Trend of Lassa fever cases and factors associated with mortality in Liberia, 2016 - 2021: a secondary data analysis.

Introduction: Lassa fever (LF) is endemic in Liberia and is immediately reportable. Suspected cases are confirmed at the National Public Health Reference Laboratory. However, there is limited information on the trend and factors associated with mortality. We described the epidemiological characteristics of LF cases and determined factors associated with mortality in Liberia from 2016 to 2021. Methods: we reviewed 867 case-based LF surveillance data from 2016 to 2021 obtained from the National Public Health Institute of Liberia (NPHIL). The cases that met the suspected LF case definition were tested with RT-PCR. Using Epi Info 7.2.5.0. We conducted univariate, bivariate, and multivariate and analysis. We calculated frequencies, proportions. Positivity rate, case fatality rate, and factors associated with LF mortality using chi-square statistics and logistics regression at 5% level of significance. Results: eighty-five percent (737/867) of the suspected cases were tested and 26.0% (192/737) were confirmed LF positive. The median age of confirmed LF cases was 21(IQR: 12-34) years. Age 10-19 years accounted for 24.5% (47/192) and females 54.2% (104/192). Bong 33.9% (65/192), Grand Bassa 31.8% (61/192), and Nimba counties, 21.9% (42/192) accounted for most of the cases. The median duration from symptom onset to hospital admission was 6 (IQR: 3-9) days. A majority, 66% (126/192) of the cases were reported during the dry season (October-March) and annual incidence was highest at 12 cases per 1,000,000 population in 2019 and 2020. The overall case fatality rate was 44.8%. Non-endemic counties, Margibi, 77.8% and Montserrado, 66.7% accounted for the highest case fatality rate (CFR), while 2018, 66.7% and 2021, 60.0% recorded the highest CFR during the period. Age ≥30 years (aOR=2.1,95% CI: 1.08-4.11, p=0.027) and residing in Grand Bassa County (aOR=0.3, 95% CI: 0.13-0.73, p=0.007) were associated with LF mortality. Conclusion: Lassa fever was endemic in three of the fifteen counties of Liberia, case fatality rate remained generally high and widely varied. The high fatality of LF has been reported to the NPHIL and is currently being further investigated. There is a need to continuously train healthcare workers, especially in non-endemic counties to improve the LF treatment outcome.

Reservoir displacement by an invasive rodent reduces Lassa virus zoonotic spillover risk.

The black rat (Rattus rattus) is a globally invasive species that has been widely introduced across Africa. Within its invasive range in West Africa, R. rattus may compete with the native rodent Mastomys natalensis, the primary reservoir host of Lassa virus, a zoonotic pathogen that kills thousands annually. Here, we use rodent trapping data from Sierra Leone and Guinea to show that R. rattus presence reduces M. natalensis density within the human dwellings where Lassa virus exposure is most likely to occur. Further, we integrate infection data from M. natalensis to demonstrate that Lassa virus zoonotic spillover risk is lower at sites with R. rattus. While non-native species can have numerous negative effects on ecosystems, our results suggest that R. rattus invasion has the indirect benefit of decreasing zoonotic spillover of an endemic pathogen, with important implications for invasive species control across West Africa.

Rodent control strategies and Lassa virus: some unexpected effects in Guinea, West Africa.

The Natal multimammate mouse (Mastomys natalensis) is the host of Lassa mammarenavirus, causing Lassa haemorrhagic fever in West Africa. As there is currently no operational vaccine and therapeutic drugs are limited, we explored rodent control as an alternative to prevent Lassa virus spillover in Upper Guinea, where the disease is highly endemic in rural areas. In a seven-year experiment, we distributed rodenticides for 10-30 days once a year and, in the last year, added intensive snap trapping for three months in all the houses of one village. We also captured rodents both before and after the intervention period to assess their effectiveness by examining alterations in trapping success and infection rates (Lassa virus RNA and IgG antibodies). We found that both interventions reduced the rodent population by 74-92% but swiftly rebounded to pre-treatment levels, even already six months after the last snap-trapping control. Furthermore, while we observed that chemical control modestly decreased Lassa virus infection rates annually (a reduction of 5% in seroprevalence per year), the intensive trapping unexpectedly led to a significantly higher infection rate (from a seroprevalence of 28% before to 67% after snap trapping control). After seven years, we conclude that annual chemical control, alone or with intensive trapping, is ineffective and sometimes counterproductive in preventing Lassa virus spillover in rural villages. These unexpected findings may result from density-dependent breeding compensation following culling and the survival of a small percentage of chronically infected rodents that may spread the virus to a new susceptible generation of mice.

Spatio-temporal spread and evolution of Lassa virus in West Africa.

BACKGROUND: Lassa fever is a hemorrhagic disease caused by Lassa virus (LASV), which has been classified by the World Health Organization as one of the top infectious diseases requiring prioritized research. Previous studies have provided insights into the classification and geographic characteristics of LASV lineages. However, the factor of the distribution and evolution characteristics and phylodynamics of the virus was still limited. METHODS: To enhance comprehensive understanding of LASV, we employed phylogenetic analysis, reassortment and recombination detection, and variation evaluation utilizing publicly available viral genome sequences. RESULTS: The results showed the estimated the root of time of the most recent common ancestor (TMRCA) for large (L) segment was approximately 634 (95% HPD: [385879]), whereas the TMRCA for small (S) segment was around 1224 (95% HPD: [10301401]). LASV primarily spread from east to west in West Africa through two routes, and in route 2, the virus independently spread to surrounding countries through Liberia, resulting in a wider spread of LASV. From 1969 to 2018, the effective population size experienced two significant increased, indicating the enhanced genetic diversity of LASV. We also found the evolution rate of L segment was faster than S segment, further results showed zinc-binding protein had the fastest evolution rate. Reassortment events were detected in multiple lineages including sub-lineage IIg, while recombination events were observed within lineage V. Significant amino acid changes in the glycoprotein precursor of LASV were identified, demonstrating sequence diversity among lineages in LASV. CONCLUSION: This study comprehensively elucidated the transmission and evolution of LASV in West Africa, providing detailed insights into reassortment events, recombination events, and amino acid variations.

The Importance of Lassa Fever and Its Disease Management in West Africa.

Lassa virus (LASV) is a zoonotic pathogen endemic throughout western Africa and is responsible for a human disease known as Lassa fever (LF). Historically, LASV has been emphasized as one of the greatest public health threats in West Africa, with up to 300,000 cases and 5000 associated deaths per year. This, and the fact that the disease has been reported in travelers, has driven a rapid production of various vaccine candidates. Several of these vaccines are currently in clinical development, despite limitations in understanding the immune response to infection. Alarmingly, the host immune response has been implicated in the induction of sensorineural hearing loss in LF survivors, legitimately raising safety questions about any future vaccines as well as efficacy in preventing potential hearing loss. The objective of this article is to revisit the importance and prevalence of LF in West Africa, with focus on Nigeria, and discuss current therapeutic approaches and ongoing vaccine development. In addition, we aim to emphasize the need for more scientific studies relating to LF-associated hearing loss, and to promote critical discussion about potential risks and benefits of vaccinating the population in endemic regions of West Africa.

Lassa fever vaccine use cases and demand: Perspectives from select West African experts.

Lassa fever (LF) is a zoonotic viral hemorrhagic disease endemic to several West African countries. Approximately 300-500,000 cases occur annually across all ages with 10-20% case fatality rates. A LF vaccine is a recognized public health priority, with several candidates entering clinical trials. However, the perspectives of regional experts regarding critical vaccine properties, ideal delivery methods, and priority target populations remain unclear. Using a mixed methods approach with a standardized questionnaire, we individually interviewed 8 West African stakeholders, each with extensive knowledge and experience of LF. They strongly favored the use of a mass, proactive campaign strategy to immunize a wide age range of people in high-risk areas, including pregnant women and health care workers. We estimated that these and other plausible delivery scenarios could result in an initial demand of anywhere from 1 to 100 million doses, with most demand coming from Nigeria. These findings may help inform LF vaccine development and deployment efforts.

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

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

A spiking fever.

Long neglected, Lassa fever is surging in West Africa. Researchers want to know why.

Lassa virus in novel hosts: insights into the epidemiology of lassa virus infections in southern Nigeria.

Identification of the diverse animal hosts responsible for spill-over events from animals to humans is crucial for comprehending the transmission patterns of emerging infectious diseases, which pose significant public health risks. To better characterize potential animal hosts of Lassa virus (LASV), we assessed domestic and non-domestic animals from 2021-2022 in four locations in southern Nigeria with reported cases of Lassa fever (LF). Birds, lizards, and domestic mammals (dogs, pigs, cattle and goats) were screened using RT-qPCR, and whole genome sequencing was performed for lineage identification on selected LASV positive samples. Animals were also screened for exposure to LASV by enzyme-linked immunosorbent assay (ELISA). Among these animals, lizards had the highest positivity rate by PCR. Genomic sequencing of samples in most infected animals showed sub-lineage 2 g of LASV. Seropositivity was highest among cattle and lowest in pigs. Though the specific impact these additional hosts may have in the broader virus-host context are still unknown - specifically relating to pathogen diversity, evolution, and transmission - the detection of LASV in non-rodent hosts living in proximity to confirmed human LF cases suggests their involvement during transmission as potential reservoirs. Additional epidemiological data comparing viral genomes from humans and animals, as well as those circulating within the environment will be critical in understanding LASV transmission dynamics and will ultimately guide the development of countermeasures for this zoonotic health threat.

Spatio-temporal spread of Lassa virus and a new rodent host in the Mano River Union area, West Africa.

The spread of Lassa virus (LASV) in Guinea, Liberia and Sierra Leone, which together are named the Mano River Union (MRU) area, was examined phylogeographically. To provide a reliable evolutionary scenario, new rodent-derived, whole LASV sequences were included. These were generated by metatranscriptomic next-generation sequencing from rodents sampled between 2003 and 2020 in 21 localities of Guinea and Sierra Leone. An analysis was performed using BEAST to perform continuous phylogeographic inference and EvoLaps v36 to visualize spatio-temporal spread. LASV was identified as expected in its primary host reservoir, the Natal multimammate mouse (Mastomys natalensis), and also in two Guinean multimammate mice (Mastomys erythroleucus) in northern Sierra Leone and two rusty-bellied brush-furred mice (Lophuromys sikapusi) in southern Sierra Leone. This finding is consistent with the latter two species being secondary host reservoirs. The strains in these three species were very closely related in LASV lineage IV. Phylogenetic analysis indicated that the most recent common ancestor of lineage IV existed 316-374 years ago and revealed distinct, well-supported clades from Sierra Leone (Bo, Kabala and Kenema), Guinea (Faranah, Kissidougou-Guekedou and Macenta) and Liberia (Phebe-Ganta). The phylogeographic scenario suggests southern Guinea as the point of origin of LASV in the MRU area, with subsequent spread to towards Mali, Liberia and Sierra Leone at a mean speed of 1.6 to 1.1 km/year.

Modelling seasonality of Lassa fever incidences and vector dynamics in Nigeria.

Lassa fever (Lf) is a viral haemorrhagic disease endemic to West Africa and is caused by the Lassa mammarenavirus. The rodent Mastomys natalensis serves as the primary reservoir and its ecology and behaviour have been linked to the distinct spatial and temporal patterns in the incidence of Lf. Nigeria has experienced an unprecedented epidemic that lasted from January until April of 2018, which has been followed by subsequent epidemics of Lf in the same period every year since. While previous research has modelled the case seasonality within Nigeria, this did not capture the seasonal variation in the reproduction of the zoonotic reservoir and its effect on case numbers. To this end, we introduce an approximate Bayesian computation scheme to fit our model to the case data from 2018-2020 supplied by the NCDC. In this study we used a periodically forced seasonal nonautonomous system of ordinary differential equations as a vector model to demonstrate that the population dynamics of the rodent reservoir may be responsible for the spikes in the number of observed cases in humans. The results show that in December through to March, spillover from the zoonotic reservoir drastically increases and spreads the virus to the people of Nigeria. Therefore to effectively combat Lf, attention and efforts should be concentrated during this period.

Ecological correlates and predictors of Lassa fever incidence in Ondo State, Nigeria 2017-2021: an emerging urban trend.

Lassa fever (LF) is prevalent in many West African countries, including Nigeria. Efforts to combat LF have primarily focused on rural areas where interactions between rodents and humans are common. However, recent studies indicate a shift in its occurrence from rural to urban areas. We analysed secondary data of reported LF outbreaks from 2017 to 2021 in Ondo State, Nigeria to identify the distribution pattern, ecological variations, and other determinants of disease spread from the ward level using nearest neighbour statistics and regression analysis. Data utilised include LF incidence, ecological variables involving population, nighttime light intensity, vegetation, temperature, market presence, road length, and building area coverage. ArcGIS Pro 3.0 software was employed for spatial analysis. Results revealed spatio-temporal clustering of LF incidents between 2017 and 2021, with an increasing trend followed by a decline in 2021. All wards in Owo Local Government Area were identified as LF hotspots. The ecological variables exhibited significant correlations with the number of LF cases in the wards, except for maximum temperature. Notably, these variables varied significantly between wards with confirmed LF and those without. Therefore, it is important to prioritise strategies for mitigating LF outbreaks in urban areas of Nigeria and other LF-endemic countries.

Environmental Persistence and Disinfection of Lassa Virus.

Lassa fever, caused by Lassa virus (LASV), is endemic to West Africa, where ≈300,000 illnesses and ≈5,000 deaths occur annually. LASV is primarily spread by infected multimammate rats via urine and fomites, highlighting the need to understand the environmental fate of LASV. We evaluated persistence of LASV Josiah and Sauerwald strains on surfaces, in aqueous solutions, and with sodium hypochlorite disinfection. Tested strains were more stable in deionized water (first-order rate constant [k] for Josiah, 0.23 days; for Sauerwald, k = 0.34 days) than primary influent wastewater (Josiah, k = 1.3 days; Sauerwald, k = 1.9 days). Both strains had similar decay rates on high-density polyethylene (Josiah, k = 4.3 days; Sauerwald, k = 2.3 days) and stainless steel (Josiah, k = 5.3 days; Sauerwald, k = 2.7 days). Sodium hypochlorite was highly effective at inactivating both strains. Our findings can inform future risk assessment and management efforts for Lassa fever.

Predicting the fine-scale spatial distribution of zoonotic reservoirs using computer vision.

Zoonotic diseases threaten human health worldwide and are often associated with anthropogenic disturbance. Predicting how disturbance influences spillover risk is critical for effective disease intervention but difficult to achieve at fine spatial scales. Here, we develop a method that learns the spatial distribution of a reservoir species from aerial imagery. Our approach uses neural networks to extract features of known or hypothesized importance from images. The spatial distribution of these features is then summarized and linked to spatially explicit reservoir presence/absence data using boosted regression trees. We demonstrate the utility of our method by applying it to the reservoir of Lassa virus, Mastomys natalensis, within the West African nations of Sierra Leone and Guinea. We show that, when trained using reservoir trapping data and publicly available aerial imagery, our framework learns relationships between environmental features and reservoir occurrence and accurately ranks areas according to the likelihood of reservoir presence.

Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria.

Effective infectious disease surveillance in high-risk regions is critical for clinical care and pandemic preemption; however, few clinical diagnostics are available for the wide range of potential human pathogens. Here, we conduct unbiased metagenomic sequencing of 593 samples from febrile Nigerian patients collected in three settings: i) population-level surveillance of individuals presenting with symptoms consistent with Lassa Fever (LF); ii) real-time investigations of outbreaks with suspected infectious etiologies; and iii) undiagnosed clinically challenging cases. We identify 13 distinct viruses, including the second and third documented cases of human blood-associated dicistrovirus, and a highly divergent, unclassified dicistrovirus that we name human blood-associated dicistrovirus 2. We show that pegivirus C is a common co-infection in individuals with LF and is associated with lower Lassa viral loads and favorable outcomes. We help uncover the causes of three outbreaks as yellow fever virus, monkeypox virus, and a noninfectious cause, the latter ultimately determined to be pesticide poisoning. We demonstrate that a local, Nigerian-driven metagenomics response to complex public health scenarios generates accurate, real-time differential diagnoses, yielding insights that inform policy.

Inter-State Transmission of Lassa Fever during the 2015-2016 Lassa Outbreak in Nigeria: An Implication for Infection Prevention and Control Practices.

BACKGROUND: Lassa fever is an acute hemorrhagic viral disease caused by the Lassa virus. The Lassa virus belongs to the Arenaviridae family of RNA viruses. On 05/04/2016; two cases of Lassa fever were reported from Katsina State with the date of presentation of the first case on 23/03/2016 and 27/03/ 2016 for the second case. We investigated the outbreak to identify the agent and the source and propose recommendations as well as to assess the practice of infection, prevention and control (IPC). METHODS: We used descriptive study to describe contact tracing and facility assessment. We described the outbreak by time, place, and person. We defined a case using established guidelines and line-listed the contacts. We conducted IPC facility check in the state. Blood specimens were collected for Lassa fever detection. Microsoft Excel and Epi-info version 7.1.6 were used for data analysis. RESULTS: The index case of Lassa fever in Katsina State was seen on 23/03/2016 with a travel history from Kaduna State. The second case had contact with a positive Lassa fever case from Gwagwalada, Federal Capital Territory (FCT). A total of 82 contacts were line listed (9 developed Lassa fever). The case fatality rate was 27.3%. IPC checklist revealed 37.5% of the health facilities lacked personal protective equipment and safety boxes, 25% lacked isolation wards, and none had chlorine solution. Overall, 61% of personnel had poor knowledge of Lassa fever, 31% had fair knowledge and 8% had good knowledge. CONCLUSION: A multiple-source epidemic with sources of primary infection from outside Katsina state was noted. Most of the health facilities assessed lack basic IPC materials and knowledge on Lassa fever which should be addressed.

CONTEXTE: La fièvre de Lassa est une maladie virale hémorragique aiguë causée par le virus de Lassa. Le virus Lassa appartient à la famille des Arenaviridae, des virus à ARN. Le 05/04/2016 ; deux cas de fièvre de Lassa ont été signalés dans l'État de Katsina avec la date de présentation du premier cas le 23/03/2016 et le 27/03/2016 pour le second cas. Nous avons enquêté sur cette épidémie pour identifier l'agent et la source et proposer des recommandations ainsi que pour évaluer la pratique de l'infection, de la prévention et du contrôle (IPC). MÉTHODES: Nous avons utilisé une étude descriptive pour décrire la recherche des contacts et l'évaluation des installations. Nous avons décrit l'épidémie en fonction de la date, du lieu et de la personne. Nous avons défini un cas à l'aide de lignes directrices établies et dressé une liste des contacts. Nous avons vérifié les installations de CIP dans l'État. Des échantillons de sang ont été prélevés pour la détection de la fièvre de Lassa. Microsoft Excel et Epi-info version 7.1.6 ont été utilisés pour l'analyse des données. RÉSULTATS: Le cas index de fièvre de Lassa dans l'État de Katsina a été observé le 23/03/2016 avec des antécédents de voyage en provenance de l'État de Kaduna. Le deuxième cas a été en contact avec un cas positif de fièvre de Lassa à Gwagwalada, dans le Territoire de la capitale fédérale (FCT). Au total, 82 contacts ont été répertoriés (9 ont développé une fièvre de Lassa). Le taux de létalité était de 27,3%. La liste de contrôle IPC a révélé que 37,5 % des établissements de santé manquaient d'équipements de protection individuelle et de boîtes de sécurité, que 25 % n'avaient pas de salles d'isolement et qu'aucun n'avait de solution chlorée. Dans l'ensemble, 61 % du personnel avait une mauvaise connaissance de la fièvre de Lassa, 31 % une connaissance moyenne et 8 % une bonne connaissance. CONCLUSION: Une épidémie à sources multiples avec des sources d'infection primaire en dehors de l'État de Katsina a été observée. La plupart des établissements de santé évalués manquent de matériel IPC de base et de connaissances sur la fièvre de Lassa, ce qui devrait être corrigé. Mots clés: Épidémiologie, Contrôle des infections, Katsina, Épidémie, Fièvre de Lassa.

Circulation of Lassa virus across the endemic Edo-Ondo axis, Nigeria, with cross-species transmission between multimammate mice.

We phylogenetically compared sequences of the zoonotic Lassa virus (LASV) obtained from Mastomys rodents in seven localities across the highly endemic Edo and Ondo States within Nigeria. Sequencing 1641 nt from the S segment of the virus genome, we resolved clades within lineage II that were either limited to Ebudin and Okhuesan in Edo state (2g-beta) or along Owo-Okeluse-Ifon in Ondo state (2g-gamma). We also found clades within Ekpoma, a relatively large cosmopolitan town in Edo state, that extended into other localities within Edo (2g-alpha) and Ondo (2g-delta). LASV variants from M. natalensis within Ebudin and Ekpoma in Edo State (dated approximately 1961) were more ancient compared to those from Ondo state (approximately 1977), suggesting a broadly east-west virus migration across south-western Nigeria; a pattern not always consistent with LASV sequences derived from humans in the same localities. Additionally, in Ebudin and Ekpoma, LASV sequences between M. natalensis and M. erythroleucus were interspersed on the phylogenetic tree, but those from M. erythroleucus were estimated to emerge more recently (approximately 2005). Overall, our results show that LASV amplification in certain localities (reaching a prevalence as high as 76% in Okeluse), anthropogenically-aided spread of rodent-borne variants amidst the larger towns (involving communal accommodation such as student hostels), and virus-exchange between syntopic M. natalensis and M. erythroleucus rodents (as the latter, a savanna species, encroaches southward into the degraded forest) pose perpetual zoonotic hazard across the Edo-Ondo Lassa fever belt, threatening to accelerate the dissemination of the virus into non endemic areas.

Lassa Fever Natural History and Clinical Management.

Lassa fever is caused by Lassa virus (LASV), an Old World Mammarenavirus that is carried by Mastomys natalensis and other rodents. It is endemic in Sierra Leone, Nigeria, and other countries in West Africa. The clinical presentation of LASV infection is heterogenous varying from an inapparent or mild illness to a fatal hemorrhagic fever. Exposure to LASV is usually through contact with rodent excreta. After an incubation period of 1-3 weeks, initial symptoms such as fever, headache, and fatigue develop that may progress to sore throat, retrosternal chest pain, conjunctival injection, vomiting, diarrhea, and abdominal pain. Severe illness, including hypotension, shock, and multiorgan failure, develops in a minority of patients. Patient demographics and case fatality rates are distinctly different in Sierra Leone and Nigeria. Laboratory diagnosis relies on the detection of LASV antigens or genomic RNA. LASV-specific immunoglobulin G and M assays can also contribute to clinical management. The mainstay of treatment for Lassa fever is supportive care. The nucleoside analog ribavirin is commonly used to treat acute Lassa fever but is considered useful only if treatment is begun early in the disease course. Drugs in development, including a monoclonal antibody cocktail, have the potential to impact the management of Lassa fever.