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Humans are key players for the current unprecedented rate of biodiversity loss across the globe with climate change, pollution and the loss, fragmentation, and degradation of habitat (VITOUSEK et al 1997). According to convention on biological diversity (C B D) in 2019, defines biodiversity as “the variety of life on earth, including plants, animals and microorganisms, as well as the ecosystem of which they are part. Biodiversity includes genetic differences within species, the diversity of species and the variety of ecosystem. The development and presence of roads infrastructures is the major indicator of economic growth. Research has shown that several important indicators of economy like trade, electricity, communication, health are positive correlated with the road infrastructure. Therefore any government of a country considers it important to invest in road infrastructure for feature prospect of the country with the best possible ways. However, consequences of road construction cannot be neglected. Roads construction for mobility and accessibility of people inevitably transforms natural habitat in to a sealed and highly disturbed environment which always implies net loss of wild life habitat. The physical encroachment on the land, gives rise to disturbance and barrier effects that contribute to the overall habitat loss, fragmentation and degradation in Sierra Leone. Humans are changing the original structure of ecological communities by roads infrastructure which increases the death rate of species. This modification in earth ecological communities causes a compelling concern for ecosystem diversity loss Sierra Leone, like most developing countries trying to construct roads for mobility and accessibility. Road construction projects undertaken by government or NGOs in Sierra Leone can reduce landscape permeability. Therefore the fundamental changes in landscape structure have both direct and indirect impacts on the conservation of species and biodiversity. The direct loss refers to the reduction of the total area of an ecosystem caused by the presence of roads and its verges, i.e. by the conversion of the original land cover into artificial surfaces. The indirect loss refers to the effects such as the fragmentation (portioning of an ecosystem in to smaller and more isolated patches), and the degradation of ecosystem induce by noise, air, water pollution, artificial light. These effects cause and indirect loss of habitat in that, they reduce the capacity of and ecosystem to sustain its original biodiversity. It is explicit that, in Sierra Leone, most of the species are endangered as a result of road constructions the use of bulldozers and other machines in the operation to level the land, clear trees, and flatten the ground will destroy and displace many living organisms from their natural habitat and change their entire ways of living. The process will unable organism to adapt to drastic changes in their natural habitat.

This study aimed to investigate the serological characteristics of Ebola virus (EBOV) infection during the late phase of the Ebola outbreak in Sierra Leone. In total, 877 blood samples from 694 suspected Ebola virus disease (EVD) cases assessed from March to December 2015, were analyzed via real-time reverse transcription polymerase chain reaction (RT-PCR) for viral RNA and enzyme-linked immunosorbent assay (ELISA) and Luminex to detect antibodies against EBOV. Viral load and EBOV-specific IgM/IgG titers displayed a declining trend during March to December 2015. Viral RNA load decreased rapidly at earlier stages after disease onset, while EBOV-specific IgM and IgG still persisted in 58.1% (18/31) and 93.5% (29/31) of the confirmed EVD patients and in 3.8% (25/663) and 17.8% (118/663) of the RNA-negative suspected patients in the later phase, respectively. Dynamic analysis of longitudinally collected samples from eight EVD patients revealed typically reversed trends of declining viral load and increasing IgM and/or IgG titers in response to the EBOV infection. The present results indicate that certain populations of Sierra Leone developed immunity to an EBOV infection in the late phase of the outbreak, providing novel insights into the risk assessment of EBOV infections among human populations.

The West Africa Ebola epidemic stimulated rapid implementation of Ebola vaccine trials in the 3 highly affected countries. In Sierra Leone, we studied the recombinant vesicular stomatitis virus Ebola vaccine (rVSV∆G-ZEBOV-GP) safety and efficacy. The Sierra Leone Trial to Introduce a Vaccine against Ebola (STRIVE) was a randomized, unblinded Phase 2/3 trial with phased vaccine introduction, no placebo, and concurrent evaluation of vaccine safety and efficacy. Healthcare and frontline response workers in 5 districts were randomized to immediate or deferred (18–24 weeks later) vaccination and followed for 6 months postvaccination. We enrolled 8651 participants from April through August 2015; 7998 were vaccinated. No participants developed Ebola virus disease so an efficacy assessment was not possible. Overall, 132 (1.5%) participants experienced serious adverse events (SAEs); none were vaccine-related. In a detailed safety substudy (N = 436), vaccinated participants reported significantly more systemic adverse events (AEs) within 7 days than unvaccinated participants including fever higher than 38°C (20.5% vs 3.9%), headache (71.2% vs 22.1%), fatigue (50.7% vs 10.4%), and joint pain (31.7% vs 6.5%); most AEs were mild to moderate severity and resolved within 5 days. During days 5-28, vaccinated participants more commonly reported joint pain (17.0% vs 4.8%) and rash (7.8% vs 1.7%) (P

Background The 2014–2016 Ebola virus epidemic in West Africa was the largest outbreak of Ebola virus disease (EVD) in history. Clarifying the influence of other prevalent diseases such as human immunodeficiency virus infection and acquired immune deficiency syndrome (HIV/AIDS) will help improve treatment and supportive care of patients with EVD. Case presentation We examined HIV and hepatitis C virus (HCV) antibody prevalence among suspected EVD cases from the Sierra Leone-China Friendship Biological Safety Laboratory during the epidemic in Sierra Leone. HIV and HCV antibodies were tested in 678 EVD-negative samples by enzyme-linked immunosorbent assay. A high HIV prevalence (17.6%) and low HCV prevalence (0.22%) were observed among the suspected cases. Notably, we found decreased HIV positive rates among the suspected cases over the course of the epidemic. This suggests a potentially beneficial effect of an improved public health system after assistance from the World Health Organization and other international aid organizations. Conclusions This EVD epidemic had a considerable impact on the public health system and influenced the prevalence of HIV found among suspected cases in Sierra Leone, but also provided an opportunity to establish a better surveillance network for infectious diseases. Electronic supplementary material The online version of this article (10.1186/s40249-019-0525-9) contains supplementary material, which is available to authorized users.

Evaluations of community-based antiretroviral therapy (ART) programmes have demonstrated positive outcomes, but little is known about the impact of tapering community-based ART. The objective of this study was to assess 24-month HIV retention outcomes of a community-based ART programme and its tapered visit frequency in Koidu City, Sierra Leone. This retrospective, quasi-experimental study compared outcomes of 52 HIV-infected persons initiated on community-based ART against 91 HIV-infected persons receiving the standard of care from November 2009 to February 2013. The community-based ART pilot programme was designed to strengthen the standard of care through a comprehensive, patient-centred case management strategy. The strategy included medical, educational, psychological, social, and economic support. Starting in October 2011, the frequency of home visits was tapered from twice daily every day per week to once daily three days per week. Outcomes were retention in care at 12 and 24 months and adherence to ART over a three-month time period. Participants who received community-based ART had significantly higher retention than those receiving standard of care. At 12 months, retention rates for community-based ART and standard of care were 61.5% and 31.9%, respectively (p < .01). At 24 months, retention rates for community based ART and standard of care were 73.1% and 44.0%, respectively (p < .01). Significant differences in levels of adherence were observed when comparing community-based ART against persons receiving standard of care (p < .05). No differences in adherence levels were observed between groups of people receiving various frequencies of home visits. Our pilotprogramme in Koidu City provides new evidence that community-based ART has the potential to improve retention and adherence outcomes for HIV-infected persons, regardless of the frequency of home visits. Overcoming the barriers to HIV care requires a comprehensive, patient-centred approach that may include clinic-based and community-based interventions.Keywords: HIV/AIDS; community-based ART programme; adherence; retention in care; Sierra Leone

During the Ebola virus outbreak of 2013-2016, the Viral Special Pathogens Branch field laboratory in Sierra Leone tested approximately 26 000 specimens between August 2014 and October 2015. Analysis of the B2M endogenous control Ct values showed its utility in monitoring specimen quality, comparing results with different specimen types, and interpretation of results. For live patients, blood is the most sensitive specimen type and oral swabs have little diagnostic utility. However, swabs are highly sensitive for diagnostic testing of corpses.

The 2013-2016 West African Ebola virus disease (EVD) epidemic is the largest recorded. Triage on the basis of clinical signs had limited success, and the time to diagnosis by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) could exceed 5 days. Here we describe the development and field validation of the ReEBOV Antigen Rapid Test (ReEBOV RDT) to aid triage of individuals with suspected EVD.Samples from patients with suspected EVD were submitted to Kenema Government Hospital, Sierra Leone, for Lassa fever and EVD screening throughout 2014. Banked residual clinical samples were tested in November 2014 and January 2015 in a blinded field trial to estimate the clinical effectiveness of the ReEBOV RDT, compared with EBOV-specific qRT-PCR.Preliminary ReEBOV RDT performance demonstrated a positive percentage agreement (PPA) of 91.1% (195 of 214 results; 95% confidence interval [CI], 86.5%-94.6%) and a negative percentage agreement (NPA) of 90.2% (175 of 194; 95% CI, 85.1%-94.0%). The final estimates used by the Food and Drug Administration to determine whether to grant emergency use authorization for the test, which excluded a qRT-PCR reference method threshold cutoff, were a PPA of 62.1% (72 of 116 results; 95% CI, 52.6%-70.9%) and a NPA of 96.7% (58 of 60; 95% CI, 88.5%-99.6%), with a diagnostic likelihood of 18.6. A subsequent, independent evaluation by the World Health Organization generated results consistent with the preliminary performance estimates.The ReEBOV RDT demonstrated the potential to provide clinically effective rapid and accurate point-of-care test results and, thus, to be a powerful tool for increasing triage efficiency.

Background.Kenema Government Hospital (KGH) has developed an advanced clinical and laboratory research capacity to manage the threat of Lassa fever, a viral hemorrhagic fever (VHF). The 2013–2016 Ebola virus (EBOV) disease (EVD) outbreak is the first to have occurred in an area close to a facility with established clinical and laboratory capacity for study of VHFs. Methods.Because of its proximity to the epicenter of the EVD outbreak, which began in Guinea in March 2014, the KGH Lassa fever Team mobilized to establish EBOV surveillance and diagnostic capabilities. Results.Augustine Goba, director of the KGH Lassa laboratory, diagnosed the first documented case of EVD in Sierra Leone, on 25 May 2014. Thereafter, KGH received and cared for numbers of patients with EVD that quickly overwhelmed the capacity for safe management. Numerous healthcare workers contracted and lost their lives to EVD. The vast majority of subsequent EVD cases in West Africa can be traced back to a single transmission chain that includes this first diagnosed case. Conclusions.Responding to the challenges of confronting 2 hemorrhagic fever viruses will require continued investments in the development of countermeasures (vaccines, therapeutic agents, and diagnostic assays), infrastructure, and human resources.

Lassa fever is a severe multisystem disease that often has haemorrhagic manifestations. The epitopes of the Lassa virus (LASV) surface glycoproteins recognized by naturally infected human hosts have not been identified or characterized. Here we have cloned 113 human monoclonal antibodies (mAbs) specific for LASV glycoproteins from memory B cells of Lassa fever survivors from West Africa. One-half bind the GP2 fusion subunit, one-fourth recognize the GP1 receptor-binding subunit and the remaining fourth are specific for the assembled glycoprotein complex, requiring both GP1 and GP2 subunits for recognition. Notably, of the 16 mAbs that neutralize LASV, 13 require the assembled glycoprotein complex for binding, while the remaining 3 require GP1 only. Compared with non-neutralizing mAbs, neutralizing mAbs have higher binding affinities and greater divergence from germline progenitors. Some mAbs potently neutralize all four LASV lineages. These insights from LASV human mAb characterization will guide strategies for immunotherapeutic development and vaccine design., Lassa virus can cause haemorrhagic fever for which no specific treatment currently exists. Here the authors have cloned 113 monoclonal antibodies from the survivors of Lassa infection and show that the majority of neutralizing antibodies target a complex of GP1 and GP2 viral proteins.

Sierra Leone is the most severely affected country by an unprecedented outbreak of Ebola virus disease (EVD) in West Africa. Although successfully contained, the transmission dynamics of EVD and the impact of interventions in the country remain unclear. We established a database of confirmed and suspected EVD cases from May 2014 to September 2015 in Sierra Leone and mapped the spatiotemporal distribution of cases at the chiefdom level. A Poisson transmission model revealed that the transmissibility at the chiefdom level, estimated as the average number of secondary infections caused by a patient per week, was reduced by 43% [95% confidence interval (CI): 30%, 52%] after October 2014, when the strategic plan of the United Nations Mission for Emergency Ebola Response was initiated, and by 65% (95% CI: 57%, 71%) after the end of December 2014, when 100% case isolation and safe burials were essentially achieved, both compared with before October 2014. Population density, proximity to Ebola treatment centers, cropland coverage, and atmospheric temperature were associated with EVD transmission. The household secondary attack rate (SAR) was estimated to be 0.059 (95% CI: 0.050, 0.070) for the overall outbreak. The household SAR was reduced by 82%, from 0.093 to 0.017, after the nationwide campaign to achieve 100% case isolation and safe burials had been conducted. This study provides a complete overview of the transmission dynamics of the 2014-2015 EVD outbreak in Sierra Leone at both chiefdom and household levels. The interventions implemented in Sierra Leone seem effective in containing the epidemic, particularly in interrupting household transmission.

Multilingual abstracts in the five official working languages of the United Nations. (PDF 230 kb)

People in Western Africa suffer greatly from febrile jaundice, which is caused by a variety of pathogens. However, yellow fever virus (YFV) is the only pathogen under surveillance in Sierra Leone owing to the undeveloped medical and public health system there. Most of the results of YFV identification are negative. Elucidation of the pathogen spectrum is required to reduce the prevalence of febrile jaundice.In the present study, we used Ion Torrent semiconductor sequencing to profile the pathogen spectrum in archived YFV-negative sera from 96 patients in Sierra Leone who presented with unexplained febrile jaundice.The most frequently identified sequencing reads belonged to the following pathogens: cytomegalovirus (89.58%), Epstein-Barr virus (55.21%), hepatitis C virus (34.38%), rhinovirus (28.13%), hepatitis A virus (20.83%), coxsackievirus (10.42%), Ebola virus (8.33%), hepatitis E virus (8.33%), lyssavirus (4.17%), leptospirosis (4.17%), chikungunya virus (2.08%), Crimean-Congo hemorrhagic fever virus (1.04%), and hepatitis B virus (1.04%).The distribution of sequencing reads suggests a broader spectrum of pathogens for consideration in clinical diagnostics and epidemiological surveillance in Sierra Leone.

During the late phase of the large West-African Ebola virus disease (EVD) outbreak, the majority of patients were cared for in designated treatment centers. However, the preexisting healthcare infrastructure was already overwhelmed by the outbreak. This had a huge impact on other, non-EVD-related diseases, causing an unprecedented increase in morbidity and mortality, which most likely exceeded the toll due to EVD directly. Consequently, a crucial question is how to provide appropriate healthcare and safeguard functionality of a healthcare system that also serves patients not suspected or diagnosed to have EVD. Here, we report on the Lion Heart Medical Center's experience in Sierra Leone and note that a case definition of Ebola that is broader than those commonly applied may be better suited when it is necessary to identify atypically presenting, pauci-symptomatic cases.

BACKGROUND. Ebola virus (EBOV) causes periodic outbreaks of life-threatening EBOV disease in Africa. Historically, these outbreaks have been relatively small and geographically contained; however, the magnitude of the EBOV outbreak that began in 2014 in West Africa has been unprecedented. The aim of this study was to describe the viral kinetics of EBOV during this outbreak and identify factors that contribute to outbreak progression. METHODS. From July to December 2014, one laboratory in Sierra Leone processed over 2,700 patient samples for EBOV detection by quantitative PCR (qPCR). Viremia was measured following patient admission. Age, sex, and approximate time of symptom onset were also recorded for each patient. The data was analyzed using various mathematical models to find trends of potential interest. RESULTS. The analysis revealed a significant difference (P = 2.7 × 10–77) between the initial viremia of survivors (4.02 log10 genome equivalents [GEQ]/ml) and nonsurvivors (6.18 log10 GEQ/ml). At the population level, patient viral loads were higher on average in July than in November, even when accounting for outcome and time since onset of symptoms. This decrease in viral loads temporally correlated with an increase in circulating EBOV-specific IgG antibodies among individuals who were suspected of being infected but shown to be negative for the virus by PCR. CONCLUSIONS. Our results indicate that initial viremia is associated with outcome of the individual and outbreak duration; therefore, care must be taken in planning clinical trials and interventions. Additional research in virus adaptation and the impacts of host factors on EBOV transmission and pathogenesis is needed.

During the 2014 Ebola virus disease (EVD) outbreak, a real-time quantitative polymerase chain reaction was established to detect and identify the Zaire Ebola virus. We describe the use of this assay to screen 315 clinical samples from EVD suspected person in Sierra Leone. The detection rate in blood samples was 77.81% (207/266), and there were relatively higher detection rate (79.32% and 81.42%, respectively) during the first two weeks after onset of symptoms. In the two weeks that followed, the detection rate declined to 66.67% and 25.00%, respectively. There was the highest virus load at the first week and then decreased. The detection rate in swab samples was 89.79% (44/49). This may be benefit from the included patients. 46 of 49 swab samples were collected from died patients. Taken together, the results presented here indicate that the assay specifically and sensitively detects Zaire Ebola virus.

Thirteen international field labs in Sierra Leone (SL) support Ebola diagnosis. Never before has the role of field labs been so crucial as it has been during the Ebolavirus disease responses in SL. This analysis encourages that developed nations should not fear sending field lab to help for controlling Ebola.

Background In August 2014, the National Institute for Communicable Diseases (NICD) in South Africa established a modular high-biosafety field Ebola diagnostic laboratory (SA FEDL) near Freetown, Sierra Leone in response to the rapidly increasing number of Ebola virus disease (EVD) cases. Methods and findings The SA FEDL operated in the Western Area of Sierra Leone, which remained a “hotspot” of the EVD epidemic for months. The FEDL was the only diagnostic capacity available to respond to the overwhelming demand for rapid EVD laboratory diagnosis for several weeks in the initial stages of the EVD crisis in the capital of Sierra Leone. Furthermore, the NICD set out to establish local capacity amongst Sierra Leonean nationals in all aspects of the FEDL functions from the outset. This led to the successful hand-over of the FEDL to the Sierra Leone Ministry of Health and Sanitation in March 2015. Between 25 August 2014 and 22 June 2016, the laboratory tested 11,250 specimens mostly from the Western Urban and Western Rural regions of Sierra Leone, of which 2,379 (21.14%) tested positive for Ebola virus RNA. Conclusions The bio-safety standards and the portability of the SA FEDL, offered a cost-effective and practical alternative for the rapid deployment of a field-operated high biocontainment facility. The SA FEDL teams demonstrated that it is highly beneficial to train the national staff in the course of formidable disease outbreak and accomplished their full integration into all operational and diagnostic aspects of the laboratory. This initiative contributed to the international efforts in bringing the EVD outbreak under control in Sierra Leone, as well as capacitating local African scientists and technologists to respond to diagnostic needs that might be required in future outbreaks of highly contagious pathogens., Author summary In response to Ebola virus disease outbreak in West Africa, the National Institute for Communicable Diseases in South Africa established a modular high-biosafety field Ebola diagnostic laboratory (FEDL) near Freetown, Sierra Leone. This was the sole diagnostic capacity available to respond to the overwhelming demand for Ebola diagnosis for several weeks in the Western Area of Sierra Leone. The deployment of the FEDL capacity contributed to the overall international efforts in bringing the Ebola outbreak in West Africa under control.

Introduction Western Area (WA) of Sierra Leone including the capital, Freetown, experienced an unprecedented outbreak of Ebola from 2014 to 2015. At the onset of the epidemic, there was little information about the epidemiology, transmission dynamics, and risk factors in urban settings as previous outbreaks were limited to rural/semi-rural settings. This study, therefore, aimed to describe the epidemiology of the outbreak and the factors which had most impact on the transmission of the epidemic and whether there were different drivers from those previously described in rural settings. Methods We conducted a descriptive epidemiology study in WA, Sierra Leone using secondary data from the National Ebola outbreak database. We also reviewed the Ebola situation reports, response strategy documents, and other useful documents. Results A total of 4,955 Ebola cases were identified between June 2014 and November 2015, although there were reports of cases occurring in WA toward end of May. All wards were affected, and Waterloo Area I (Ward 330), the capital city of Western Area Rural District, recorded the highest numbers of cases (580) and deaths (236). Majority of cases (63.4%) and deaths (66.8%) were in WA Urban District (WAU); 44 cases were imported from other provinces. Only 20% of cases had a history of contact with an Ebola case, and more than 30% were death alerts. Equal numbers of males and females were infected, and very few cases (3.2%) were health workers. Overall, transmission was through contact with infected individuals, and intense transmission occurred at the community level. In WAU, transmission was mostly between neighbors and among inhabitants of shared accommodations. The drivers of transmission included high population movement to and from WA, overcrowding, fear and lack of trust in the response, and negative community behaviors. Transmission was mostly through contact and with limited transmission through sex and breast milk. Conclusion The unprecedented outbreak in WA was attributed to delayed detection, inadequate preparedness and response, intense population movements, overcrowding, and unresponsive communities. Anticipation, strengthening preparedness for early detection, and swift and effective response remains critical in mitigating a potential urban explosion of similar future outbreaks.

BACKGROUND In light of the decline in donor HIV funding HIV programmes increasingly need to assess their available and potential resources and maximize their utilization. This article presents lessons learned related to how countries have addressed the sustainability of HIV programmes in a stakeholder-driven sustainability analysis. METHODOLOGY During HIV/AIDS Programme Sustainability Analysis Tool (HAPSAT) applications in six countries (Benin Guyana Kenya Lesotho Sierra Leone and South Sudan) stakeholders identified key sustainability challenges for their HIV responses. Possible policy approaches were prepared and those related to prioritization and resource mobilization are analysed in this article. RESULTS The need to prioritize evidence-based interventions and apply efficiency measures is being accepted by countries. Five of the six countries in this study requested that the HAPSAT team prepare prioritization strategies. Countries recognize the need to prepare for an alternative to universal access by 2015 acknowledging that their capacity might be insufficient to reach such high-coverage levels by then. There is further acceptance of the importance of reaching the most-at-risk marginalized populations as seen for example in South Sudan and Sierra Leone. However the pace at which resources are shifting towards these populations is slow. Finally only two of the six countries Kenya and Benin chose to examine options for generating additional financial resources beyond donor funding. In Kenya three non-donor sources were recommended yet even if all were to be implemented it would cover only 25% of the funding needed. CONCLUSIONS Countries are increasingly willing to address the challenges of HIV programme sustainability yet in different ways and with varying urgency. To secure achievements made to date and maximize future impact countries would benefit from strengthening their strategic plans operational plans and funding proposals with concrete timelines and responsibilities for addressing sustainability issues.

We performed Ebola virus disease diagnosis and viral load estimation for Ebola cases in Sierra Leone during the late stage of the 2014-2015 outbreak (January-March 2015) and analyzed antibody and cytokine levels and the viral genome sequences. Ebola virus disease was confirmed in 86 of 1001 (9.7%) patients, with an overall case fatality rate of 46.8%. Fatal cases exhibited significantly higher levels of viral loads, cytokines, and chemokines at late stages of infection versus early stage compared with survivors. The viruses converged in a new clade within sublineage 3.2.4, which had a significantly lower case fatality rate.

BACKGROUND The 2013-2016 West African Ebola virus disease (EVD) epidemic is the largest recorded. Triage on the basis of clinical signs had limited success, and the time to diagnosis by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) could exceed 5 days. Here we describe the development and field validation of the ReEBOV Antigen Rapid Test (ReEBOV RDT) to aid triage of individuals with suspected EVD. METHODS Samples from patients with suspected EVD were submitted to Kenema Government Hospital, Sierra Leone, for Lassa fever and EVD screening throughout 2014. Banked residual clinical samples were tested in November 2014 and January 2015 in a blinded field trial to estimate the clinical effectiveness of the ReEBOV RDT, compared with EBOV-specific qRT-PCR. RESULTS Preliminary ReEBOV RDT performance demonstrated a positive percentage agreement (PPA) of 91.1% (195 of 214 results; 95% confidence interval [CI], 86.5%-94.6%) and a negative percentage agreement (NPA) of 90.2% (175 of 194; 95% CI, 85.1%-94.0%). The final estimates used by the Food and Drug Administration to determine whether to grant emergency use authorization for the test, which excluded a qRT-PCR reference method threshold cutoff, were a PPA of 62.1% (72 of 116 results; 95% CI, 52.6%-70.9%) and a NPA of 96.7% (58 of 60; 95% CI, 88.5%-99.6%), with a diagnostic likelihood of 18.6. A subsequent, independent evaluation by the World Health Organization generated results consistent with the preliminary performance estimates. CONCLUSIONS The ReEBOV RDT demonstrated the potential to provide clinically effective rapid and accurate point-of-care test results and, thus, to be a powerful tool for increasing triage efficiency.

SummaryThe 2013-2016 epidemic of Ebola virus disease in West Africa was of unprecedented magnitude, duration and impact. Extensive collaborative sequencing projects have produced a large collection of over 1600 Ebola virus genomes, representing over 5% of known cases, unmatched for any single human epidemic. In this comprehensive analysis of this entire dataset, we reconstruct in detail the history of migration, proliferation and decline of Ebola virus throughout the region. We test the association of geography, climate, administrative boundaries, demography and culture with viral movement among 56 administrative regions. Our results show that during the outbreak viral lineages moved according to a classic ‘gravity’ model, with more intense migration between larger and more proximate population centers. Notably, we find that despite a strong attenuation of international dispersal after border closures, localized cross-border transmission beforehand had already set the seeds for an international epidemic, rendering these measures relatively ineffective in curbing the epidemic. We use this empirical evidence to address why the epidemic did not spread into neighboring countries, showing that although these regions were susceptible to developing significant outbreaks, they were also at lower risk of viral introductions. Finally, viral genome sequence data uniquely reveals this large epidemic to be a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help inform approaches to intervention in such epidemics in the future.

Sierra Leone was the most severely affected country in Western Africa during the 2013-2016 outbreak of Ebola virus disease (EVD). Previous genome surveillance studies have revealed the origin, diversity, and evolutionary dynamics of the Ebola virus (EBOV); however, the information regarding EBOV sequences is insufficient, especially the clinical outcomes, given that the correlation between the clinical outcomes and the genetic evolution of EBOV is still not clear. Here, we collected and curated a comprehensive data set that includes 514 EBOV genome sequences from patients with confirmed EVD (including 60 sequences not previously studied), >87.5% of which have residence information and definitive clinical outcomes. Phylogenetic reconstruction revealed 11 lineages of EBOV in Sierra Leone. The median-joining haplotype network showed that haplotypes that are associated with lethal outcomes tend to contribute more to the spread of the EBOV in Sierra Leone than those with live outcomes. Analyses of the spatial-temporal distribution unraveled the lineage-distinctive distribution patterns. Different viral lineages have different case fatality rates (CFRs) during the same stage of the outbreak, implying that several lineages featuring SNPs may correlate with increased/decreased CFRs. This study provides invaluable data sets of EBOV infection and highlights the potential SNPs for further in-depth investigation.

SUMMARYThe current Ebola virus disease (EVD) epidemic in West Africa is unprecedented in scale, and Sierra Leone is the most severely affected country. The case fatality risk (CFR) and hospitalization fatality risk (HFR) were used to characterize the severity of infections in confirmed and probable EVD cases in Sierra Leone. Proportional hazards regression models were used to investigate factors associated with the risk of death in EVD cases. In total, there were 17 318 EVD cases reported in Sierra Leone from 23 May 2014 to 31 January 2015. Of the probable and confirmed EVD cases with a reported final outcome, a total of 2536 deaths and 886 recoveries were reported. CFR and HFR estimates were 74·2% [95% credibility interval (CrI) 72·6–75·5] and 68·9% (95% CrI 66·2–71·6), respectively. Risks of death were higher in the youngest (0–4 years) and oldest (⩾60 years) age groups, and in the calendar month of October 2014. Sex and occupational status did not significantly affect the mortality of EVD. The CFR and HFR estimates of EVD were very high in Sierra Leone.

Background During 2014-2015, an outbreak of Ebola virus disease (EVD) swept across parts of West Africa. No approved antiviral drugs are available for Ebola treatment currently. Methods A retrospective clinical case series was performed for EVD patients in Sierra Leone-China Friendship Hospital. Patients with confirmed EVD were sequentially enrolled and treated with either World Health Organization (WHO)-recommended supportive therapy (control group) from 10 to 30 October, or treated with WHO-recommended therapy plus favipiravir (T-705) from 1 to 10 November 2014. Survival and virological characteristics were observed for 85 patients in the control group and 39 in the T-705 treatment group. Results The overall survival rate in the T-705 treatment group was higher than that of the control group (56.4% [22/39] vs 35.3% [30/85]; P = .027). Among the 35 patients who finished all designed endpoint observations, the survival rate in the T-705 treatment group (64.8% [11/17]) was higher than that of the control group (27.8% [5/18]). Furthermore, the average survival time of the treatment group (46.9 ± 5.6 days) was longer than that of the control group (28.9 ± 4.7 days). Most symptoms of patients in the treatment group improved significantly. Additionally, 52.9% of patients who received T-705 had a >100-fold viral load reduction, compared with only 16.7% of patients in the control group. Conclusions Treatment of EVD with T-705 was associated with prolonged survival and markedly reduced viral load, which makes a compelling case for further randomized controlled trials of T-705 for treating EVD.

Background The heterogeneity of the pre-antiretroviral (pre-ART) population calls for more granular depictions of the cascade of HIV care. Methods We studied a prospective cohort of persons newly diagnosed with HIV infection from a single center in Freetown, Sierra Leone, over a 12-month period and then traced those persons who were lost to follow-up (LTFU) during pre-ART care (before ART initiation). ART eligibility was based on a CD4 cell count result of ≤ 350 mm/cells and/or WHO clinical stage 3 or 4. Persons who attended an appointment in the final three months were considered to be retained in care. Adherence to ART was measured using pharmacy refill dates. “Effective HIV care” was defined as completion of the cascade of care at 12-months regardless of whether patients are on ART. Tracing outcomes were obtained for those who were LTFU during pre-ART care. Results 408 persons newly diagnosed with HIV infection were screened, 338 were enrolled, and 255 persons were staged for ART. ART-ineligible persons had higher retention rates than ART-eligible persons (59.6% vs 41.8%, p = 0.03). 77 (22.8%) of 338 persons received effective HIV care. Most attrition (61.9%) occurred with persons during pre-ART care. 123 of 138 persons (89.1%) who were LTFU prior to ART initiation were found, and 91 of those 123 (74.0%) were alive. Of the 74 persons who were alive and described their engagement in care, 40 (54.1%) stopped care. Nearly half (42.5%) of those 40 stopped after assessment of ART-eligibility but before ART initiation. The main limitation of this study was the lack of tracing outcomes for those lost during ART care. Conclusions The majority of the pre-ART LTFU population stopped their care, particularly after ART-eligibility but before ART initiation. Interventions to hasten ART initiation and retain this at-risk group may have significant downstream impact on effective HIV care.

The 2014-2015 West African outbreak of Ebola Virus Disease (EVD) claimed the lives of more than 11,000 people and infected over 27,000 across seven countries. Traditional approaches to containing EVD proved inadequate and new approaches for controlling the outbreak were required. The Ministry of Health & Sanitation and King’s Sierra Leone Partnership developed a model for Ebola Holding Units (EHUs) at Government Hospitals in the capital city Freetown. The EHUs isolated screened or referred suspect patients, provided initial clinical care, undertook laboratory testing to confirm EVD status, referred onward positive cases to an Ebola Treatment Centre or negative cases to the general wards, and safely stored corpses pending collection by burial teams. Between 29th May 2014 and 19th January 2015, our five units had isolated approximately 37% (1159) of the 3097 confirmed cases within Western Urban and Rural district. Nosocomial transmission of EVD within the units appears lower than previously documented at other facilities and staff infection rates were also low. We found that EHUs are a flexible and effective model of rapid diagnosis, safe isolation and early initial treatment. We also demonstrated that it is possible for international partners and government facilities to collaborate closely during a humanitarian crisis.

To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing of cases and contacts was required. The ability to quickly identify unknown sources and chains of transmission is key to ending the EVD epidemic and of even greater importance in the context of recent reports of Ebola virus (EBOV) persistence in survivors. Phylogenetic analysis of complete EBOV genomes can provide important information on the source of any new infection. A local deep sequencing facility was established at the Mateneh Ebola Treatment Centre in central Sierra Leone. The facility included all wetlab and computational resources to rapidly process EBOV diagnostic samples into full genome sequences. We produced 554 EBOV genomes from EVD cases across Sierra Leone. These genomes provided a detailed description of EBOV evolution and facilitated phylogenetic tracking of new EVD cases. Importantly, we show that linked genomic and epidemiological data can not only support contact tracing but also identify unconventional transmission chains involving body fluids, including semen. Rapid EBOV genome sequencing, when linked to epidemiological information and a comprehensive database of virus sequences across the outbreak, provided a powerful tool for public health epidemic control efforts., info:eu-repo/semantics/published

Knowledge of epidemiologic, clinical, and viral features of the outbreak is critical for optimizing control and treatment measures., During 2014–2015, an outbreak of Ebola virus disease (EVD) swept across parts of West Africa. The China Mobile Laboratory Testing Team was dispatched to support response efforts; during September 28–November 11, 2014, they conducted PCR testing on samples from 1,635 suspected EVD patients. Of those patients, 50.4% were positive, of whom 84.6% lived within a 3-km zone along main roads connecting rural towns and densely populated cities. The median time from symptom onset to testing was 5 days. At testing, 75.7% of the confirmed patients had fever, and 94.1% reported at least 1 gastrointestinal symptom; all symptoms, except rash and hemorrhage, were more frequent in confirmed than nonconfirmed patients. Virus loads were significantly higher in EVD patients with fever, diarrhea, fatigue, or headache. The case-fatality rate was lower among patients 15–44 years of age and with virus loads of

Background: Anecdotal evidence suggests that much of the continuing infection of health care workers (HCWs) with Ebola virus during the current outbreak in Sierra Leone has occurred in settings other than Ebola isolation units, and it is likely that some proportion of acquisition by HCWs occurs outside the workplace. There is a critical need to define more precisely the pathways of Ebola infection among HCWs, to optimise measures for reducing risk during current and future outbreaks. Methods: We conducted a retrospective descriptive study of Ebola acquisition among health workers in Sierra Leone during May-December 2014. The data used were obtained mainly from the national Ebola database, a cross-sectional survey conducted through administration of a structured questionnaire to infected HCWs, and key informant interviews of select health stakeholders. Results: A total of 293 HCWs comprising 277 (95 %) confirmed, 6 (2 %) probable, and 10 (3 %) suspected cases of infection with Ebola virus were enrolled in the study from nine districts of the country. Over half of infected HCWs (153) were nurses; others included laboratory staff (19, 6.5 %), doctors (9, 3.1 %), cleaners and porters (9, 3.1 %), Community Health Officers (8, 2.7 %), and pharmacists (2, 0.7 %). HCW infections were mainly reported from the Western Area (24.9 %), Kailahun (18.4 %), Kenema (17.7 %), and Bombali (13.3 %) districts. Almost half of the infected HCWs (120, 47.4 %) believed that their exposure occurred in a hospital setting. Others believed that they were exposed in the home (48, 19 %), at health centres (45, 17.8 %), or at other types of health facilities (13, 5.1 %). Only 27 (10.7 %) of all HCW infections were associated with Ebola virus disease (EVD) isolation units. Over half (60 %, 150) of infected HCWs said they had been trained in infection prevention and control prior to their infection, whereas 34 % (85) reported that they had not been so trained. Conclusions: This study demonstrated the perception that most HCW infections are associated with general health care and home settings and not with dedicated EVD settings, which should provide substantial reassurance to HCWs that measures in place at dedicated EVD facilities generally provide substantial protection when fully adhered to.

A novel Ebola virus (EBOV) first identified in March 2014 has infected more than 25,000 people in West Africa, resulting in more than 10,000 deaths. Preliminary analyses of genome sequences of 81 EBOV collected from March to June 2014 from Guinea and Sierra Leone suggest that the 2014 EBOV originated from an independent transmission event from its natural reservoir followed by sustained human-to-human infections. It has been reported that the EBOV genome variation might have an effect on the efficacy of sequence-based virus detection and candidate therapeutics. However, only limited viral information has been available since July 2014, when the outbreak entered a rapid growth phase. Here we describe 175 full-length EBOV genome sequences from five severely stricken districts in Sierra Leone from 28 September to 11 November 2014. We found that the 2014 EBOV has become more phylogenetically and genetically diverse from July to November 2014, characterized by the emergence of multiple novel lineages. The substitution rate for the 2014 EBOV was estimated to be 1.23 × 10(-3) substitutions per site per year (95% highest posterior density interval, 1.04 × 10(-3) to 1.41 × 10(-3) substitutions per site per year), approximating to that observed between previous EBOV outbreaks. The sharp increase in genetic diversity of the 2014 EBOV warrants extensive EBOV surveillance in Sierra Leone, Guinea and Liberia to better understand the viral evolution and transmission dynamics of the ongoing outbreak. These data will facilitate the international efforts to develop vaccines and therapeutics.

The aim of this survey was to gain an insight into the level of knowledge, perception of risk and attitude of Sierra Leone Military personnel towards colleagues with HIV/AIDS. Four hundred and fifty (450) randomly selected male and female military personnel including officers and other ranks from six battalions were surveyed with a standard questionnaire. Results of this survey demonstrated a relatively low level of knowledge of HIV and AIDS amongst the survey population as evidenced by the 40% and 52% of participants stating that HIV is transmitted by mosquito bites and from public toilets respectively. An equally low perception of risk of the infection was demonstrated from the responses of the participants about attitude towards HIV infected colleagues. Three-fourth of the participants indicated that nobody should be informed if a colleague is HIV positive, with almost all the participants expressing their willingness to take care of an HIV/AIDS person in their household. Varying responses obtained demonstrate the necessity for scaling-up HIV education within the Republic of Sierra Leone Armed Forces. More resources most therefore be made available to the HIV/AIDS office of the Republic of Sierra Leone Armed Forces so that HIV education activities can be extended to all the brigades and battalions. Keywords: Knowledge, Perception, Attitude, HIV/AIDS.

Background Voluntary counselling and testing (VCT) is an important component of national HIV programs, which are necessary to realize the right to health. VCT data also provide valuable information on regional HIV epidemiology. Methods The study examines data on the population that obtained HIV VCT in Kenema District, Sierra Leone, from 2004 to 2006, using descriptive statistics and exploring potential HIV risk factors using bivariate and multivariable logistic regression. Analysis was performed separately for two subpopulations: those accessing VCT routinely as part of antenatal care and those specifically seeking VCT. Results During this period, 2230 people accessed VCT: 1213 through antenatal testing and 1017 specifically seeking VCT. The HIV prevalence was 0.6% in women presenting for antenatal care, 12.6% in women specifically accessing VCT, and 6.7% in men specifically accessing VCT. In both bivariate and multivariable analyses, being female was statistically significantly associated with testing positive in people specifically seeking VCT. Conclusions These data from the VCT service in Kenema will be used to improve the accessibility of HIV testing. Questions raised by the analysis will be used to enhance data collection and to inform further research on risk factors.

Understanding the growth and spatial expansion of (re)emerging infectious disease outbreaks, such as Ebola and avian influenza, is critical for the effective planning of control measures; however, such efforts are often compromised by data insufficiencies and observational errors. Here, we develop a spatial–temporal inference methodology using a modified network model in conjunction with the ensemble adjustment Kalman filter, a Bayesian inference method equipped to handle observational errors. The combined method is capable of revealing the spatial–temporal progression of infectious disease, while requiring only limited, readily compiled data. We use this method to reconstruct the transmission network of the 2014–2015 Ebola epidemic in Sierra Leone and identify source and sink regions. Our inference suggests that, in Sierra Leone, transmission within the network introduced Ebola to neighbouring districts and initiated self-sustaining local epidemics; two of the more populous and connected districts, Kenema and Port Loko, facilitated two independent transmission pathways. Epidemic intensity differed by district, was highly correlated with population size ( r = 0.76, p = 0.0015) and a critical window of opportunity for containing local Ebola epidemics at the source ( ca one month) existed. This novel methodology can be used to help identify and contain the spatial expansion of future (re)emerging infectious disease outbreaks.

Summary The 2013–2015 Ebola virus disease (EVD) epidemic is caused by the Makona variant of Ebola virus (EBOV). Early in the epidemic, genome sequencing provided insights into virus evolution and transmission and offered important information for outbreak response. Here, we analyze sequences from 232 patients sampled over 7 months in Sierra Leone, along with 86 previously released genomes from earlier in the epidemic. We confirm sustained human-to-human transmission within Sierra Leone and find no evidence for import or export of EBOV across national borders after its initial introduction. Using high-depth replicate sequencing, we observe both host-to-host transmission and recurrent emergence of intrahost genetic variants. We trace the increasing impact of purifying selection in suppressing the accumulation of nonsynonymous mutations over time. Finally, we note changes in the mucin-like domain of EBOV glycoprotein that merit further investigation. These findings clarify the movement of EBOV within the region and describe viral evolution during prolonged human-to-human transmission., Graphical Abstract, Highlights • In Sierra Leone, transmission has primarily been within-country, not between-country • Infectious doses are large enough for intrahost variants to transmit between hosts • A prolonged epidemic removes deleterious mutations from the viral population • There is preliminary evidence for human RNA editing effects on the Ebola genome, Ebola virus genomes from 232 patients sampled over 7 months in Sierra Leone were sequenced. Transmission of intrahost genetic variants suggests a sufficiently high infectious dose during transmission. The human host may have caused direct alterations to the Ebola virus genome.