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The burden of anemia in Senegal is high, particularly in children and women in rural households. The main objectives of the study reported here were (i) to measure and compare the prevalence of anemia and intestinal parasitic infections in farmers and family members and sheep in two agro-ecological zones in Senegal and (ii) to examine the association between anemia and age or sex in farmers and family members. The study was conducted in Mpal (250 km from Dakar, the capital city) and Diawara (700 km from Dakar, a remote location near the Malian border). In humans, the prevalence of anemia was higher in Diawara (64/86 = 74%), compared to Mpal (13/29 = 45%) (p

Porcine circovirus-2 (PCV-2) is associated with several disease syndromes in domestic pigs that have a significant impact on global pig production and health. Currently, little is known about the status of PCV-2 in Africa. In this study, a total of 408 archived DNA samples collected from pigs in Burkina Faso, Cameroon, Cape Verde, Ethiopia, the Democratic Republic of the Congo, Mozambique, Nigeria, Senegal, Tanzania, and Zambia between 2000 and 2018 were screened by PCR for the presence of PCV-2. Positive amplicons of the gene encoding the viral capsid protein (ORF2) were sequenced to determine the genotypes circulating in each country. Four of the nine currently known genotypes of PCV-2 were identified (i.e. PCV-2a, PCV-2b, PCV-2d and PCV-2g) with more than one genotype being identified in Burkina Faso, Ethiopia, Nigeria, Mozambique, Senegal and Zambia. Additionally, a phylogeographic analysis which included 38 additional ORF2 gene sequences of PCV-2s previously identified in Mozambique, Namibia and South Africa from 2014 to 2016 and 2019 to 2020 and available in public databases, demonstrated the existence of several African-specific clusters and estimated the approximate time of introduction of PCV-2s into Africa from other continents. This is the first in-depth study of PCV-2 in Africa and it has important implications for pig production at both the small-holder and commercial farm level on the continent. This article is protected by copyright. All rights reserved.

International audience; Bluetongue (BT) is an infectious, arthropod-borne viral disease of domestic and wild ruminants. The disease causes animal mortality, production decrease and commercial limits for herds. Despite the active circulation of the disease in the world, few studies have been carried out in Senegal. The objective of this study was to assess the current prevalence of BT in small ruminants and the serotypes circulating in Senegal. A cross-sectional study was conducted in the fourteen regions of Senegal. After the sampling campaign, sera collected in sheep and goats herds were screened for the presence of Bluetongue virus (BTV) specific antibodies using c-Elisa. The whole blood of seropositive animals was further analyzed by RT-qPCR and positive samples were typed to identify BTV serotypes. Analysis of several risk factors such as age, sex and species of animals was performed using logistic regression. The overall seroprevalence of BTV in Senegal was 72.6% (95% CI: 70.3-74.9%) with 75.9% (95% CI: 72.2-79.5%) in goat and 70.6% (95% CI: 67.5-73.6%) in sheep. Female (prevalence=77.1%) and adult (prevalence=80%) animals showed the highest seropositivity to BTV compared respectively to male (55.7%, p=6.133e-09) and young (49.4%, p < 2.2e-16). The RT-qPCR results showed the presence of BT viral genome in 359 small ruminants. The results obtained from serological and genotyping studies showed an active spread of the Bluetongue virus in domestic ruminants and phylogenetic analysis showed that the BTV-2 is one of the circulating serotypes in Senegal. This study allows having baseline information for controlling Bluetongue in Senegal.

Rift Valley fever virus (RVFV), an arbovirus belonging to the Phlebovirus genus of the Phenuiviridae family, causes the zoonotic and mosquito-borne RVF. The virus, which primarily affects livestock (ruminants and camels) and humans, is at the origin of recent major outbreaks across the African continent (Mauritania, Libya, Sudan), and in the South-Western Indian Ocean (SWIO) islands (Mayotte). In order to be better prepared for upcoming outbreaks, to predict its introduction in RVFV unscathed countries, and to run efficient surveillance programmes, the priority is harmonising and improving the diagnostic capacity of endemic countries and/or countries considered to be at risk of RVF. A serological inter-laboratory proficiency test (PT) was implemented to assess the capacity of veterinary laboratories to detect antibodies against RVFV. A total of 18 laboratories in 13 countries in the Middle East, North Africa, South Africa, and the Indian Ocean participated in the initiative. Two commercial kits and two in-house serological assays for the detection of RVFV specific IgG antibodies were tested. Sixteen of the 18 participating laboratories (88.9%) used commercial kits, the analytical performance of test sensitivity and specificity based on the seroneutralisation test considered as the reference was 100%. The results obtained by the laboratories which used the in-house assay were correct in only one of the two criteria (either sensitivity or specificity). In conclusion, most of the laboratories performed well in detecting RVFV specific IgG antibodies and can therefore be considered to be prepared. Three laboratories in three countries need to improve their detection capacities. Our study demonstrates the importance of conducting regular proficiency tests to evaluate the level of preparedness of countries and of building a network of competent laboratories in terms of laboratory diagnosis to better face future emerging diseases in emergency conditions.

Rift Valley fever (RVF) is a mosquito-borne disease mostly affecting wild and domestic ruminants. It is widespread in Africa, with spillovers in the Arab Peninsula and the southwestern Indian Ocean. Although RVF has been circulating in West Africa for more than 30 years, its epidemiology is still not clearly understood. In 2013, an RVF outbreak hit Senegal in new areas that weren’t ever affected before. To assess the extent of the spread of RVF virus, a national serological survey was implemented in young small ruminants (6–18 months old), between November 2014 and January 2015 (after the rainy season) in 139 villages. Additionally, the drivers of this spread were identified. For this purpose, we used a beta-binomial (BB) logistic regression model. An Integrated Nested Laplace Approximation (INLA) approach was used to fit the spatial model. Lower cumulative rainfall, and higher accessibility were both associated with a higher RVFV seroprevalence. The spatial patterns of fitted RVFV seroprevalence pointed densely populated areas of western Senegal as being at higher risk of RVFV infection in small ruminants than rural or southeastern areas. Thus, because slaughtering infected animals and processing their fresh meat is an important RVFV transmission route for humans, more human populations might have been exposed to RVFV during the 2013–2014 outbreak than in previous outbreaks in Senegal.

Estimating the epidemic potential of vector-borne diseases, along with the relative contribution of underlying mechanisms, is crucial for animal and human health worldwide. In West African Sahel, several outbreaks of Rift Valley fever (RVF) have occurred over the last decades, but uncertainty remains about the conditions necessary to trigger these outbreaks. We use the basic reproduction number (R0) as a measure of RVF epidemic potential in Northern Senegal, and map its value in two distinct ecosystems, namely the Ferlo and the Senegal river delta and valley. We consider three consecutive rainy seasons (July-November 2014, 2015 and 2016) and account for several vector and animal species. Namely, we parametrize our model with estimates of Aedes vexans arabiensis, Culex poicilipes, Culex tritaeniorhynchus, cattle, sheep and goats abundances. The impact of RVF virus introduction is assessed every week, in 4367 pixels of 3,5km2. The results of our analysis indicate that September was the month with highest epidemic potential in each study area, while at-risk locations varied between seasons. We show that decreased vector densities do not highly reduce R0 and that cattle immunity has a greater impact on reducing transmission than small ruminants immunity. The host preferences of vectors and the temperature-dependent time interval between their blood meals are crucial parameters needing further biological investigations.HighlightsSeptember is a period of high Rift Valley fever epidemic potential in northern Senegal regardless of the year, but exact locations where epidemics might start change between rainy seasons.Decreased vector densities during the rainy season did not highly reduce the epidemic potential of at-risk locations.High levels of immunity in cattle populations reduce more Rift Valley fever virus transmission than a high immunity in small ruminants in our study area. This aspect should be investigated further for targeted vaccination campaigns.Precise estimates of vector feeding preferences and the temperature-dependent lenght of their gonotrophic cycle are key to ensure a good detection of at-risk pixels.

Since November 2018, several countries in West and Central Africa have reported mortalities in donkeys and horses. Specifically, more than 66,000 horses and donkeys have succumbed to disease in Burkina Faso, Chad, Cameroon, The Gambia, Ghana, Mali, Niger, Nigeria, and Senegal. Strangles caused by Streptococcus equi subsp equi, African Horse Sickness (AHS) virus, and Equine influenza virus (EIV) were all suspected as potential causative agents. This study reports the identification of EIV in field samples collected in Niger and Senegal. Phylogenetic analysis of the hemagglutinin and neuraminidase genes revealed that the identified viruses belonged to clade 1 of the Florida sublineage and were very similar to viruses identified in Nigeria in 2019. Interestingly, they were also more similar to EIVs from recent outbreaks in South America than to those in Europe and the USA. This is one of the first reports providing detailed description and characterization of EIVs in West and Central Africa region.

Rift Valley fever (RVF) is a mosquito-borne viral infection mostly encountered in Africa. In its acute form, it severely affects domestic and wild ruminants, dromedaries, and humans. It is considered as an emerging disease, with increased frequency in several regions, and a spread potential to many areas under the influence of two main drivers: environmental (including climatic) changes and animal mobility (livestock trade, transhumance). In this chapter, we discuss the peculiarities of RVF epidemiology in Sahelian Africa and we show how the joint influence of these two drivers may trigger RVF epidemics. The public health impact of RVF can be severe, with tens of thousands of human cases and hundreds of fatalities recorded during large epidemics. Beyond its direct, negative effects on public and animal health, RVF has large economic consequences related to bans on livestock importation from infected countries. Solutions are available to improve surveillance and control of RVF in Sahelian Africa according to well-defined, risk-based strategies. The implementation of coordinated actions between Public Health and Animal Health authorities would represent an important advance in the One Health joint approach of RVF for better prevention, early detection, and reaction.

In recent years very virulent (VV) IBDV strains and classical (CV) IBDV strains re-emerged and caused devastating outbreaks in different parts of the world. In this study, genetic evolution of fifteen IBDVs collected in Senegal in 1979, 1999, 2007, 2012, 2013 and 2014 was characterized to gain information for a better control of IBD. Following RT-PCR, nucleotide sequence of the VP2 hypervariable region was determined and compared with sequences available in GenBank. Phylogenetic analysis showed that the viruses diverged into two genotypes: Very virulent (VV) IBDV and classical virulent (CV) IBDV. The Senegalese field strains of the first genotype (VV) IBDV had 98.9 to 100% identity among themselves, whereas their identity with reported Nigerian (VV) IBDVs ranged between 96.7 and 99%. The close phylogenetic relationship of the Senegalese and Nigerian strains suggests that they likely derived from a common ancestor. In the phylogenetic tree, all the Senegalese (VV) IBDV strains belonged to the African very virulent types (VV2). The genotyping of senegalese field IBDV strains indicated that the majority of viruses circulating in Senegal are (VV) IBDVs and highlights a genetic stability. Key words: Infectious bursal disease, phylogenetic analysis, Senegal.

Au Senegal, des foyers de la maladie de Gumboro sont souvent observes dans les elevages ou elle provoque des pertes economiques importantes. Une etude portant sur cette maladie dans les elevages avicoles semi-intensifs de la region de Dakar a ete conduite. Elle a consiste a identifier sur le plan moleculaire les souches circulant et a etudier les liens de parente genetique qui existent entre les souches senegalaises et celles etrangeres en vue de mieux readapter les strategies de lutte. Pour cela, la region hypervariable du genome viral codant pour le « domaine variable de la proteine VP2 » a ete sequencee. Les sequences d’acides nucleidiques et amines comparees a des sequences publiees sur la base de donnees de GenBank. Ainsi, les resultats indiquent une forte prevalence des souches « hypervirulentes ». Toutes les huit souches etudiees appartiennent au genotype des souches « hypervirulentes ». Parmi ces souches, une est classee dans le sous-genotype VV3 et les autres dans VV2. Les souches de ce sous-genotype sont tres proches des souches nigerianes et constituent avec des souches tanzaniennes, zambiennes et ethiopiennes la lignee africaine VV2. Toutefois, des investigations portant sur le segment B permettraient d’apporter plus de precisions sur l’origine des souches qui circulent a Dakar. Mots cles : Caracterisation moleculaire, souches hypervirulentes, Senegal, Maladie de Gumboro. English Title: Molecular characterization of Gumboro disease virus isolate from semiintensive poultry farms in Dakar, Senegal In Senegal, outbreaks of Gumboro disease are often observed with significant economic losses. A study of this disease in semi-intensive poultry farms was carried in Dakar. The research work consisted to identify by molecular biology the viral strains circulating and study the genetic relationship between Senegalese strains and foreign strains in order to better rehabilitate the control strategies. To do so, the hypervariable region of the viral genome encoding “the VP2 variable domain” was sequenced. The nucleic and amino acid sequences were compared to sequences published on the GenBank data base. Thus, the results indicate a high prevalence of "hypervirulent" strains. All eight strains studied belong to the genotype of "hypervirulent" strains. Among these trains, one strain is classified in sub genotype VV3 and the others in VV2. The strains of this sub genotype are very close to the nigerian strains and constitute with the tanzanian, zambian and ethiopian strains the African sub genotype VV2. However, investigations on segment B would provide more details on the origin of viral strains circulating in Dakar. Keywords : Molecular characterization, hypervirulent strains, Senegal, Gumboro disease.

International audience; Understanding human and animal mobility patterns is a key to predict local and global disease spread. We analysed the nomad herds' movement network in a pilot area of northern Senegal and used exponential random graph models (ERGM) to investigate the reasons behind these movements. We interviewed 132 nomadic herders to collect information about nomad herd structures, movements, and reasons for taking specific routes or gathering in certain areas. We constructed a spatially explicit network with villages as the nodes and nomad herds' movements as the connecting edges. The final ERGM showed that node and edge attributes such as presence of cattle in the herd (odds ratio = 12, CI: 5.3, 27.3), morbidity (odds ratio = 3.6, CI: 2.3, 5.7), and lack of water (odds ratio = 2, CI: 1.3, 3.1) were important predictors of nomad herds' movements. This study not only provides valuable information for monitoring important livestock diseases such as Rift Valley Fever in Senegal, but also helps implement outreach, education, and intervention programs for other emerging and endemic diseases affecting nomadic herds.

West Nile fever is an arthropod-borne viral disease of public health importance transmitted by mosquitoes from the genus Culex. Birds are the main hosts/reservoirs of West Nile virus (WNV; Flaviviridae, Flavivirus) and ensure its spread worldwide toward migration. The WNV is continuously spreading across the world with significant health and economic impact in human and animals, especially in newly infected areas where many human and animal losses are reported. However, in most of the African countries where the disease is endemic, no or few human or animal cases are reported in contrast with the high prevalence of the disease and the recurrent circulation of the virus. These gaps could be related to the fact that clinical signs are similar to those of dominant pathologies in human or equine encephalitis in animal health allowing to a misdiagnosis.

Sandfly fever virus (SFV) serotypes sandfly fever Naples virus, sandfly fever Sicilian virus, and sandfly fever Cyprus virus cause febrile diseases, whereas Toscana virus (TOSV) is responsible for aseptic meningoencephalitis. Diagnosis and surveillance of TOSV depend heavily on virus serology, and various commercial assays utilizing various antigen sources and formats have been available. The aim of this study was to perform comparative evaluation of commercially available serological assays for anti-TOSV immunoglobulins.A collection of 120 sera from healthy blood donors from an endemic region, previously identified to be reactive for antibodies against various SFV serotypes by indirect immunofluorescence test (IIFT), was reevaluated for IgG/IgM via IIFT, enzyme-linked immunosorbent assay, and an immunoblot assay manufactured by Euroimmun, Diesse, and Mikrogen, respectively. Virus neutralization test (VNT) was performed for 99 sera using standard TOSV, sandfly fever Sicilian virus, and sandfly fever Naples virus strains.A total of 89 samples (74.2%) were reactive for TOSV IgG in at least one of the commercial assays, and 31 samples (31.3%) were reactive in VNT for various SFV serotypes. Average percentage agreements among commercial assays and between VNT and the commercial assays were noted as 57.8% and 62.6%, respectively. No significant correlation between assay results and VNT titers was observed. SFV IgM antibodies were detected in a total of eight samples (6.7%) via IIFT, which were nonreactive in enzyme-linked immunosorbent assay and VNT.Commercial diagnostic immunoassays displayed slight to fair agreement for TOSV IgG as assessed via kappa and percentage agreement values. The results could only be confirmed via virus neutralization in a portion of the samples, and overall agreement between the commercial assays and VNT was slight. Commercial assays such as immunoblot can be used in addition to VNT for confirmation of TOSV exposure.

Au Senegal, la maladie de Gumboro constitue un veritable obstacle pour le developpement de l’aviculture semi-intensive. Une etude epidemiologique portant sur cette affection dans les exploitations semiintensives a ete conduite en decembre 2015 dans les regions de Dakar et Thies. Elle a consiste a evaluer l’association entre des facteurs de risque et l’apparition de la maladie. Pour cela, les gestionnaires de 56 exploitations infectees et 112 indemnes ont constitue les cibles de cette enquete. Les foyers etaient suspectes sur la base des manifestations cliniques et confirmes par la detection du virus avec la RT-PCR. Ainsi, les resultats indiquent une faible liaison entre la presence d’oiseaux domestiques ou sauvages et l’apparition de la maladie (Odds Ratio = 1,44). Par contre, la presence de rongeurs (Odds = 22), la gestion des cadavres (Odds Ratio = 7,56) et l’acces des personnes etrangeres (Odds Ratio = 4,47) sont fortement lies a l’apparition de la maladie. La sensibilisation sur la gestion des poulets infectes et morts contribuerait a limiter la dissemination du virus et les pertes attribuables a la maladie. Mots cles : Epidemiologie, facteurs de risque, Odds Ratio, Senegal, Maladie de Gumboro. English Title: Risk factors related to the appearance of Gumboro disease in semi-intensive poultry farms in Senegal English Abstract In Senegal, Gumboro disease is a real obstacle to the development of semi-intensive poultry farming. An epidemiological study of this disease in semi-intensive poultry farms was carried out in December 2015 in the regions of Dakar and Thies. The study consisted to assess the association between risk factors at the onset of the disease. To do so, 56 chicken coop managers of infected farms and 112 disease-free farms were targeted for the survey. The outbreaks of infectious bursal disease virus were suspected on the basis of the clinical manifestations, and confirmed by the detection of virus with RT-PCR. Thus, the results indicated that a weak linkage between the presence of domestic or wild birds and the onset of the disease (Odds Ratio = 1.44). On the other hand, the presence of rodents (Odds = 22), cadaver management (Odds Ratio = 7.56) and the access of foreign people in the farm (Odds Ratio = 4.47) are strongly related to the onset of Gumboro disease. Sensitization on the management of infected and dead chickens would help to limit the spread of the virus and the losses attributable to the disease. Keywords : Epidemiology, Risk factor, Odds ratio, Senegal, Gumboro, disease.

Background Rapid diagnostics are not available for several human pathogens in the genus Phlebovirus of the Bunyaviridae. Objectives To develop RT-PCR assays for Sandfly Fever Sicilian virus (SFSV), Sandfly Fever Naples virus (SFNV), Toscana virus (TOSV) and Rift Valley Fever virus (RVFV). Study design RNA standards were generated and used to test the performance of the assays. Results A detection limit of 10–100 RNA molecules was determined for the SFSV, TOSV and RVFV assays. The sensitivity of the SFNV assay was not determined. The TOSV and the RVFV assays detected recent isolates from Spain and Africa, respectively. Conclusion The assays should help to improve surveillance of pathogenic Phleboviruses.

Summary Peste des petits ruminants (PPR) is a contagious and often fatal disease affecting sheep and goats. Currently, it is endemic in Africa, the Middle and Near East, the Indian subcontinent and China. Understanding the molecular epidemiology and evolution of PPR virus (PPRV) can assist in the control of the transboundary spread of this economically important disease. We isolated PPRV from pathological and swab samples collected 42 years apart (1969 and 2011) in Benin, West Africa, and sequenced the full genome of two isolates (Benin/B1/1969 and Benin/10/2011). Phylogenetic analysis showed that all of the characterized isolates clustered within viral lineage II and that the 2011 isolates fell into two distinct subgroups. Comparison of the full genome sequences revealed a 95.3% identity at the nucleotide level, while at the protein level, the matrix protein was the most conserved between the two viruses with an identity of 99.7% and only one amino acid substitution over the 42-year sampling period. An analysis of specific amino acid residues of known or putative function did not identify any significant changes between the two viruses. A molecular clock analysis of complete PPRV genomes revealed that the lineage II viruses sampled here arose in the early 1960s and that these viruses have likely persisted in Benin since this time.

We report the complete genome sequence of a lineage I peste des petits ruminants virus (E32/1969) isolated in a Senegalese laboratory in 1969. This is the earliest peste des petits ruminants virus of any lineage sequenced to date and only the second lineage I virus available in public databases.

During September–October 2010, an unprecedented outbreak of Rift Valley fever was reported in the northern Sahelian region of Mauritania after exceptionally heavy rainfall. Camels probably played a central role in the local amplifi cation of the virus. We describe the main clinical signs (hemorrhagic fever, icterus, and nervous symptoms) observed during the outbreak.

Sandfly fever viruses (SFVs) cause febrile diseases as well as aseptic meningitis/encephalitis and include serotypes sandfly fever Sicilian virus (SFSV), sandfly fever Naples virus (SFNV) and Toscana virus (TOSV). Infections are endemic in the Mediterranean basin and data on SFV activity in Turkey are limited. In this study, sera from 1533 blood donors from the Ankara, Konya, Eskisehir and Zonguldak provinces of Turkey were evaluated for SFV exposure by indirect immunofluorescence test (IIFT) and confirmed by virus neutralization test (VNT). One hundred and two patients with central nervous system (CNS) infections of unknown aetiology were also tested via IIFT and real-time reverse-transcription PCR for SFV/TOSV. Rate of overall IgG reactivity in IIFT was 32.9% (505/1533) among blood donors. TOSV exposure was confirmed by VNT in all study regions. Exposure to the recently-identified serotype sandfly fever Turkish virus, as evaluated by VNT, was revealed in Konya and Ankara. SFNV exposure was identified in Konya and SFSV was observed to be present in all regions except Zonguldak. TOSV RNA was detected in 15.7% (16/102) and was accompanied by TOSV IgM in 25% (4/16) of the patients. Partial L and S sequences suggested that TOSV circulating in Turkey can be grouped into TOSV genotype A strains. Exposure to TOSV and other SFV serotypes was revealed in blood donors and CNS infections by TOSV were identified for the first time in Turkey. Infections are observed to be endemic in central Anatolia and should be considered as aetiologic agents in cases/outbreaks of fever and meningoencephalitis. peerReviewed