Lassa Fever in Post-Conflict Sierra Leone

Background: Lassa fever (LF), an often-fatal hemorrhagic disease caused by Lassa virus (LASV), is a major public health threat in West Africa. When the violent civil conflict in Sierra Leone (1991 to 2002) ended, an international consortium assisted in restoration of the LF program at Kenema Government Hospital (KGH) in an area with the world's highest incidence of the disease. Methodology/Principal Findings Clinical and laboratory records of patients presenting to the KGH Lassa Ward in the post-conflict period were organized electronically. Recombinant antigen-based LF immunoassays were used to assess LASV antigenemia and LASV-specific antibodies in patients who met criteria for suspected LF. KGH has been reestablished as a center for LF treatment and research, with over 500 suspected cases now presenting yearly. Higher case fatality rates (CFRs) in LF patients were observed compared to studies conducted prior to the civil conflict. Different criteria for defining LF stages and differences in sensitivity of assays likely account for these differences. The highest incidence of LF in Sierra Leone was observed during the dry season. LF cases were observed in ten of Sierra Leone's thirteen districts, with numerous cases from outside the traditional endemic zone. Deaths in patients presenting with LASV antigenemia were skewed towards individuals less than 29 years of age. Women self-reporting as pregnant were significantly overrepresented among LASV antigenemic patients. The CFR of ribavirin-treated patients presenting early in acute infection was lower than in untreated subjects. Conclusions/Significance: Lassa fever remains a major public health threat in Sierra Leone. Outreach activities should expand because LF may be more widespread in Sierra Leone than previously recognized. Enhanced case finding to ensure rapid diagnosis and treatment is imperative to reduce mortality. Even with ribavirin treatment, there was a high rate of fatalities underscoring the need to develop more effective and/or supplemental treatments for LF

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. These regions are enriched for genes involved in pathogen defence and immunity and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. We used these genomes to improve the mouse reference genome, resulting in the completion of 10 new gene structures. Also, 62 new coding loci were added to the reference genome annotation. These genomes identified a large, previously unannotated, gene (Efcab3-like) encoding 5,874 amino acids. Mutant Efcab3-like mice display anomalies in multiple brain regions, suggesting a possible role for this gene in the regulation of brain development

Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever

Infection with Lassa virus (LASV) can cause Lassa fever, a haemorrhagic illness with an estimated fatality rate of 29.7%, but causes no or mild symptoms in many individuals. Here, to investigate whether human genetic variation underlies the heterogeneity of LASV infection, we carried out genome-wide association studies (GWAS) as well as seroprevalence surveys, human leukocyte antigen typing and high-throughput variant functional characterization assays. We analysed Lassa fever susceptibility and fatal outcomes in 533 cases of Lassa fever and 1,986 population controls recruited over a 7 year period in Nigeria and Sierra Leone. We detected genome-wide significant variant associations with Lassa fever fatal outcomes near GRM7 and LIF in the Nigerian cohort. We also show that a haplotype bearing signatures of positive selection and overlapping LARGE1, a required LASV entry factor, is associated with decreased risk of Lassa fever in the Nigerian cohort but not in the Sierra Leone cohort. Overall, we identified variants and genes that may impact the risk of severe Lassa fever, demonstrating how GWAS can provide insight into viral pathogenesis

Age distribution of cases presenting to the KGH Lassa Ward, 2008–12.

<p>Panel A: Age distributions of patients presenting while antigenemic (Ag+/IgM±). Panel B: Age distributions of nonantigenemic patients presenting with serum anti-LASV IgM (Ag−/IgM+). Panel C: Age distributions of nonantigenemic patients presenting without anti-LASV IgM seropositivity (Ag−/IgM−). In Panels A–C yellow portion of bars represent patients who were discharged and black portion of bars represent patients who died. Panel D: Age demographic for the population of Sierra Leone (2010 estimate). Among patients who died, the age distributions differed significantly between the Ag+/IgM± and Ag−/IgM− groups (p = .005). Distributional comparisons were carried out using the Kolmogorov-Smirnov technique (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002748#pntd.0002748.s006" target="_blank">Table S5</a>).</p

CFRs in suspected LF cases presenting to the KGH Lassa Ward by serostatus, 2008–12.

<p>Panel A: CFR by serostatus. The presence of LASV Ag and anti-LASV IgM in serum of patients with verifiable outcomes was assessed by recombinant Ag− and IgM− capture ELISA, respectively. Panel B: Alternative calculation of CFRs. Ag+/IgM± plus Ag−/IgM+ compared to Ag−/IgM−. Statistical significance was determined using a logistic regression model predicting CFR (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002748#pntd.0002748.s004" target="_blank">Table S3</a>). NS = not significant.</p

Geographic distribution of patients presenting to the KGH with LASV antigenemia and anti-LASV IgM serpositivity, 2008–12.

<p>Confirmed cases of LF as assessed by LASV Ag in serum or cases anti-LASV IgM are shown by year of presentation, district of residence and frequency of cases. Panel A: Patients presenting in 2008–9. Panel B: Patients presenting in 2010. Panel C: Patients presenting in 2011. Panel D: Patients presenting in 2012.</p

Suspected cases of LF evaluated at the KGH Lassa Laboratory and numbers of patients admitted to the KGH Lassa Ward, 2008–12.

<p>Non-admitted patients include those where only blood samples were submitted for screening from referral health-posts, patients dying en route to the hospital (DOA = dead on arrival), and patients not meeting the LF suspected case criteria (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002748#pntd-0002748-t001" target="_blank">Table 1</a>). Characteristics of study patients are compiled in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002748#pntd.0002748.s002" target="_blank">Table S1</a>.</p

Monthly distribution of suspected LF cases presenting to the KGH Lassa Ward by serostatus, 2008–2012.

<p>Panel A: antigenemic Lassa fever cases (Ag+/IgM±). Panel B: Patients with serum anti-LASV IgM (Ag−/IgM+). Panel C: Patients with no Lassa virus seropositivity (Ag−/IgM−). The monthly frequency distributions differed between each of the serostatus group comparisons as assessed using a Poisson regression model (p<.001 for all serostatus comparisons; data not shown).</p

Gender and self-reported pregnancy status of suspected Lassa fever cases presenting to the KGH Lassa Ward, 2008–2012.

<p>Panel A: Frequency of suspected Lassa fever cases by gender and serostatus. Panel B: Cases fatality rates by gender and serostatus. Panel C: Percentage of female patients of childbearing age with self-reported pregnancy status by serostatus. Panel D: Case fatality rates in female patients with self-reported pregnancy status Pregnancies are self-reported and therefore likely underestimated as pregnancy tests were not routinely available. Logistic regression was used for group comparisons (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002748#pntd.0002748.s007" target="_blank">Tables S6</a> and <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002748#pntd.0002748.s008" target="_blank">S7</a>). NS = not significant.</p