Determining Ancestry between Rodent- and Human-Derived Lassa Virus Sequences in Endemic Foci within West Africa: Indications of Reverse Zoonosis

2019 ◽  
Author(s):  
Ayodeji Olayemi ◽  
Adetunji Samuel Adesina ◽  
Thomas Strecker ◽  
N’Faly Magassouba ◽  
Elisabeth Fichet-Calvet
Keyword(s):  
West Africa ◽  
Lassa Virus

scholarly journals Identification of Common CD8+ T Cell Epitopes from Lassa Fever Survivors in Nigeria and Sierra Leone

2020 ◽  
Vol 94 (12) ◽  
Author(s):  
Saori Sakabe ◽  
Jessica N. Hartnett ◽  
Nhi Ngo ◽  
Augustine Goba ◽  
Mambu Momoh ◽  
...  
Keyword(s):  
T Cell ◽  
West Africa ◽  
Sierra Leone ◽  
T Cell Responses ◽  
Lassa Fever ◽  
Health Concern ◽  
Lassa Virus ◽  
T Cell Epitopes ◽  
Virus Surface ◽  
Cell Responses

ABSTRACT Early and robust T cell responses have been associated with survival from Lassa fever (LF), but the Lassa virus-specific memory responses have not been well characterized. Regions within the virus surface glycoprotein (GPC) and nucleoprotein (NP) are the main targets of the Lassa virus-specific T cell responses, but, to date, only a few T cell epitopes within these proteins have been identified. We identified GPC and NP regions containing T cell epitopes and HLA haplotypes from LF survivors and used predictive HLA-binding algorithms to identify putative epitopes, which were then experimentally tested using autologous survivor samples. We identified 12 CD8-positive (CD8+) T cell epitopes, including epitopes common to both Nigerian and Sierra Leonean survivors. These data should be useful for the identification of dominant Lassa virus-specific T cell responses in Lassa fever survivors and vaccinated individuals as well as for designing vaccines that elicit cell-mediated immunity. IMPORTANCE The high morbidity and mortality associated with clinical cases of Lassa fever, together with the lack of licensed vaccines and limited and partially effective interventions, make Lassa virus (LASV) an important health concern in its regions of endemicity in West Africa. Previous infection with LASV protects from disease after subsequent exposure, providing a framework for designing vaccines to elicit similar protective immunity. Multiple major lineages of LASV circulate in West Africa, and therefore, ideal vaccine candidates should elicit immunity to all lineages. We therefore sought to identify common T cell epitopes between Lassa fever survivors from Sierra Leone and Nigeria, where distinct lineages circulate. We identified three such epitopes derived from highly conserved regions within LASV proteins. In this process, we also identified nine other T cell epitopes. These data should help in the design of an effective pan-LASV vaccine.

Fluctuation of Abundance and Lassa Virus Prevalence in Mastomys natalensis in Guinea, West Africa

2007 ◽  
Vol 7 (2) ◽  
pp. 119-128 ◽  
Author(s):  
Elisabeth Fichet-Calvet ◽  
Emilie Lecompte ◽  
Lamine Koivogui ◽  
Barré Soropogui ◽  
Amadou Doré ◽  
...  
Keyword(s):  
West Africa ◽  
Lassa Virus ◽  
Mastomys Natalensis ◽  
Virus Prevalence

scholarly journals Phylogeography of Lassa Virus in Nigeria

2019 ◽  
Vol 93 (21) ◽  
Author(s):  
Deborah U. Ehichioya ◽  
Simon Dellicour ◽  
Meike Pahlmann ◽  
Toni Rieger ◽  
Lisa Oestereich ◽  
...  
Keyword(s):  
West Africa ◽  
Case Fatality ◽  
Hemorrhagic Fever ◽  
Lassa Fever ◽  
Future Research ◽  
Lassa Virus ◽  
Southeastern Part ◽  
Data Set ◽  
Content Type ◽  
Virus Strains

ABSTRACT Lassa virus is genetically diverse with several lineages circulating in West Africa. This study aimed at describing the sequence variability of Lassa virus across Nigeria and inferring its spatiotemporal evolution. We sequenced and isolated 77 Lassa virus strains from 16 Nigerian states. The final data set, including previous works, comprised metadata and sequences of 219 unique strains sampled between 1969 and 2018 in 22 states. Most of this data originated from Lassa fever patients diagnosed at Irrua Specialist Teaching Hospital, Edo State, Nigeria. The majority of sequences clustered with the main Nigerian lineages II and III, while a few sequences formed a new cluster related to Lassa virus strains from Hylomyscus pamfi. Within lineages II and III, seven and five sublineages, respectively, were distinguishable. Phylogeographic analysis suggests an origin of lineage II in the southeastern part of the country around Ebonyi State and a main vector of dispersal toward the west across the Niger River, through Anambra, Kogi, Delta, and Edo into Ondo State. The frontline of virus dispersal appears to be in Ondo. Minor vectors are directed northeast toward Taraba and Adamawa and south toward Imo and Rivers. Lineage III might have spread from northern Plateau State into Kaduna, Nasarawa, Federal Capital Territory, and Bauchi. One sublineage moved south and crossed the Benue River into Benue State. This study provides a geographic mapping of lineages and phylogenetic clusters in Nigeria at a higher resolution. In addition, we estimated the direction and time frame of virus dispersal in the country. IMPORTANCE Lassa virus is the causative agent of Lassa fever, a viral hemorrhagic fever with a case fatality rate of approximately 30% in Africa. Previous studies disclosed a geographical pattern in the distribution of Lassa virus strains and a westward movement of the virus across West Africa during evolution. Our study provides a deeper understanding of the geography of genetic lineages and sublineages of the virus in Nigeria. In addition, we modeled how the virus spread in the country. This knowledge allows us to predict into which geographical areas the virus might spread in the future and prioritize areas for Lassa fever surveillance. Our study not only aimed to generate Lassa virus sequences from across Nigeria but also to isolate and conserve the respective viruses for future research. Both isolates and sequences are important for the development and evaluation of medical countermeasures to treat and prevent Lassa fever, such as diagnostics, therapeutics, and vaccines.

scholarly journals Predicting the evolution of Lassa Virus endemic area and population at risk over the next decades

2021 ◽  
Author(s):  
Raphaëlle Klitting ◽  
Liana E. Kafetzopoulou ◽  
Wim Thiery ◽  
Gytis Dudas ◽  
Sophie Gryseels ◽  
...  
Keyword(s):  
At Risk ◽  
West Africa ◽  
Endemic Area ◽  
Hemorrhagic Fever ◽  
Lassa Fever ◽  
Environmental Data ◽  
World Health ◽  
Lassa Virus ◽  
Viral Genomes ◽  
Health Organization

AbstractLassa fever is listed among the diseases that pose the greatest risks to public health by the World Health Organization. This severe viral hemorrhagic fever is caused by Lassa virus, a zoonotic pathogen that repeatedly spills over to humans from its rodent reservoirs. It is currently not known how climate change, transformations in land use, and human population growth could affect the endemic area of this virus, currently limited to parts of West Africa. By exploring the environmental data associated with virus occurrence, we show how temperature, precipitation and the presence of pastures determine ecological suitability for virus circulation. We project that regions in Central and East Africa will likely become suitable for Lassa virus over the next decades and estimate that the total population living in areas suitable for Lassa virus may grow from about 100 million to 700 million by 2070. By analysing geotagged viral genomes, we find that in the event of Lassa virus being introduced into a new suitable region, its spread might remain spatially limited over the first decades. Our results highlight how the endemic area of Lassa virus may expand well beyond West Africa in the next decades due to human impact on the environment, putting hundreds of million more people at risk of infection.

scholarly journals The Impact of Human Conflict on the Genetics of Mastomys natalensis and Lassa Virus in West Africa

PLoS ONE ◽  
2012 ◽  
Vol 7 (5) ◽  
pp. e37068 ◽  
Author(s):  
Aude Lalis ◽  
Raphaël Leblois ◽  
Emilie Lecompte ◽  
Christiane Denys ◽  
Jan ter Meulen ◽  
...  
Keyword(s):  
West Africa ◽  
Lassa Virus ◽  
Mastomys Natalensis ◽  
Human Conflict ◽  
The Impact

scholarly journals Molecular confirmation of Lassa fever imported into Ghana

2016 ◽  
Vol 5 (1) ◽  
Author(s):  
Joseph H.K. Bonney ◽  
Edward O. Nyarko ◽  
Sally-Ann Ohene ◽  
Joseph Amankwa ◽  
Ralph K. Ametepi ◽  
...  
Keyword(s):  
West Africa ◽  
Gene Segment ◽  
Lassa Fever ◽  
Molecular Diagnostic ◽  
Military Hospital ◽  
Lassa Virus ◽  
Haemorrhagic Fever ◽  
Blood Samples ◽  
Viral Haemorrhagic Fever ◽  
Close Contacts

Background: Recent reports have shown an expansion of Lassa virus from the area where it was first isolated in Nigeria to other areas of West Africa. Two Ghanaian soldiers on a United Nations peacekeeping mission in Liberia were taken ill with viral haemorrhagic fever syndrome following the death of a sick colleague and were referred to a military hospital in Accra, Ghana, in May 2013. Blood samples from the soldiers and five asymptomatic close contacts were subjected to laboratory investigations.Objective: We report the results of these investigations to highlight the importance of molecular diagnostic applications and the need for heightened awareness about Lassa fever in West Africa.Methods: We used molecular assays on sera from the two patients to identify the causativeorganism. Upon detection of positive signals for Lassa virus ribonucleic material by two differentpolymerase chain reaction assays, sequencing and phylogenetic analyses were performed.Results: The presence of Lassa virus in the soldiers’ blood samples was shown by L-gene segment homology to be the Macenta and las803792 strains previously isolated in Liberia, with close relationships then confirmed by phylogenetic tree construction. The five asymptomatic close contacts were negative for Lassa virus.Conclusions: The Lassa virus strains identified in the two Ghanaian soldiers had molecular epidemiological links to strains from Liberia. Lassa virus was probably responsible for the outbreak of viral haemorrhagic fever in the military camp. These data confirm Lassa fever endemicity in West Africa.

scholarly journals Lassa fever infection from West Africa, dynamic and epidemiology of the virus on the population 1969–2019: a systematic review and meta-analysis

2019 ◽  
Author(s):  
Roland Eric YESSINOU ◽  
Alain Richi Kamga Waladjo ◽  
Dramou Ignace ◽  
Justin Adinsi ◽  
Elsie Sangnidjo ◽  
...  
Keyword(s):  
West Africa ◽  
Meta Analysis ◽  
Hospital Staff ◽  
Lassa Fever ◽  
Lassa Virus ◽  
Health Authorities ◽  
Review Period ◽  
Pooled Prevalence ◽  
Public Health Authorities ◽  
High Level

Abstract Background Lassa virus (LASV) is a highly prevalent arenavirus that affects two to three million people in West Africa. This rodent borne virus which has serious consequences on the population and hospital staff in endemic areas. In this article, we review prevalence of LASV with a focus on the dynamic and epidemiology of the disease of 1969-2019. What informs on the evolution and the extent of the disease in this at-risk zone in order to prepare response measures in the event of an epidemic. Methods We was conducted a retrospective review through literatures search using the AGORA, PubMed, Science Direct, Scopus, researchgate and Google scholar Database on Lassa fever (LF) from West Africa. A total 34 articles were studied from 11 countries. Studies were categorized by host and country, and meta-analysis conducted to determine pooled prevalence estimates for each category Analysis was done using the metaprop command in STATA version 15 and MetaXL software. Results A total of 18.111 individual samples from 11 countries, described in 34 articles were studied. Meta-analysis of twenty six studies have indicated that the pooled prevalence was 19.0% [95% CI (15.0-23.0%), I2 = 97.93%]. There was a high level of heterogeneity between studies; however, the high prevalence of LASV was noted in several countries as Nigeria (12-42%), followed by Sierra Leone (8-43%), and then Guinea (9-40%). Pooled prevalence of LASV for human in studies conducted over the entire review period was 22.0% [95% CI (17.0-28.0%), I2 = 98.0%]; eighteen studies), while she was 9.0% [95% CI (4.0-15.0%), I2 = 97.0%]; eight studies) for Mastomys spp. Conclusion The knowledge of the geographical distribution and epidemiology may have help for disease control efforts and limit the risk of transmission, both locally and internationally. This study is also important in order to guide interventions, public health authorities and inform on the evolution of the disease and its magnitude in the population.

scholarly journals Bayesian estimation of Lassa virus epidemiological parameters: implications for spillover prevention using wildlife vaccination

2019 ◽  
Author(s):  
Scott L. Nuismer ◽  
Christopher H. Remien ◽  
Andrew Basinski ◽  
Tanner Varrelman ◽  
Nathan Layman ◽  
...  
Keyword(s):  
West Africa ◽  
Surveillance Data ◽  
Model Parameters ◽  
Lassa Virus ◽  
Vaccination Programs ◽  
Public Health Burden ◽  
Health Burden ◽  
Human Infections ◽  
Rodent Populations ◽  
Epidemiological Parameters

AbstractLassa virus is a significant burden on human health throughout its endemic region in West Africa, with most human infections the result of spillover from the primary rodent reservoir of the virus, the natal multimammate mouse,M. natalensis. Here we develop a Bayesian methodology for estimating epidemiological parameters of Lassa virus within its rodent reservoir and for generating probabilistic predictions for the efficacy of rodent vaccination programs. Our approach uses Approximate Bayesian Computation (ABC) to integrate mechanistic mathematical models, remotely-sensed precipitation data, and Lassa virus surveillance data from rodent populations. Using simulated data, we show that our method accurately estimates key model parameters, even when surveillance data are available from only a relatively small number of points in space and time. Applying our method to previously published data from two villages in Guinea estimates the time-averagedR0of Lassa virus to be 1.658 and 1.453 for rodent populations in the villages of Bantou and Tanganya, respectively. Using the posterior distribution for model parameters derived from these Guinean populations, we evaluate the likely efficacy of vaccination programs relying on distribution of vaccine-laced baits. Our results demonstrate that effective and durable reductions in the risk of Lassa virus spillover into the human population will require repeated distribution of large quantities of vaccine.Author SummaryLassa virus is a chronic source of illness throughout West Africa, and is considered to be a threat for widespread emergence. Because most human infections result from contact with infected rodents, interventions that reduce the number of rodents infected with Lassa virus represent promising opportunities for reducing the public health burden of this disease. Evaluating how well alternative interventions are likely to perform is complicated by our relatively poor understanding of viral epidemiology within the reservoir population. Here we develop a novel statistical approach that couples mathematical models and viral surveillance data from rodent populations to robustly estimate key epidemiological parameters. Applying our method to existing data from Guinea yields well-resolved parameter estimates and allows us to simulate a variety of rodent vaccination programs. Together, our results demonstrate that rodent vaccination alone is unlikely to be an effective tool for reducing that public health burden of Lassa fever within West Africa.

scholarly journals Bridging the gap: Using reservoir ecology and human serosurveys to estimate Lassa virus spillover in West Africa

2021 ◽  
Vol 17 (3) ◽  
pp. e1008811
Author(s):  
Andrew J. Basinski ◽  
Elisabeth Fichet-Calvet ◽  
Anna R. Sjodin ◽  
Tanner J. Varrelman ◽  
Christopher H. Remien ◽  
...  
Keyword(s):  
Machine Learning ◽  
West Africa ◽  
Human Population ◽  
Risk Model ◽  
Lassa Virus ◽  
Training Models ◽  
Infection Dynamics ◽  
Wildlife Vaccination ◽  
Risk Forecast ◽  
Human Infections

Forecasting the risk of pathogen spillover from reservoir populations of wild or domestic animals is essential for the effective deployment of interventions such as wildlife vaccination or culling. Due to the sporadic nature of spillover events and limited availability of data, developing and validating robust, spatially explicit, predictions is challenging. Recent efforts have begun to make progress in this direction by capitalizing on machine learning methodologies. An important weakness of existing approaches, however, is that they generally rely on combining human and reservoir infection data during the training process and thus conflate risk attributable to the prevalence of the pathogen in the reservoir population with the risk attributed to the realized rate of spillover into the human population. Because effective planning of interventions requires that these components of risk be disentangled, we developed a multi-layer machine learning framework that separates these processes. Our approach begins by training models to predict the geographic range of the primary reservoir and the subset of this range in which the pathogen occurs. The spillover risk predicted by the product of these reservoir specific models is then fit to data on realized patterns of historical spillover into the human population. The result is a geographically specific spillover risk forecast that can be easily decomposed and used to guide effective intervention. Applying our method to Lassa virus, a zoonotic pathogen that regularly spills over into the human population across West Africa, results in a model that explains a modest but statistically significant portion of geographic variation in historical patterns of spillover. When combined with a mechanistic mathematical model of infection dynamics, our spillover risk model predicts that 897,700 humans are infected by Lassa virus each year across West Africa, with Nigeria accounting for more than half of these human infections.

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