Next-generation Sequencing Study of Pathogens in Serum from Patients with Febrile Jaundice in Sierra Leone

Objective 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. Methods 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. Results 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%). Conclusion The distribution of sequencing reads suggests a broader spectrum of pathogens for consideration in clinical diagnostics and epidemiological surveillance in Sierra Leone.

Assessing people at risk of developing type 2 diabetes in Freetown, Sierra Leone

Objective:This study aims to estimate the proportion of adults that are at high risk of developing Type 2 diabetes mellitus,and to investigate the association of participants at high risk for developing diabetes with various risk factors.Methods:A 2-yearprospective community based cross-sectional design was carried out in Freetown using the standardized Finnish Diabetes Risk Score assessment questionnaire,at two community pharmacies in the East,Central Freetown,and at a Peripheral Health Unit in the west where participants were randomly selected.Results:The study included a total of 1013 adults(ages 18 years and above)which reveals that 36.5%had a family history of diabetes mellitus and 42.8%were physically inactive.Assessment of obesity depicted 35.4%have class 1–2 obesity,with 19.4%males and 35.4%females having central obesity respectively.In terms of risk score,17.8%of total participants were found to be at high risk for developing type 2 diabetes.Conclusion:There is a high prevalence of risk for developing diabetes among residents of Freetown.Major risk factors such as,age,family history of Diabetes,obesity,high blood pressure contributed to this.Increase in obesity rate was also seen especially among females having a wider waist circumference and Body Mass Index.Interventions to adequately address issues of physical inactivity,poor dietary habits are highly needed to prevent those at high risk of developing type 2 diabetes mellitus.

Serological Investigation of Laboratory-Confirmed and Suspected Ebola Virus Disease Patients During the Late Phase of the Ebola Outbreak in Sierra Leone

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.

Rapid assessment of knowledge,attitudes,practices,and risk perception related to the prevention and control of Ebola virus disease in three communities of Sierra Leone

Background:The recent outbreak of the Ebola virus disease(EVD)in Sierra Leone has been characterized by the World Health Organization as one of the most challenging EVD outbreaks to date.The first confirmed case in Sierra Leone was a young woman who was admitted to a government hospital in Kenema following a miscarriage on 24 May 2014.On 5 January 2015,intensified training for an EVD response project was initiated at the medical university of Sierra Leone in Jui.To understand the knowledge,attitudes,practices,and perceived risk of EVD among the public,especially after this training,a rapid assessment was conducted from 10 to 16 March 2015.Methods:Interviews were conducted with 466 participants based on questionnaires that were distributed from 10 to 16 March 2015 by cluster sampling in three adjacent communities,namely Jui,Grafton,and Kossoh Town,in the Western Area Rural District of Sierra Leone.Results:It was found that knowledge about EVD was comprehensive and high.Positive attitude towards prevention was found to be satisfactory.Nearly all participants knew the reporting phone number 117 and had reported some change in behavior since learning about Ebola.More than half(62%)of the participants had a history of travelling to urban areas,which increases the risk of infection.The multivariable logistic regression analysis showed that community and occupation were variables associated with perceived risk of EVD.Conclusions:Our study showed that community level social mobilization and community engagement were an effective strategy in the special context.

Impact of five annual rounds of mass drug administration with ivermectin on onchocerciasis in Sierra Leone

Background:Onchocerciasis is endemic in 12 of the 14 health districts of Sierra Leone.Good treatment coverage of community-directed treatment with ivermectin was achieved between 2005 and 2009 after the 11-year civil conflict.Sentinel site surveys were conducted in 2010 to evaluate the impact of five annual rounds of ivermectin distribution.Methods:In total,39 sentinel villages from hyper-and meso-endemic areas across the 12 endemic districts were surveyed using skin snips in 2010.Results were analyzed and compared with the baseline data from the same 39 villages.Results:The average microfilaridermia(MF)prevalence across 39 sentinel villages was 53.10%at baseline.The MF prevalence was higher in older age groups,with the lowest in the age group of 1-9 years(11.00%)and the highest in the age group of 40-49 years(82.31%).Overall mean MF density among the positives was 28.87 microfilariae(mf)/snip,increasing with age with the lowest in the age group of 1-9 years and the highest in the age group of 40-49 years.Males had higher MF prevalence and density than females.In 2010 after five rounds of mass drug administration,the overall MF prevalence decreased by 60.26%from 53.10%to 21.10%;the overall mean MF density among the positives decreased by 71.29%from 28.87 mf/snip to 8.29 mf/snip;and the overall mean MF density among all persons examined decreased by 88.58%from 15.33 mf/snip to 1.75 mf/snip.Ten of 12 endemic districts had>50%reduction in MF prevalence.Eleven of 12 districts had≥50%reduction in mean MF density among the positives.Conclusions:A significant reduction of onchocerciasis MF prevalence and mean density was recorded in all 12 districts of Sierra Leone after five annual MDAs with effective treatment coverage.The results suggested that the onchocerciasis elimination programme in Sierra Leone was on course to reach the objective of eliminating onchocerciasis in the country by the year 2025.Annual MDA with ivermectin should continue in all 12 districts and further evaluations are needed across the country to assist the NTDP with programme decision making.

Soil-transmitted helminth infection in school age children in Sierra Leone after a decade of preventive chemotherapy interventions

Background:Baseline mapping of soil-transmitted helminth(STH)infections among school age children(SAC)in 2008-2009 found high or moderate prevalence in 13 of the 14 districts in Sierra Leone.Following these surveys,mass drug administration(MDA)of mebendazole/albendazole was conducted biannually at national level targeting pre-school children(PSC)aged 12-59 months and intermittently at sub-national level targeting SAC.In addition,MDA with ivermectin and albendazole for eliminating lymphatic filariasis(LF)has been conducted nationwide since 2010 targeting individuals over 5 years of age.Each MDA achieved high coverage,except in 2014 when all but one round of MDA for PSC was cancelled due to the Ebola emergency.The objective of the current study was to determine the prevalence and intensity of STH infections among SAC after a decade of these deworming campaigns.Methods:Seventy-three schools in 14 districts were purposefully selected,including 39 schools from the baseline surveys,with approximately two sites from each of low,moderate and high prevalence categories at baseline per district.Fresh stool samples were collected from 3632 children aged 9-14 years(male 51%,female 49%)and examined using the Kato Katz technique.Results:The prevalence of STH infections in Sierra Leone decreased in 2016 compared to 2008:Ascaris lumbricoides 4.4%(95%confidence interval[CI]:3.7-5.1%)versus 6.6%(95%CI:0-25%),Trichuris trichiura 0.7%(95%CI:0.5-1.1%)versus 1.8%(95%CI:0-30.2%),hookworm 14.9%(95%CI:13.8-16.1)versus 38.5%(95%CI:5.4-95.1%),and any STH 18.3%(95%CI:17.0-19.5%)versus 48.3%(CI:5.4-96.3%),respectively.In 2016,no district had high hookworm prevalence and four districts had moderate prevalence,compared with eight and four districts respectively in 2008.In 2016,the arithmetic mean hookworm egg count in all children examined was light:45.5 eggs per gram(EPG)of faeces,(95%CI:\35.96-55.07 EPG);three(0.08%)children had heavy infections and nine(0.25%)children had moderate infections.Conclusions:Sierra Leone has made considerable progress toward controlling STH as a public health problem among SAC.As LF MDA phases out(between 2017 and 2021),transition of deworming to other platforms and water and sanitation strategies need to be strengthened to maintain STH control and ultimately interrupt transmission.

Dissemination of Antibiotic Resistance Genes Among Patients with Diarrhea — Freetown, Sierra Leone, 2018

What is already known about this topic?Antibiotic resistance(AR)is a serious public health threat worldwide.However,the AR and antibiotic resistance genes(ARGs)data from West Africa,especially from Sierra Leone,are limited.What is added by this report?The study revealed ARGs’common dissemination,and multiplex antibiotic resistance genes in one sample.Genes blaNDM and blaOXA-48-like were first discovered in Sierra Leone.What are the implications for public health practice?Basic information is provided for AR research and surveillance and highlights that effective AR surveillance among diarrhea patients is necessary for Sierra Leone and West Africa.

Sustainable Laboratory Capacity Building in Sierra Leone:From Ebola to COVID-19

The onset of the Ebola outbreak in 2014 originated in Guinea and proceeded to swiftly reach Sierra Leone and Liberia(1).Unfortunately,these nations were critically deficient in their capacity for pathogenic testing and diagnostics,the availability of healthcare workers,and their supply of epidemic prevention materials,thereby impeding their ability to address the outbreak efficiently(2).This grave scenario underscored the need for support from the worldwide community.

Intra-host Ebola viral adaption during human infection

The onsite next generation sequencing(NGS)of Ebola virus(EBOV)genomes during the 2013–2016 Ebola epidemic in Western Africa provides an opportunity to trace the origin,transmission,and evolution of this virus.Herein,we have diagnosed a cohort of EBOV patients in Sierra Leone in 2015,during the late phase of the outbreak.The surviving EBOV patients had a recovery process characterized by decreasing viremia,fever,and biochemical parameters.EBOV genomes sequenced through the longitudinal blood samples of these patients showed dynamic intra-host substitutions of the virus during acute infection,including the previously described short stretches of 13 serial TNC mutations.Remarkably,within individual patients,samples collected during the early phase of infection possessed Ts at these nucleotide sites,whereas they were replaced by Cs in samples collected in the later phase,suggesting that these short stretches of TNC mutations could emerge independently.In addition,up to a total of 35 nucleotide sites spanning the EBOV genome were mutated coincidently.Our study showed the dynamic intra-host adaptation of EBOV during patient recovery and gave more insight into the complex EBOV-host interactions.

HIV prevalence in suspected Ebola cases during the 2014-2016 Ebola epidemic in Sierra Leone

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.