In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78 patients in Sierra Leone to ∼2000× coverage. We observed a rapid accumulation of interhost and intrahost genetic variation, allowing us to characterize patterns of viral transmission over the initial weeks of the epidemic. This West African variant likely diverged from central African lineages around 2004, crossed from Guinea to Sierra Leone in May 2014, and has exhibited sustained human-to-human transmission subsequently, with no evidence of additional zoonotic sources. Because many of the mutations alter protein sequences and other biologically meaningful targets, they should be monitored for impact on diagnostics, vaccines, and therapies critical to outbreak response.

BACKGROUND Limited clinical and laboratory data are available on patients with Ebola virus disease (EVD). The Kenema Government Hospital in Sierra Leone, which had an existing infrastructure for research regarding viral hemorrhagic fever, has received and cared for patients with EVD since the beginning of the outbreak in Sierra Leone in May 2014. METHODS We reviewed available epidemiologic, clinical, and laboratory records of patients in whom EVD was diagnosed between May 25 and June 18, 2014. We used quantitative reverse-transcriptase–polymerase-chain-reaction assays to assess the load of Ebola virus (EBOV, Zaire species) in a subgroup of patients. RESULTS Of 106 patients in whom EVD was diagnosed, 87 had a known outcome, and 44 had detailed clinical information available. The incubation period was estimated to be 6 to 12 days, and the case fatality rate was 74%. Common findings at presentation included fever (in 89% of the patients), headache (in 80%), weakness (in 66%), dizziness (in 60%), diarrhea (in 51%), abdominal pain (in 40%), and vomiting (in 34%). Clinical and laboratory factors at presentation that were associated with a fatal outcome included fever, weakness, dizziness, diarrhea, and elevated levels of blood urea nitrogen, aspartate aminotransferase, and creatinine. Exploratory analyses indicated that patients under the age of 21 years had a lower case fatality rate than those over the age of 45 years (57% vs. 94%, P = 0.03), and patients presenting with fewer than 100,000 EBOV copies per milliliter had a lower case fatality rate than those with 10 million EBOV copies per milliliter or more (33% vs. 94%, P = 0.003). Bleeding occurred in only 1 patient. CONCLUSIONS The incubation period and case fatality rate among patients with EVD in Sierra Leone are similar to those observed elsewhere in the 2014 outbreak and in previous outbreaks. Although bleeding was an infrequent finding, diarrhea and other gastrointestinal manifestations were common. (Funded by the National Institutes of Health and others.)

An unfolded state ensemble is generated by using a self-avoiding statistical coil model that is based on backbone conformational frequencies in a coil library, a subset of the Protein Data Bank. The model reproduces two apparently contradicting behaviors observed in the chemically denatured state for a variety of proteins, random coil scaling of the radius of gyration and the presence of significant amounts of local backbone structure (NMR residual dipolar couplings). The most stretched members of our unfolded ensemble dominate the residual dipolar coupling signal, whereas the uniformity of the sign of the couplings follows from the preponderance of polyproline II and ␤ conformers in the coil library. Agreement with the NMR data substantially improves when the backbone conformational preferences include correlations arising from the chemical and conformational identity of neighboring residues. Although the unfolded ensembles match the experimental observables, they do not display evidence of nativelike topology. By providing an accurate representation of the unfolded state, our statistical coil model can be used to improve thermodynamic and kinetic modeling of protein folding. denatured state ͉ protein folding ͉ residual dipolar coupling ͉ nearest neighbor ͉ radius of gyration D enatured proteins are the initial state for mechanistic and thermodynamic studies of folding. The recent resurgence of interest in the unfolded state is partly motivated by the development of NMR methods that are capable of providing site-resolved structural information (1-7). These measurements indicate that unfolded proteins have far richer structural diversity than earlier believed, possibly even encoding the native topology (1,(8)(9)(10)(11).These works seem at odds with the classic studies by Tanford et al. (12,13), who demonstrated by using hydrodynamic methods that the global dimensions of denatured proteins exhibit the size dependence expected for self-avoiding ''random coil'' polymers. More recent measurements of the radius of gyration, R g , using small-angle scattering methods exhibit the same random coil scaling behavior with length R g ϰ N 0.585 (8,14). These observations are consistent with denatured proteins being random coils in good solvent conditions (15). This finding leads to the so-called ''reconciliation problem'' between the random coil scaling behavior and the presence of significant amounts of local structure in unfolded state (14, 16).However, Rose and Fitzkee (17) demonstrate that even a ''deliberately extreme'' model of chains composed of native-like segments connected by flexible residues also can reproduce random coil scaling behavior. Hence, the recapitulation of the scaling behavior provides only a weak test for any unfolded state model. Nevertheless, spectroscopic measurements, such as circular dichroism, indicate that most unfolded states, particularly chemicaldenatured proteins (8,13,18), have little secondary structure. Accordingly, the unrealistic native-like segment model is ruled out. More exacting...