀/ml).</p><p>++ = Ct 30–35 = (100–2000 TCID₅₀/ml).</p><p>+ = Ct 35–39 = (5–100 TCID₅₀/ml).</p>*<p>Pool of 3 tissue sections.</p