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Item Whole-genome sequencing and phylogenetic analysis of the first and second confirmed cases of human infection with Monkeypox virus from Sierra Leone(Elsevier BV, 2025-08-12) Yu, ShuoWhole-genome sequencing and phylogenetic analysis of the first and second confirmed cases of human infection with Monkeypox virus from Sierra LeoneTo the Editor, We read with great interest the letter by Yadav and colleagues, which detailed the need to focus on understanding the evolutionary trajectory of monkeypox virus. 1 The monkeypox virus (MPXV) is genetically classified into four primary clades (Ia, Ib, IIa, IIb).Notably, the newly identified clade Ib has emerged as the dominant strain in the current Public Health Emergency of International Concern (PHEIC), exemplified by the ongoing outbreak in the Democratic Republic of the Congo. 2 Concurrently, global transmission of clade IIb MPXV persists, underscoring that the ongoing epidemic warrants serious attention.On January 10-11, 2025, Sierra Leone released the case reports of its first two human infections with monkeypox virus during the PHEIC, becoming the final member of the Mano River Alliance to document such cases.Here, we present the two case studies with viral sequencing insights, shedding light on MPXV evolution in West Africa.Case 1 was a male in his twenties working as a car dealer who presented to the hospital in early January.He had traveled to Lungi (Port Loko District) from 26 December 2024 to 5 January 2025 (Fig. 1A).Symptom onset occurred on 6 January.Case 2, a male staff at a restaurant over 20 years old, developed symptoms on 6 January and sought hospital care in January.Both of the vesicle samples were confirmed MPXV-positive by real-time PCR using Monkeypox Virus Nucleic Acid Detection Kit at the Molecular Laboratory of 34th Military Hospital in Sierra Leone on January 10 and 11, respectively (Fig. 1A; Fig. S1 in the Appendix).Mean cycle threshold values were 20.29 for Case 1 and 15.14 for Case 2. The patients were admitted to the infectious disease isolation unit and were managed appropriately.Pre-rash symptoms included fever and headache, with rash involvement of the face, palms, and other cutaneous sites (Fig. S2 in the Appendix).Case 2 additionally presented with genital rashes with dysuria.Both patients denied animal/known case exposure, blood transfusions, travel (except for Case 1's documented trip, Journal of Infection 91 (2025) 106587Item Whole-genome sequencing of Lassa virus from dry blood spots: a comparative evaluation(BioMed Central, 2025-10-13) Bangura, UmaruBACKGROUND: Whole blood samples are often used to generate whole genome sequences, which provide valuable insights into the genetic make-up of viruses. However, the collection and management present significant challenges, particularly in remote and resource-limited communities, where maintaining a cold chain is often difficult and costly. The use of dry blood spots (DBS) is gradually increasing to overcome these logistical barriers with reduced biosafety constraints. We propose an alternative approach using native DBS Lassa virus (LASV)-positive samples as a substitute for whole blood. FINDINGS: Next-generation sequencing (NGS) was performed on RNA extracted from whole blood and DBS samples using Illumina technology. RNA concentration, cycle threshold (Ct) values and sequence read counts were statistically compared. A total of 78 samples from 39 LASV-positive Mastomys atalensis were analysed. Whole blood had significantly higher mean RNA concentration (26.5 ± 1.9) than DBS (3.4 ± 0.3), P < 0.05. Mean Ct values in whole blood were significantly lower than in DBS (P = 0.0001). Log mean sequence reads and NGS coverage for both S and L segments were significantly higher in whole blood (P = 0.0001). RNA concentration showed no association with sequence coverage (P = 0.382), while Ct values showed a strong association (P = 0.0001). CONCLUSIONS: Our study demonstrates that DBS is a viable alternative for whole genome sequencing of LASV, although whole blood samples consistently outperform DBS in terms of RNA concentration, Ct values and NGS coverage.Item Upscaling MPhil and PhD Completion Rates: Approaches That Work for Universities(RELX Group (Netherlands), 2025) Dumbuya, EmmanuelItem The enduring story of Lassa fever: Advancing the case for sustainable management strategies(Elsevier BV, 2025-07-03) Awoniyi, Adedayo MichaelLassa fever (LF) is an acute viral hemorrhagic illness caused by the Lassa virus (LASV), an enveloped, spherical virus belonging to the Arenaviridae family. LASV possess a single-stranded RNA genome of negative polarity and exhibits high genetic diversity, corresponding to the geographical distribution of its seven principal distinct clades across West Africa\[1\]. LASV was first isolated in 1969 from an American missionary nurse stationed in the rural town of Lassa, Borno State, Nigeria, following her return from a brief vacation in the United States\[2\]. Although she had travelled through Sierra Leone and made a stop in Jos, Nigeria, before arriving at her station, the virus was contentiously named after Lassa town. LF is endemic in several West African countries, particularly within the Mano River Union countries (Guinea, Liberia and Sierra Leone) and Nigeria, where annual outbreaks are consistently reported. Additionally, cases of LF or the detection of the virus have been reported in other West African countries, including Benin, Côte d’Ivoire, Mali and Togo. Sporadic exported cases have also been reported in Asia, Europe and North America, highlighting LF’s potential as a global health threat if not adequately addressed\[3\]. LASV is primarily hosted by the multimammate rat Mastomys natalensis, which typically remains asymptomatic and can harbor the virus throughout its lifespan. Infected rats shed LASV through their urine, faeces\[4\], saliva, and respiratory secretions, contaminating household surfaces, foodstuffs and other environmental materials. Human infection occurs predominantly through direct contact with infected rats or indirectly via exposure to contaminated items, especially the consumption of contaminated foodstuffs, and rarely through human-to-human transmission via contact with bodily fluids of an infected person or contaminated medical equipment\[3\]. LF presents with a wide clinical symptoms, ranging from asymptomatic to mild or severe illness and in severe cases, LF can lead to life-threatening complications including hemorrhage, respiratory distress, neurological disorder and multiple organ failure, particularly when diagnosis and treatment are delayed\[5\]. LF affects an estimated 897700 people annually, with 18000 deaths in the West Africa region\[6\]. The true burden of LF is likely underestimated due to several factors: early symptoms often mimic those of other common febrile illnesses, diagnostic capacity in many endemic areas is limited, and underreporting is exacerbated by social isolation “stigma” stemming from LF’s association with rats–disease of poverty, and certain cultural/religious beliefs seldom discourage victims from seeking medical care. Fatal outcomes are particularly high among pregnant women, where LF can lead to spontaneous abortion and elevated maternal mortality\[7\]. Survivors may suffer from long-term complications, such as sensorineural hearing loss, neurological impairments and other chronic health conditions, all of which can significantly diminish quality of life and increase economic burden on individuals, families and the government\[5,7\]. At a broader level, LF imposes a substantial socio-economic burden on affected countries through both direct costs such as medical treatment and indirect costs, including lost productivity due to the illness, long-term disability, and premature death. These impacts are especially devastating for families where the affected individual is the primary breadwinner, often leaving dependents in poverty or financial instability. Given the substantial socioeconomic burden posed by LF and other zoonoses, exacerbated by recent global experiences such as the COVID-19 pandemics, there is growing interest in strengthening the management of zoonotic threats. While advancements in vaccine development and public health interventions have led to notable reductions in the morbidity and mortality of many infectious diseases, similar progress has been limited for rodent-borne diseases like LF. To date, there is no World Health Organization (WHO)-licensed vaccine against LASV\[8\]. This general bottleneck in LF management could be in part due to LASV’s extensive genetic diversity, complex transmission dynamics shaped by environmental and socioeconomic conditions, and the persistent difficulty of controlling the rat reservoir responsible for maintaining viral circulation in endemic regions. As efforts towards vaccine development continue, it is important to implement integrated preventive strategies, such as improved housing and sanitation, public education to minimize human exposure to rats, to reduce human risk of LF and other rodent-borne diseases. In contrast to many high-income countries, many nations in the Global South, particularly in LF-endemic regions lack national or regional specific policies dedicated to rodent surveillance and population management, despite prominent rodent public health- and economic-related problems in the regions. Funding and institutional support for rodent- and rodent-borne disease research remain minimal if not non-existent, especially when compared to vector-borne diseases such as malaria. Additionally, there is marked shortage of trained rodent control specialists within endemic regions. Consequently, vulnerable communities are often left without effective or sustainable mitigation strategies. In many cases, local populations resort to the indiscriminate use of rodenticides, which are not only ineffective in the long-term but also pose significant risks to non-target species, including humans, due to accidental poisoning. The continued escalation of factors driving rat proliferation, such as climate change, rapid urbanization, overcrowding, increasing slum inhabitants, inadequate personal hygiene, precarious sanitation infrastructure, poor waste management and deepening poverty, pose a growing threat, particularly in LF endemic regions. These deteriorating conditions, common in both rural and urban communities across West Africa, could increase the frequency and intensity of human-rat interactions. Given the well-documented association between rat abundance and rodent-borne disease transmission risk, public health experts are sounding alarm over the heightened potential for future zoonotic outbreaks. It is no gainsaying to warn that LF-endemic regions are metaphorically “sitting on a powder keg” poised for emergence of potentially new zoonotic threats unless substantial interventions are prioritized. Such event could have devastating socioeconomic consequences, especially in communities of West Africa that are already grappling with persistent LF outbreaks and the recently declared viral mpox outbreak\[9\]. In conclusion, the complex transmission dynamics of LF, compounded by diagnostic challenges, limited treatment options and the lack of WHO-licensed vaccine, underscore the need for a comprehensive and multisectoral response. With case number rising steadily over the past decade, effective mitigation must extend beyond clinical management to address the socio-environmental determinants of transmission. Specifically, governments/policymakers should implement (a) sustained health education campaigns to raise community awareness about LF risk factors, transmission pathways and preventive practices; (b) coordinated investment in integrated research and action involving key stakeholders, including local community, academia, healthcare providers, ministries of health, agriculture, information and education, waste management authorities and the currently non-existent national rodent and vector control agencies. Such collaboration should aim to develop locally tailored protocols for rodent surveillance and population management to reduce human-rodent interactions and subsequent spillover of pathogens into human population; (c) enhanced case surveillance, early detection and rapid response mechanisms to limit potential outbreaks; (d) national policies to promote improved personal and community hygiene and sanitation practices to minimize LASV contamination; (e) stigma reduction strategies, including anti-discrimination policies and post-recovery reintegration programs to encourage timely health-seeking behavior and community support for survivors; (f) policies to discourage the consumption of bushmeat, particularly rodents, and encourage safer agricultural practices–such as storing harvested crops in rodent-proof containers; and (g) investment in the laboratory infrastructure and workforce (re)training to strengthen prompt confirmation and treatment. Collectively, these interventions will not only curb LF incidence but also reduce the risk of other zoonotic disease spillovers, thereby enhancing the overall resilience and wellbeing of the vulnerable populations, especially in endemic regions. Conflict of interest statement No conflict of interest was declared by the authors. Funding The study received no specific funding for the study. Authors’ contributions AMA conceived and designed the study and wrote the first draft of the paper. Both AMA and UB contributed to literature search, critically revised and improved the presentation of the paper and approved the final manuscript. Publisher’s note The Publisher of the Journal remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Edited by Zhang Q, Lei Y, Pan YItem Surgical Volume in Sierra Leone: A Comparison Between Population and Facility‐Based Data Collection(Springer Science+Business Media, 2025-08-15) Martens, Janine P. J.INTRODUCTION: Surgical volume obtained from health facility records is one of the six indicators proposed by the Lancet Commission on Global Surgery. An alternative approach to assess surgical volume is from household surveys, which might be more suitable for low-income settings. The aim of this study was to describe the annual surgical volume in Sierra Leone through a population-based approach and compare this with health facility data. METHODS: This study is part of the PRESSCO 2020 (PREvalence Study on Surgical COnditions) study, a cross-sectional countrywide descriptive study based on a randomly selected national representative sample. Data on surgeries performed annually, including type and location, were collected through interviews and compared with facility-based data. RESULTS: In total, 10,001 household members were included from 1854 households, who reported 152 major surgical procedures the year preceding the interview. Amounting an annual nation-wide surgical volume of 1520 (95% CI 1300-1780) per 100,000 population. The most common procedures were hernia repairs (30.9%), caesarean sections (23.7%), and appendicectomies (13.8%). The population-based data collection identified 4.1 times more procedures compared with 372 procedures in facility-based study from the same year. CONCLUSION: The substantial difference between population- and facility-based data reveals a likely underreporting in facilities and possible overreporting in the household survey. Interpretation of facility-based surgical volume data should be carried out with caution and rigorous description of methodology is essential for proper interpretation. Independent of the method of data collection, the surgical volume in Sierra Leone is far below the recommended global benchmark. TRIAL REGISTRATION: ISRCTN registry under no 12353489.Item Strengthening health system resilience during COVID-19: a qualitative study of national-level decision-makers in Guinea and Sierra Leone(BMJ, 2025-12-01) Fischer, Hanna-TinaINTRODUCTION: 4 years after the Ebola outbreak, the arrival of COVID-19 presented West Africa with a new shock. Despite widespread disruptions, malaria service continuity remained a priority in both countries. In Sierra Leone, the proportion of pregnant women receiving at least three doses of intermittent preventive treatment increased from 36% in 2018 to 50% in 2021. Similarly, insecticide-treated net ownership in Guinea rose from 44% to 63%, reflecting the ability of national programmes to sustain essential interventions despite pandemic-related constraints. Against this backdrop, this study investigates the strategies used to strengthen health system resilience in Guinea and Sierra Leone during the pandemic. Specifically, it explores how both countries responded to the pandemic's demands and mitigated potential negative effects on health service delivery, using malaria as an example of routine care. METHODS: We conducted a document review and interviewed 36 key informants (16 in Guinea and 20 in Sierra Leone) leading malaria elimination efforts and the national COVID-19 response. The review included malaria surveillance data and health performance reports to contextualise our qualitative findings. Interviews identified strategic responses by decision-makers overseeing malaria and COVID-19 efforts. This qualitative approach offers an in-depth understanding of decision-making within broader health systems. RESULTS: Three major themes were shared between countries: (1) 'Responding quickly and decisively to COVID-19', (2) 'Ensuring continuity of essential services during the pandemic' and (3) 'Improving health system responsiveness, despite contextual challenges'. The document review confirmed sustained malaria service delivery, with minimal declines in outpatient consultations compared to Ebola. CONCLUSIONS: Strategies used in both countries enabled the health systems to absorb the acute shock of COVID-19, adapt to the challenges and transform aspects to improve responsiveness. Institutionalising these policies and fostering agility could enhance pandemic preparedness and contribute to stronger health systems in these and other low-income countries in the region.Item Public Data for: Computer Assisted Verbal Autopsy: Comparing Large Language Models to Physicians for Assigning Causes to 6939 Deaths in Sierra Leone from 2019-2022(Harvard University, 2025-12-07) Wen, RichardPublic data on 6939 deaths in Sierra Leone from 2019-2022 acquired through verbal autopsy. The data was collected for a study comparing GPT and OpenVA models to physician coding of deaths.Item Physical and insecticidal durability of PermaNet® 3.0 and Olyset® plus piperonyl butoxide-synergist insecticide-treated nets in Sierra Leone: results of durability monitoring from 2020 to 2023(BioMed Central, 2025-07-13) Sudoi, Raymond KipropThe performance of two piperonyl butoxide (PBO-synergist) insecticide-treated net (ITN) brands, PermaNet ® 3.0 and Olyset ® Plus, were evaluated under field conditions in two neighboring districts in Sierra Leone over 36 months to estimate median ITN survival, understand insecticidal efficacy, and identify factors influencing ITN durability. This assessment can help guide future PBO-synergist ITN procurement and replacement strategies. This prospective study tracked 370 households and 652 campaign-distributed ITNs from 2020, followed annually for 36 months. Districts were purposefully selected based on shared characteristics. Household surveys were conducted, and 30 ITNs per round were tested for bioefficacy and chemical residue. Key indicators included ITN survival, 24-h mosquito mortality, and chemical content reduction compared to manufacturer targets doses. Cox proportional hazard models identified factors influencing ITN survival. Median useful life was 3.0 (95% CI 2.7–3.5) years for PermaNet ® 3.0 ITNs in Bo and 2.2 (95% CI 2.0–2.4) years for Olyset ® Plus ITNs in Moyamba. PermaNet ® 3.0 ITNs displayed 13% 24-h mortality against pyrethroid-resistant mosquitoes on roof panels, with a 46% reduction in PBO content 34 months post-distribution. Olyset ® Plus ITNs had 3% f24-hour mortality against pyrethroid-resistant mosquitoes, with a 77% reduction in PBO content. Several factors were associated with improved ITN survival, including cohort ITNs from Bo (adjusted hazard ratio \[aHR\] = 0.33, p < 0.001), households without children under five (CU5) (aHR = 0.64, p = 0.003), highest socio-economic status tertile (aHR = 0.63, p = 0.016), exposure to social and behaviour change (SBC) messages combined with positive net attitudes (aHR = 0.63, p = 0.008), lack of food storage in sleeping spaces (aHR = 0.56, p = 0.006), exclusive adult use of ITNs (aHR = 0.72, p = 0.048), net folding when not in use (aHR = 0.67, p = 0.015), and drying nets outside (aHR = 0.44, p = 0.008). ITNs in Bo outperformed those in Moyamba in both physical and insecticidal performance. However, ITN survival is highly context specific, and further investigation into field performance of new ITN types is necessary across diverse epidemiological settings.Item Pandemic preparedness: what difference does experience make?(Cambridge University Press, 2025-04-11) Nyakoi, MarionThis ethnographic study, conducted as part of the Pandemic Preparedness Project, explores the pandemic preparedness of communities in NG and its satellite settlements within Kailahun District, Eastern Province, Sierra Leone. The research site was particularly significant due to its history as one of the hardest-hit areas during the 2014-16 Ebola outbreak. NG is served by a Peripheral Health Unit (PHU) that provides health services to seven villages, as well as one distant village far from its designated facility. The study employed long-term observational research methods, where the researcher lived within the community, becoming an integrated observer familiar with local customs and daily life. This ethnographic approach aimed to understand the health-seeking behaviors of residents following the Ebola crisis. The onset of the Covid-19 pandemic during the study period shifted the focus to examine how the community understood and responded to a new pandemic threat. Additionally, the study reflects on the challenges faced by female social scientists in Sierra Leone, where few are trained in ethnographic methods. This article offers insights into the process of conducting ethnographic research in a challenging context, providing valuable guidance for other female researchers seeking to engage in similar bio-social studies.Item Non-exanthematous mpox infections in Nigeria: a possible explanation of the sporadic outbreaks in city centers?(African Field Epidemiology Network, 2025) Cadmus, Simeon**Introduction:** non-exanthematous presentations in mpox infection are increasingly reported, posing a risk of underestimating the true burden of the disease. In Nigeria, border towns play a unique role in shaping the dynamics of mpox transmission, yet they have received relatively little research attention. This study aims to address this gap by investigating the prevalence of mpox infection in a potential hotspot region of Nigeria. **Methods:** a cross-sectional study was conducted during a free medical outreach in Iboko, Izzi Local Government Area, Ebonyi State, Nigeria, from April 15 to May 20, 2024. Participants were educated on the study objectives and provided informed consent for clinical evaluation and sample collection. Blood samples from 75 participants were tested for the mpox virus using quantitative PCR. Socio-demographic data and clinical presentations were also recorded. **Results:** the mean age of participants was 51.3 ± 18.0 years, and 73.3% were female. Most participants (78.7%) were farmers, and 52.0% had no formal education. Headache (69.3%) and body pain (37.3%) were the most common clinical symptoms, with only 3.6% presenting with fever. Mpox virus DNA was detected in two participants (2.67%) designated K3 and K4. Both cases lacked exanthematous lesions but reported headache and body pain. **Conclusion:** this study identified the presence of non-exanthematous mpox infections in Nigeria, emphasizing the need to recognize and address "subclinical" spreaders to mitigate sporadic outbreaks of mpox infection. In addition, the findings highlight the importance of integrating targeted awareness campaigns to enhance surveillance and improve case detection of asymptomatic mpox in Nigeria.