Usutu virus in Africa.

Usutu virus (USUV) was discovered in South Africa in 1959. Since then, it has been reported in several African countries including Senegal, Central African Republic, Nigeria, Uganda, Burkina Faso, Cote d'Ivoire, and Morocco. In 2001, USUV has been identified for the first time outside of Africa, namely in Europe, where it caused a significant mortality among blackbirds in Vienna, Austria. In 2009, the first two human cases of USUV infection in Europe have been reported in Italy, causing encephalitis in immunocompromised patients. The host range in Africa includes mainly Culex mosquitoes, birds, and also humans with one benign and one severe case. Given its role as a potential human pathogen and the similar appearance compared with other emerging arboviruses, it is essential to investigate the natural history and ecology of USUV in Africa. In this regard, we review the emergence of USUV in Africa, summarizing data about isolations, host range, and potential vectors, which should help to improve our understanding of the factors underlying the circulation of USUV in Europe and Africa

Vector competence of Aedes vexans (Meigen), Culex poicilipes (Theobald) and Cx. quinquefasciatus Say from Senegal for West and East African lineages of Rift Valley fever virus

Background Rift Valley fever virus (RVFV; Phlebovirus, Bunyaviridae) is a mosquito–borne, zoonotic pathogen. In Senegal, RVFV was first isolated in 1974 from Aedes dalzieli (Theobald) and thereafter from Ae. fowleri (de Charmoy), Ae. ochraceus Theobald, Ae. vexans (Meigen), Culex poicilipes (Theobald), Mansonia africana (Theobald) and Ma. uniformis (Theobald). However, the vector competence of these local species has never been demonstrated making hypothetical the transmission cycle proposed for West Africa based on serological data and mosquito isolates. Methods Aedes vexans and Cx. poicilipes, two common mosquito species most frequently associated with RVFV in Senegal, and Cx. quinquefasciatus, the most common domestic species, were assessed after oral feeding with three RVFV strains of the West and East/central African lineages. Fully engorged mosquitoes (420 Ae. vexans, 563 Cx. quinquefasciatus and 380 Cx. poicilipes) were maintained at 27 ± 1 °C and 70–80 % relative humidity. The saliva, legs/wings and bodies were tested individually for the RVFV genome using real-time RT-PCR at 5, 10, 15 and 20 days post exposure (dpe) to estimate the infection, dissemination, and transmission rates. Genotypic characterisation of the 3 strains used were performed to identify factors underlying the different patterns of transmission. Results The infection rates varied between 30.0–85.0 % for Ae. vexans, 3.3–27 % for Cx. quinquefasciatus and 8.3–46.7 % for Cx. poicilipes, and the dissemination rates varied between 10.5–37 % for Ae. vexans, 9.5–28.6 % for Cx. quinquefasciatus and 3.0–40.9 % for Cx. poicilipes. However only the East African lineage was transmitted, with transmission rates varying between 13.3–33.3 % in Ae. vexans, 50 % in Cx. quinquefasciatus and 11.1 % in Cx. poicilipes. Culex mosquitoes were less susceptible to infection than Ae. vexans. Compared to other strains, amino acid variation in the NSs M segment proteins of the East African RVFV lineage human-derived strain SH172805, might explain the differences in transmission potential. Conclusion Our findings revealed that all the species tested were competent for RVFV with a significant more important role of Ae. vexans compared to Culex species and a highest potential of the East African lineage to be transmitted

Multinomial logistic model for coinfection diagnosis between arbovirus and malaria in Kedougou

In tropical regions, populations continue to suffer morbidity and mortality from malaria and arboviral diseases. In Kedougou (Senegal), these illnesses are all endemic due to the climate and its geographical position. The co-circulation of malaria parasites and arboviruses can explain the observation of coinfected cases. Indeed there is strong resemblance in symptoms between these diseases making problematic targeted medical care of coinfected cases. This is due to the fact that the origin of illness is not obviously known. Some cases could be immunized against one or the other of the pathogens, immunity typically acquired with factors like age and exposure as usual for endemic area. Then, coinfection needs to be better diagnosed. Using data collected from patients in Kedougou region, from 2009 to 2013, we adjusted a multinomial logistic model and selected relevant variables in explaining coinfection status. We observed specific sets of variables explaining each of the diseases exclusively and the coinfection. We tested the independence between arboviral and malaria infections and derived coinfection probabilities from the model fitting. In case of a coinfection probability greater than a threshold value to be calibrated on the data, duration of illness above 3 days and age above 10 years-old are mostly indicative of arboviral disease while body temperature higher than 40{\textdegree}C and presence of nausea or vomiting symptoms during the rainy season are mostly indicative of malaria disease

Molecular Diagnostics of Ebola Patient Samples by Institut Pasteur de Dakar Mobile Laboratory in Guinea 2014–2016

As part of the laboratory response to the Ebola virus outbreak in Guinea, the Institut Pasteur de Dakar mobile laboratory (IPD-ML) was set up in Donka hospital from 2014 to 2016. EBOV suspected samples collected at Ebola Treatment Centers (ETC) and from community deaths were sent daily to IPD-ML. Analysis was performed using dried oligonucleotide mixes for real-time RT-PCR designed for field diagnostic. From March 2014 to May 2015, a total of 6055 patient samples suspected for EBOV collected from seven regions of Guinea were tested by real-time RT-PCR. These patients’ clinical included serum samples (n = 2537 samples) and swabs (n = 3518 samples) with positivity rates of 36.74 and 6.88% respectively. Females were significantly more affected than males with positivity rates of 22.39 and 17.22% respectively (p-value = 5.721e-7). All age groups were exposed to the virus with significant difference (p-value <= 2.2e-16). The IPD-ML contributed significantly to the surveillance and patient management during the EBOV outbreak in Guinea. Furthermore, dried reagents adapted for field diagnostic of EVD suspect cases could be useful for future outbreak preparedness and response

Study of The Fermentescibilty of Typha Domingensis in Mode Mesophilic

To assess the energy potential of the species Typha domingensis, tests were conducted in the laboratory to determine assess the amount of biogas produced per liter of fermentor per kg dry matter (ms). Thus, after 37 days of fermentation in a digester 1000ml containing 150g biomass production cumulative biogas obtained is 8955 ml titrating 40.4% methane, is 59.70 ml / g of biomass (1 , 61l /g/ j) or 0.24 l /l /j). This plant species has an identical biogas that of Euphorbia Tirucalli digested in the same conditions of temperature and preparation. However Typha biogas produces less than the stomachs of cattle (0,65l / lj) but more than the sewage sludge (0,11l / lj)

Contribution of Dehydration and Malnutrition to the Mortality of Children 0-59 Month of Age in a Senegalese Pediatric Hospital

In-hospital mortality is an indicator of the quality of care. We analyzed the mortality of under five years children of Pediatric ward of Aristide Le Dantec teaching hospital to update our data, after an previous study conducted ten years earlier.Methods: This was a retrospective study involving children 0-59 months of age, hospitalized from January 1, 2012 to December 31, 2012.For each child, nutritional status was assessed according to 2006 World Health Organization growth standards; clinical and biological data were recorded. The outcome of the disease was specified. Bivariate and multivariable were used to identify risk factors for death.Results: 393 children were included. Overall mortality rate was 10% (39/393). Factors associated with death were severe wasting [OR = 8.27, 95% CI [3.79-18], male gender (OR = 2.98, 95% CI [1.25-7.1]), dehydration (OR = 5.4, 95% CI [2.54-13.43]) in the model using the weight-for- height z score, male gender (OR = 2.5, 95% CI [1.11-5.63]), dehydration (OR = 8.43, 95% CI [3.83-18.5]) in using the height- for- age z score, male gender (OR = 2.7, 95% CI [1.19-6.24]), dehydration (OR = 7.5, 95% CI [3.39-16.76]), severe underweight (OR = 2.4, 95% CI [1.11-5.63]), in the model using the weight-for- age z score, and male gender (OR = 2.5, 95% CI [1.11-5.63]), dehydration (OR = 8.43, 95% CI [3.83-18.5]) in that using MUAC.Dehydration and malnutrition are two independent factors of mortality. Our management protocols of dehydration and malnutrition have to be updated. Screening malnutrition has to be done systematically for each child by anthropometric measurements using WHO growth standards

Development and validation of sensitive real-time RT-PCR assay for broad detection of rabies virus

Rabies virus (RABV) remains one of the most important global zoonotic pathogens. RABV causes rabies, an acute encephalomyelitis associated with a high rate of mortality in humans and animals and affecting different parts of the world, particularly in Asia and Africa. Confirmation of rabies diagnosis relies on laboratory diagnosis, in which molecular techniques such as detection of viral RNA by reverse transcription polymerase chain reaction (RT-PCR) are increasingly being used.&nbsp; In this study, two real-time quantitative RT-PCR assays were developed for large-spectrum detection of RABV, with a focus on African isolates. The primer and probe sets were targeted highly conserved regions of the nucleoprotein (N) and polymerase (L) genes.&nbsp; The results indicated the absence of non-specific amplification and cross-reaction with a range of other viruses belonging to the same taxonomic family, i.e Rhabdoviridae, as well as negative brain tissues from various host species. Analytical sensitivity ranged between 100 to 10 standard RNA copies detected per reaction for N-gene and L-gene assays, respectively. Effective detection and high sensitivity of these assays on African isolates showed that they can be successfully applied in general research and used in diagnostic process and epizootic surveillance in Africa using a double-check strategy

Mobile laboratory reveals the circulation of Dengue virus serotype I of Asian origin in Medina Gounass (Guediawaye), Senegal

With the growing success of controlling malaria in Sub-Saharan Africa, the incidence of fever due to malaria is in decline, whereas the proportion of patients with non-malaria febrile illness (NMFI) is increasing. Clinical diagnosis of NMFI is hampered by unspecific symptoms but early diagnosis is a key factor for better patient care and for disease control. The aim of this study was to determine the arboviral aetiologies of NMFI in a low resources settings using a mobile laboratory based on Recombinase Polymerase Amplification (RPA) assays. The panel of tests for this study was expanded to five arboviruses including (Dengue virus (DENV), Zika virus (ZIKV), Yellow fever virus (YFV), Chikungunya virus (CHIKV), and Rift valley fever virus (RVFV). One hundred and four children aged between one month and 115 months were enrolled and screened. Three of 104 blood samples of children < 10 years presenting at an outpatient clinic tested positive for DENV. The results were confirmed by real-time RT-PCR, partial sequencing, and non structural protein 1 (NS1) antigen capture ELISA (Biorad, France). Phylogenetic analysis of the derived DENV-1 sequences clustered them with sequences of DENV-1 isolates from Guangzhou in China in 2014. In conclusion, this mobile setup proved reliable for the rapid identification of the causative agent of NMFI, with results consistent with those obtained in the reference laboratory`s settings

Larval ecology of mosquitoes in sylvatic arbovirus foci in southeastern Senegal

BACKGROUND: Although adult mosquito vectors of sylvatic arbovirus [yellow fever (YFV), dengue-2 (DENV-2) and chikungunya (CHIKV)] have been studied for the past 40 years in southeastern Senegal, data are still lacking on the ecology of larval mosquitoes in this area. In this study, we investigated the larval habitats of mosquitoes and characterized their seasonal and spatial dynamics in arbovirus foci. METHODS: We searched for wet microhabitats, classified in 9 categories, in five land cover classes (agriculture, forest, savannah, barren and village) from June, 2010 to January, 2011. Mosquito immatures were sampled monthly in up to 30 microhabitats of each category per land cover and bred until adult stage for determination. RESULTS: No wet microhabitats were found in the agricultural sites; in the remaining land covers immature stages of 35 mosquito species in 7 genera were sampled from 9 microhabitats (tree holes, fresh fruit husks, decaying fruit husks, puddles, bamboo holes, discarded containers, tires, rock holes and storage containers). The most abundant species was Aedes aegypti formosus, representing 30.2% of the collections, followed by 12 species, representing each more than 1% of the total, among them the arbovirus vectors Ae. vittatus (7.9%), Ae. luteocephalus (5.7%), Ae. taylori (5.0%), and Ae. furcifer (1.3%). Aedes aegypti, Cx. nebulosus, Cx. perfuscus, Cx. tritaeniorhynchus, Er. chrysogster and Ae. vittatus were the only common species collected from all land covers. Aedes furcifer and Ae. taylori were collected in fresh fruit husks and tree holes. Species richness and dominance varied significantly in land covers and microhabitats. Positive associations were found mainly between Ae. furcifer, Ae. taylori and Ae. luteocephalus. A high proportion of potential enzootic vectors that are not anthropophilic were found in the larval mosquito fauna. CONCLUSIONS: In southeastern Senegal, Ae. furcifer and Ae. taylori larvae showed a more limited distribution among both land cover and microhabitat types than the other common species. Uniquely among vector species, Ae. aegypti formosus larvae occurred at the highest frequency in villages. Finally, a high proportion of the potential non-anthropophilic vectors were represented in the larval mosquito fauna, suggesting the existence of unidentified sylvatic arbovirus cycles in southeastern Senegal