Real-Time RT-PCR Assays for Detection and Genotyping of West Nile Virus Lineages Circulating in Africa

West Nile virus (WNV) is an emerging arbovirus, circulating worldwide between birds and mosquitoes, which impacts human and animal health. Since the mid-1990s, WNV outbreaks have emerged in Europe and America and represent currently the primary cause of encephalitis in the United States. WNV exhibits a great genetic diversity with at least eight different lineages circulating in the world, and four (1, 2, Koutango, and putative new) are present in Africa. These different WNV lineages are not readily differentiated by serology, and thus, rapid molecular tools are required for diagnostic. We developed here real-time RT-PCR assays for detection and genotyping of African WNV lineages. The specificity of the assays was tested using other flaviviruses circulating in Africa. The sensitivity was determined by testing serial 10-fold dilutions of viruses and RNA standards. The assays provided good specificity and sensitivity and the analytical detection limit was 10 copies/ reaction. The RT-PCR assays allowed the detection and genotyping of all WNV isolates in culture medium, human serum, and vertebrate tissues, as well as in field and experimental mosquito samples. Comparing the ratios of genome copy number/infectious virion (plaque-forming units), our study finally revealed new insight on the replication of these different WNV lineages in mosquito cells. Our RT-PCR assays are the first ones allowing the genotyping of all WNV African variants, and this may have important applications in surveillance and epidemiology in Africa and also for monitoring of their emergence in Europe and other continents

Large-scale delivery of seasonal malaria chemoprevention to children under 10 in Senegal: an economic analysis.

Seasonal Malaria Chemoprevention (SMC) is recommended for children under 5 in the Sahel and sub-Sahel. The burden in older children may justify extending the age range, as has been done effectively in Senegal. We examine costs of door-to-door SMC delivery to children up to 10 years by community health workers (CHWs). We analysed incremental financial and economic costs at district level and below from a health service perspective. We examined project accounts and prospectively collected data from 405 CHWs, 46 health posts, and 4 district headquarters by introducing questionnaires in advance and completing them after each monthly implementation round. Affordability was explored by comparing financial costs of SMC to relevant existing health expenditure levels. Costs were disaggregated by administration month and by health service level. We used linear regression models to identify factors associated with cost variation between health posts. The financial cost to administer SMC to 180 000 children over one malaria season, reaching ∼93% of children with all three intended courses of SMC was $234 549 (constant 2010 USD) or$0.50 per monthly course administered. Excluding research-participation incentives, the financial cost was $0.32 per resident (all ages) in the catchment area, which is 1.2$278 922 or $0.59 per course administered and varied widely between health posts, from$0.38 to $2.74 per course administered. Substantial economies of scale across health posts were found, with the smallest health posts incurring highest average costs per monthly course administered. SMC for children up to 10 is likely to be affordable, particularly where it averts substantial curative care costs. Estimates of likely costs and cost-effectiveness of SMC in other contexts must account for variation in average costs across delivery months and health posts

Application of Functional Data Analysis to Identify Patterns of Malaria Incidence, to Guide Targeted Control Strategies.

We introduce an approach based on functional data analysis to identify patterns of malaria incidence to guide effective targeting of malaria control in a seasonal transmission area. Using functional data method, a smooth function (functional data or curve) was fitted from the time series of observed malaria incidence for each of 575 villages in west-central Senegal from 2008 to 2012. These 575 smooth functions were classified using hierarchical clustering (Ward's method), and several different dissimilarity measures. Validity indices were used to determine the number of distinct temporal patterns of malaria incidence. Epidemiological indicators characterizing the resulting malaria incidence patterns were determined from the velocity and acceleration of their incidences over time. We identified three distinct patterns of malaria incidence: high-, intermediate-, and low-incidence patterns in respectively 2% (12/575), 17% (97/575), and 81% (466/575) of villages. Epidemiological indicators characterizing the fluctuations in malaria incidence showed that seasonal outbreaks started later, and ended earlier, in the low-incidence pattern. Functional data analysis can be used to identify patterns of malaria incidence, by considering their temporal dynamics. Epidemiological indicators derived from their velocities and accelerations, may guide to target control measures according to patterns

Large-scale delivery of seasonal malaria chemoprevention to children under 10 in Senegal: an economic analysis

Seasonal Malaria Chemoprevention (SMC) is recommended for children under 5 in the Sahel and sub-Sahel. The burden in older children may justify extending the age range, as has been done effectively in Senegal. We examine costs of door-To-door SMC delivery to children up to 10 years by community health workers (CHWs). We analysed incremental financial and economic costs at district level and below from a health service perspective. We examined project accounts and prospectively collected data from 405 CHWs, 46 health posts, and 4 district headquarters by introducing questionnaires in advance and completing them after each monthly implementation round. Affordability was explored by comparing financial costs of SMC to relevant existing health expenditure levels. Costs were disaggregated by administration month and by health service level. We used linear regression models to identify factors associated with cost variation between health posts. The financial cost to administer SMC to 180 000 children over one malaria season, reaching â 1/493% of children with all three intended courses of SMC was 234 549 (constant 2010 USD) or 0.50 per monthly course administered. Excluding research-participation incentives, the financial cost was 0.32 per resident (all ages) in the catchment area, which is 1.2% of Senegal's general government expenditure on health per capita. Economic costs were 18.7% higher than financial costs at 278 922 or 0.59 per course administered and varied widely between health posts, from 0.38 to 2.74 per course administered. Substantial economies of scale across health posts were found, with the smallest health posts incurring highest average costs per monthly course administered. SMC for children up to 10 is likely to be affordable, particularly where it averts substantial curative care costs. Estimates of likely costs and cost-effectiveness of SMC in other contexts must account for variation in average costs across delivery months and health posts

Effectiveness of Seasonal Malaria Chemoprevention in Children under Ten Years of Age in Senegal: A Stepped-Wedge Cluster-Randomised Trial.

BACKGROUND: Seasonal Malaria Chemoprevention (SMC) with sulfadoxine-pyrimethamine (SP) plus amodiaquine (AQ), given each month during the transmission season, is recommended for children living in areas of the Sahel where malaria transmission is highly seasonal. The recommendation for SMC is currently limited to children under five years of age, but, in many areas of seasonal transmission, the burden in older children may justify extending this age limit. This study was done to determine the effectiveness of SMC in Senegalese children up to ten years of age. METHODS AND FINDINGS: SMC was introduced into three districts over three years in central Senegal using a stepped-wedge cluster-randomised design. A census of the population was undertaken and a surveillance system was established to record all deaths and to record all cases of malaria seen at health facilities. A pharmacovigilance system was put in place to detect adverse drug reactions. Fifty-four health posts were randomised. Nine started implementation of SMC in 2008, 18 in 2009, and a further 18 in 2010, with 9 remaining as controls. In the first year of implementation, SMC was delivered to children aged 3-59 months; the age range was then extended for the latter two years of the study to include children up to 10 years of age. Cluster sample surveys at the end of each transmission season were done to measure coverage of SMC and the prevalence of parasitaemia and anaemia, to monitor molecular markers of drug resistance, and to measure insecticide-treated net (ITN) use. Entomological monitoring and assessment of costs of delivery in each health post and of community attitudes to SMC were also undertaken. About 780,000 treatments were administered over three years. Coverage exceeded 80% each month. Mortality, the primary endpoint, was similar in SMC and control areas (4.6 and 4.5 per 1000 respectively in children under 5 years and 1.3 and 1.2 per 1000 in children 5-9 years of age; the overall mortality rate ratio [SMC: no SMC] was 0.90, 95% CI 0.68-1.2, p = 0.496). A reduction of 60% (95% CI 54%-64%, p < 0.001) in the incidence of malaria cases confirmed by a rapid diagnostic test (RDT) and a reduction of 69% (95% CI 65%-72%, p < 0.001) in the number of treatments for malaria (confirmed and unconfirmed) was observed in children. In areas where SMC was implemented, incidence of confirmed malaria in adults and in children too old to receive SMC was reduced by 26% (95% CI 18%-33%, p < 0.001) and the total number of treatments for malaria (confirmed and unconfirmed) in these older age groups was reduced by 29% (95% CI 21%-35%, p < 0.001). One hundred and twenty-three children were admitted to hospital with a diagnosis of severe malaria, with 64 in control areas and 59 in SMC areas, showing a reduction in the incidence rate of severe disease of 45% (95% CI 5%-68%, p = 0.031). Estimates of the reduction in the prevalence of parasitaemia at the end of the transmission season in SMC areas were 68% (95% CI 35%-85%) p = 0.002 in 2008, 84% (95% CI 58%-94%, p < 0.001) in 2009, and 30% (95% CI -130%-79%, p = 0.56) in 2010. SMC was well tolerated with no serious adverse reactions attributable to SMC drugs. Vomiting was the most commonly reported mild adverse event but was reported in less than 1% of treatments. The average cost of delivery was US$0.50 per child per month, but varied widely depending on the size of the health post. Limitations included the low rate of mortality, which limited our ability to detect an effect on this endpoint. CONCLUSIONS: SMC substantially reduced the incidence of outpatient cases of malaria and of severe malaria in children, but no difference in all-cause mortality was observed. Introduction of SMC was associated with an overall reduction in malaria incidence in untreated age groups. In many areas of Africa with seasonal malaria, there is a substantial burden in older children that could be prevented by SMC. SMC in older children is well tolerated and effective and can contribute to reducing malaria transmission. TRIAL REGISTRATION: ClinicalTrials.gov NCT00712374

Correction: A Seroepidemiological Study of Serogroup A Meningococcal Infection in the African Meningitis Belt.

[This corrects the article DOI: 10.1371/journal.pone.0147928.]

Diversité des agricultures familiales

Dans un contexte d’interrogation sur les modèles agricoles et de profondes transformations des agricultures et des marchés, cet ouvrage s’attache à revisiter la diversité des formes familiales de production et leurs mutations de par le monde. Dès lors, l’analyse intègre les liens aux marchés, aux territoires et à l’Ailleurs — par le fait migratoire — les enjeux d’autonomie et de sécurité alimentaire, les stratégies de survie et d’accumulation ainsi que les formes d’action collective et politique. L’ouvrage est construit autour de dix-huit études de cas, menées dans les cinq continents. Elles ont toutes été conduites avec un cadre méthodologique, identique et original, inspiré du Sustainable Rural Livehoods (cadre d’identification des moyens de subsistance durables en milieu rural). Revisitée pour cet ouvrage, cette méthode d’observations et d’analyses permet aux auteurs de préciser finement « ce qui fait famille », d’analyser les adaptations du travail des actifs familiaux et les mettre en perspective avec le contexte territorial et les politiques publiques de chaque pays. Écrit à plusieurs mains, par un réseau de chercheurs, cet ouvrage contribue autant à l’approfondissement des savoirs scientifiques sur les agricultures familiales dans le monde qu’à la mise à l’épreuve d’un cadre méthodologique d’analyse et d’observations en milieu rural. Il vise un public de chercheurs, d’enseignants et d’étudiants, agronomes, économistes, sociologues et historiens. Les experts du développement agricole et rural y trouveront un grand intérêt. Plus largement, toute personne qui s’intéresse aux agricultures familiales et à leurs évolutions dans divers contextes sociaux trouvera avantage à cette lecture. Les chercheurs qui ont coordonné cet ouvrage sont agronomes, économistes et géographes, au Cirad ou à l’Inra où ils mènent des recherches sur les systèmes agricoles familiaux à des échelles locales, nationales ou internationales. Cet ouvrage est le fruit d’une démarche de recherche collective et partagée permettant à de nombreux scientifiques des pays du Sud d’exprimer la diversité des réalités agraires contemporaines. Certains coordinateurs ou auteurs de cet ouvrage ont également collaboré à Agricultures familiales et mondes à venir, titre paru en 2014 chez Quae. Ce livre est également disponible en anglais sous le titreDiversity of Family Farming Around the Worldauprès des éditions Springer -www.springer.co

Les violence basees sur le genre dans les ménages: représentations, connaissances, prévalence et prise en charge

Ce texte analyse les manifestations des violences basées sur le genre dans les ménagesCRD

Analyse de données fonctionnelles pour la classification de profils épidémiques : application au paludisme

International audienc

Targeting Malaria Hotspots to Reduce Transmission Incidence in Senegal.

International audienc