Molecular Evidence of Human Monkeypox Virus Infection, Sierra Leone.

Monkeypox virus is a zoonotic disease endemic to Africa. In 2017, we confirmed a case of human monkeypox virus in Sierra Leone by molecular and serologic methods. Sequencing analysis indicated the virus belongs to the West African clade and data suggest it was likely transmitted by wild animals.

Detection and Analysis of Ebola Virus in Sierra Leone-China Friendship Biosafety Laboratory from March 11 to April 20, 2015.

Ebola virus disease reemerged in Western Africa in 2014. Chinese Center for Disease Control and Prevention dispatched the first Ebola virus (EBOV) detection team to run newly established Sierra Leone-China Friendship Biological Safety Laboratory. The aims of study were to understand epidemiology, clinical manifestations and survival time of EBOV in patient's blood. A total of 913 specimens were tested between March 11 and April 20, 2015. EBOV positivity occurred in 7.37% of the blood and 0.53% in throat swabs. Most commonly reported symptoms of laboratory confirmed patients were intense fatigue, anorexia, and fever. EBOV RNAs persisted in blood for almost 4 weeks and the real-time RT-PCR Ct values showed close correlation with the sampling time after onset.

Spatial-temporal heterogeneity and determinants of HIV prevalence in the Mano River Union countries.

BACKGROUND: Utilizing population-based survey data in epidemiological research with a spatial perspective can integrate valuable context into the dynamics of HIV prevalence in West Africa. However, the situation in the Mano River Union (MRU) countries is largely unknown. This research aims to perform an ecological study to determine the HIV prevalence patterns in MRU. METHODS: We analyzed Demographic and Health Survey (DHS) and AIDS Indicator Survey (AIS) data on HIV prevalence in MRU from 2005 to 2020. We examined the country-specific, regional-specific and sex-specific ratios of respondents to profile the spatial-temporal heterogeneity of HIV prevalence and determine HIV hot spots. We employed Geodetector to measure the spatial stratified heterogeneity (SSH) of HIV prevalence for adult women and men. We assessed the comprehensive correct knowledge (CCK) about HIV/AIDS and HIV testing uptake by employing the Least Absolute Shrinkage and Selection Operator (LASSO) regression to predict which combinations of CCKs can scale up the ratio of HIV testing uptake with sex-specific needs. RESULTS: In our analysis, we leveraged data for 158,408 respondents from 11 surveys in the MRU. From 2005-2015, Cote d'Ivoire was the hot spot for HIV prevalence with a Gi_Bin score of 3, Z-Score 8.0-10.1 and P < 0.001. From 2016 to 2020, Guinea and Sierra Leone were hot spots for HIV prevalence with a Gi_Bin score of 2, Z-Score of 3.17 and P < 0.01. The SSH confirmed the significant differences in HIV prevalence at the national level strata, with a higher level for Cote d'Ivoire compared to other countries in both sexes with q-values of 0.61 and 0.40, respectively. Our LASSO model predicted different combinations of CCKs with sex-specific needs to improve HIV testing uptake. CONCLUSIONS: The spatial distribution of HIV prevalence in the MRU is skewed and the CCK about HIV/AIDS and HIV testing uptake are far below the threshold target set by UNAIDS for ending the epidemic in the sub-region. Geodetector detected statistically significant SSH within and between countries in the MRU. Our LASSO model predicted that different emphases should be implemented when popularizing the CCK about HIV/AIDS for adult women and men.

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.

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.

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 T>C 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 T>C 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.

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.

South African Ebola diagnostic response in Sierra Leone: A modular high biosafety field laboratory.

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.

[Establishment of Quality Control System of Nucleic Acid Detection for Ebola Virus in Sierra Leone-China Friendship Biological Safety Laboratory].

The quality control process throughout the Ebola virus nucleic acid detection in Sierra Leone-China Friendship Biological Safety Laboratory (SLE-CHN Biosafety Lab) was described in detail, in order to comprehensively display the scientific, rigorous, accurate and efficient practice in detection of Ebola virus of first batch detection team in SLE-CHN Biosafety Lab. Firstly, the key points of laboratory quality control system was described, including the managements and organizing, quality control documents and information management, instrument, reagents and supplies, assessment, facilities design and space allocation, laboratory maintenance and biosecurity. Secondly, the application of quality control methods in the whole process of the Ebola virus detection, including before the test, during the test and after the test, was analyzed. The excellent and professional laboratory staffs, the implementation of humanized management are the cornerstone of the success; High-level biological safety protection is the premise for effective quality control and completion of Ebola virus detection tasks. And professional logistics is prerequisite for launching the laboratory diagnosis of Ebola virus. The establishment and running of SLE-CHN Biosafety Lab has landmark significance for the friendship between Sierra Leone and China, and the lab becomes the most important base for Ebola virus laboratory testing in Sierra Leone.

Good laboratory practices guarantee biosafety in the Sierra Leone-China friendship biosafety laboratory.

BACKGROUND: The outbreak of Ebola virus disease (EVD) in West Africa between 2014 and 2015 was the largest EDV epidemic since the identification of Ebola virus (EBOV) in 1976, and the countries most strongly affected were Sierra Leone, Guinea, and Liberia. FINDINGS: The Sierra Leone-China Friendship Biological Safety Laboratory (SLE-CHN Biosafety Lab), a fixed Biosafety Level 3 laboratory in the capital city of Sierra Leone, was established by the Chinese government and has been active in EBOV detection since 11 March 2015. Complete management and program documents were created for the SLE-CHN Biosafety Lab, and it was divided into four zones (the green, yellow, brown, and red zones) based on the risk assessment. Different types of safe and appropriate personnel protection equipment (PPE) are used in different zones of the laboratory, and it fully meets the Biosafety Level 3 laboratory standards of the World Health Organization. CONCLUSION: Good preparedness, comprehensive risk assessment and operation documents, appropriate PPE, effective monitoring and intensive training, together with well-designed and reasonable laboratory sectioning are essential for guaranteeing biosafety.

Multi-Locus Sequence Typing (MLST) and Repetitive Extragenic Palindromic Polymerase Chain Reaction (REP-PCR), characterization of shigella spp. over two decades in Tianjin China.

To understand the change of the dominant serogroup of Shigella spp., their antimicrobial resistance over more than two decades in Tianjin, their phylogenetic similarity and to determine their evolutionary biology by using REP-PCR and MLST in order to study their epidemiological character. Multi-locus Sequence Typing was performed to determine their lineage and phylogenetic similarity. REP-PCR typing was used to study the homology of their genomic DNA. The isolated rate of group D Shigella in 2009 and 2010 had obviously increased. Antimicrobial susceptibility test results showed that the resistant rates of the 1981-1983 Shigella flexneri to tetracycline, streptomycin and chloramphenicol varied from 76.47 to 100%, they were all sensitive to other antibiotics. During 2009-2010, the resistance rates of the isolated Shigella flexneri to gentamicin, amikacin, third and fourth Generation Cephalosporins and quinolones had increased. MLST results produced five sequence types and two sequence type complexes. REP-PCR showed DNA band similarities between the 1981-1983 and 2009-2010 strains. The dominant serogroup of Shigella in Tianjin has changed from Shigella flexneri to Shigella sonnei. Increased drug resistance of Shigella flexneri is higher than Shigella sonnei because a great variety of antibiotics has been used. The MLST results showed that the 1981-1983 strains had the same sequence type with some of the 2009-2010 strains. Combination of MLST and REP-PCR produced better discriminatory power than using either method alone.